diff --git a/locale/de/LC_MESSAGES/01_Sample_preparation.po b/locale/de/LC_MESSAGES/01_Sample_preparation.po new file mode 100644 index 000000000..96f4a5078 --- /dev/null +++ b/locale/de/LC_MESSAGES/01_Sample_preparation.po @@ -0,0 +1,708 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-19 07:07-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../01_Sample_preparation/Considerations.md:1 +msgid "Considerations for different sample types" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:3 +msgid "" +"There are many different options for types of samples to image, and " +"advances in sample preparation techniques and imaging modalities are " +"continually enabling the imaging of more diverse and complex biological " +"specimens. As with many other aspects of experimental design, sample type" +" selection comes with tradeoffs. Samples that are amenable to simple " +"preparation and imaging tend to be small, thin, and relatively clear, " +"like a monolayer of cultured cells. Such samples have obvious advantages " +"and can be imaged in a high-throughput manner, but they're not suitable " +"for every biological question. Sometimes a thicker specimen, like an " +"organoid, or whole or sectioned tissue is needed, especially when the " +"biological question involves interactions between different types of " +"cells. Carefully consider what biological context is appropriate for your" +" question and what measurements you'd ultimately like to be able to make." +" Below, we summarize some common sample types" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md +msgid "๐Ÿค” What are my options?" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:7 +msgid "" +"Here we present some major categories for sample types. Note that there " +"are not hard boundaries between these different categories (e.g., both " +"cells and organoids can be cultured in 3D, many of these specimens can be" +" imaged live or after {term}`fixation`), but some general advantages and " +"disadvantages are summarized below." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:11 +msgid "**Cultured cells**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:13 +msgid "" +"Many different types of cells can be cultured, or grown in a dish. Cells " +"can be grown in a monoculture, with only one cell type, or in a co-" +"culture with multiple cell types." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:15 +#: ../../01_Sample_preparation/Considerations.md:31 +#: ../../01_Sample_preparation/Considerations.md:49 +#: ../../01_Sample_preparation/Considerations.md:67 +msgid "_Advantages_" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:17 +msgid "" +"Cultured cells tend to be relatively simple to image and for many " +"questions can be imaged with widefield microscopy (see " +"[Acquisition](content/microscope_selection)), which is faster and more " +"accessible than confocal or superresolution methods. Additionally, high-" +"throughput microscopes integrated with robotics can enable automation of " +"experiments and imaging with cultured cells." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:19 +msgid "" +"Cells can be frozen, thawed, and grown much faster than work with more " +"complex specimens like organoids or whole organisms, compressing the " +"timeline to perform an experiment" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:21 +#: ../../01_Sample_preparation/Considerations.md:37 +#: ../../01_Sample_preparation/Considerations.md:55 +#: ../../01_Sample_preparation/Considerations.md:71 +msgid "_Disadvantages_" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:23 +msgid "" +"Most applications in microscopy require imaging through a glass coverslip" +" of a specific thickness and tolerance. However, many cell types do not " +"survive or cannot grow on glass and require additional coatings and " +"manipulations of the coverslip to ensure the health of the sample. As an " +"alternative some companies manufacture imaging chambers (multi well " +"plates, 35 mm dishesโ€ฆ) with proprietary polymers that have similar " +"properties to glass (optical polymers), thus enabling high resolution " +"imaging. It is imperative to understand whether the immersion oil used " +"during imaging affects the integrity of these polymers, as the solvents " +"in some immersion media can crack or dissolve the polymer layer." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:27 +msgid "**Organoids**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:29 +msgid "" +"Organoids are cultured cells that are grown in 3D to mimic the structure " +"and sometimes functions of organs. Organoids are typically grown from " +"stem cells that self-organize into a more complex structure, including " +"differentiating into different cell types. Organoids are well suited to " +"questions of development, modeling disease, and for understanding tissue " +"and organ regeneration." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:33 +msgid "" +"Because organoids contain multiple cell types and reflect some structure " +"and cell relationships seen in organs _in vivo_, they are well-suited to " +"more complex questions about disease and cell-cell interactions. They can" +" also be used to model processes and structures that are necessarily 3D " +"and not recapitulated well in a flat layer of cells, like many " +"developmental processes." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:35 +msgid "" +"Organoids can be made from induced pluripotent stem cells (iPSCs) from " +"human or animal samples, and thus can model disease processes specific to" +" a given human donor." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:39 +msgid "" +"Organoids can take more complex resources and protocols to grow and can " +"take more time than just growing cultured cells on glass or plastic." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:41 +msgid "" +"Because organoids are 3D structures, they often are not amenable to " +"widefield imaging and may require spinning disk or point-scanning " +"confocal microscopy." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:45 +msgid "**Tissue**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:47 +msgid "" +"Tissues are formed when cells act together to perform a specific " +"function. Tissues can be cultured by taking a piece of an animal or plant" +" and allowing it to continue to survive and grow in a dish. Tissues can " +"also be harvested from plants or animals and stained for the presence of " +"different molecules. Tissues are typically cut into pieces (aka " +"{term}`tissue sectioning`), and can be fixed, fresh, or frozen, or even " +"alive in {term}`ex-vivo imaging`." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:51 +msgid "" +"Tissues have more intact cell-cell interactions that are generally more " +"representative of what happens _in vivo_ than in cell culture." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:53 +msgid "" +"Repositories of donated human tissues enable biomedical research to study" +" a diverse sample of patients with a particular disease." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:57 +msgid "" +"Primary cells and tissues tend to be sensitive to environment than " +"immortalized cell lines and can be more difficult to grow and may require" +" specialized protocols depending on cell type." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:59 +msgid "" +"Tissues harvested from a whole animal or plant require time for the " +"development and growth of that specimen before harvesting." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:63 +msgid "**Whole organism / embryo**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:65 +msgid "" +"Some whole organisms are thin and transparent enough to image. Some " +"animals also have near-transparent embryonic stages, like the zebrafish. " +"Additionally, {term}`intravital imaging` is the imaging of cellular " +"structures or biological processes inside a live animal in real time, " +"without extracting the organs or fixing the sample. In general, it " +"requires specific instrumentation or modalities with improved light " +"penetration, such as multiphoton microscopy and is limited to the ability" +" to access the specific organ, often through optical windows." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:69 +msgid "" +"Imaging whole organisms or embyros provides the most possible intact " +"biological context when studying a particular process or structure." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:73 +msgid "" +"Imaging of thicker specimens may require processing ({term}`tissue " +"clearing`) of the sample to make its {term}`refractive index` match that " +"of the imaging media and reduce absorption and scattering of light." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:75 +msgid "" +"Intravital imaging often requires specific surgical techniques and is " +"overseen by bioethical committees and needs to be approved by IACUC " +"and/or other institutional committees." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md +msgid "โš ๏ธ Where can things go wrong?" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:80 +msgid "" +"**Photobleaching and phototoxicity** - Photobleaching can be defined as " +"the irreversible destruction of a fluorophore in its excited state, " +"meaning, that fluorophore will not be able to emit more light and the " +"fluorescence signal will therefore degrade over time, affecting signal to" +" noise ratio and intensity measurements. In order to minimize " +"photobleaching during acquisition, there are a number of photobleaching " +"reagent agents that can be added to the media. These agents minimize " +"photobleaching of fluorophores to a different extent, and therefore it is" +" important to contact the manufacturer to ensure they are optimal for the" +" specific fluorophore. For example addition of oxygen scavengers to the " +"imaging media such as glucose oxidase or pyranose 2-oxidase can " +"significantly reduce photobleaching. It is important to understand that " +"the use of {term}`oxygen scavengers` may affect live cell imaging, as " +"these scavengers can affect the ATP and oxygen levels within the sample, " +"compromising its health and therefore biological function." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:82 +msgid "" +"**Cells are dying** - Fluorescent light induces DNA damage and oxidation " +"of cellular components (phototoxicity). In addition, fluorophore " +"photobleaching can further induce phototoxicity by creating reactive " +"oxygen species (ROS). The addition of antioxidants and removal of certain" +" molecules (e.g., riboflavin) from the imaging media can reduce the ROS " +"produced during imaging, improving the health of the " +"sample.{cite}`Stockley2017`" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:85 +msgid "" +"**My fixed cells don't looked as expected** - Fixation can change the " +"localization and fluorescence of different proteins. Where possible, " +"always compare the distribution of a protein or molecule of interest with" +" and without fixation. Also consider whether a different {term}`fixation`" +" method may be more appropriate for your specimen." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:88 +msgid "" +"**My sample is too opaque** - Thicker specimens, like thick tissue " +"sections, pigmented cells, or whole organisms can be challenging to image" +" due to light absorption and scattering induced by the inhomogeneities in" +" {term}`refractive index` within the tissue itself, resulting in poor " +"light penetration. To facilitate imaging of tissues, researchers often " +"cut thick tissues into slices of different thicknesses. This process is " +"called tissue sectioning. In most cases the samples are fixed and " +"embedded in paraffin or frozen in tissue freezing medium and later cut " +"into thin slices by a machine like a cryostat, microtome, or vibratome " +"and sections collected into a tube or onto a slide. Alternatively, most " +"components in any complex biological system such as an organ are not " +"contained within this two-dimensional volume, and therefore, this " +"approach compromises the understanding of the spatial relationships among" +" cellular components. Tissue clearing focused on reducing the " +"inhomogeneities in the tissue by equilibrating the {term}`refractive " +"index` throughout the sample. This allows light to pass through the " +"tissue and therefore enables high resolution, volumetric imaging of whole" +" organs and tissues using conventional microscopy techniques such as " +"confocal microscopy without the need to physically section the sample." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md +msgid "๐Ÿ“š๐Ÿคทโ€โ™€๏ธ Where can I learn more?" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:94 +#, python-format +msgid "" +"๐Ÿ“„ [Organoids " +"Primer](https://www.nature.com/articles/s43586-022-00174-y#:~:text=An%20organoid%20is%20a%20self,%2C9%2C10%2C11.)" +" {cite}`Zhao2022-rm`" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:95 +msgid "" +"๐Ÿ“„ [Tutorial: guidance for quantitative confocal " +"microscopy](https://doi.org/10.1038/s41596-020-0313-9) " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:96 +msgid "" +"๐Ÿ“„ [Hypothesis-driven quantitative fluorescence microscopy - the " +"importance of reverse-thinking in experimental " +"design](https://pubmed.ncbi.nlm.nih.gov/33154172/) {cite}`Wait2020-gq`" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:1 +msgid "Experimental design decisions" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:3 +msgid "" +"A number of critical decisions must be made when designing a quantitative" +" bioimaging experiment. Many of these decisions will be deeply dependent " +"on what is possible given the biology you wish to study, for example:" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:4 +msgid "" +"You will always prefer live imaging to fixed imaging if it is important " +"to assess the dynamics of a given process" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:5 +msgid "" +"You may need to perform special processes such as tissue clearing if it " +"is important to image deep into a relatively opaque specimen" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:6 +msgid "" +"You cannot rely on genetic tagging with fluorescent proteins if your " +"model system is not genetically tractable to such manipulations" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:7 +msgid "" +"You have to image at a particularly high resolution to confidently assess" +" interactions between two molecules imaged in the same system" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:9 +msgid "" +"It is therefore _**extremely**_ important to think through all of the " +"aspects of your biological question before ever picking up a pipette or a" +" slide. Many sample preparation decisions are deeply entwined with the " +"availability and suitability of particular microscopes; see [that " +"section](content/microscope_selection) for more information." +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:11 +msgid "Mounting" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:13 +msgid "Glass coverslips" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:15 +msgid "" +"Many imaging applications involve mounting on glass coverslips, either " +"directly or using a coverslip mounted into a dish. While there is a wide " +"range of coverslip sizes and shapes, the most important attribute is the " +"coverslip thickness. Coverslip grade dictates the expected thickness and " +"tolerance. These factors are important because most microscope " +"manufacturers assume a specific coverslip thickness (0.17mm) in the " +"design of objective lenses to minimize aberrations. These aberrations " +"tend to affect the brightness and axial resolution, reducing signal to " +"noise ratio, sharpness, and resolution. The tolerance of the coverslip " +"(to minimize the variability in thickness) is essential for super-" +"resolution techniques or intensity measurements in images collected with " +"high numerical aperture objectives. Other applications do not require the" +" mounting of samples onto glass or plastic but instead have the sample " +"and the objective lens immersed in the same medium." +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:17 +msgid "Comparison of coverslip grades" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:21 +msgid "Grade" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:22 +msgid "Nominal thickness [mm]" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:23 +msgid "Thickness range [mm]" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:24 +msgid "#1.5" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:25 +#: ../../01_Sample_preparation/Experimental_design.md:28 +msgid "0.17" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:26 +msgid "0.16 - 0.19" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:27 +msgid "#1.5H" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:29 +msgid "0.165 - 0.175" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:32 +msgid "Mounting media" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:34 +msgid "" +"The {term}`refractive index` the sample is placed in, as well as the " +"refractive index of the glass and the medium between the objective and " +"the sample are all critical to determining the achievable resolution. The" +" {term}`mounting media` can have other important optical and/or " +"experimental properties; it is important to use the correct mounting " +"media for experiment planned." +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:43 +msgid "effects of mounting media" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:43 +msgid "" +"**Effects of mounting media on staining with various fluorophores**. " +"Adapted from Jonkman J., Brown C.M., Wright G.D _et al_. Tutorial: " +"guidance for quantitative confocal microscopy. _Nat Prot_ **15**, (2020) " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:46 +msgid "Fluorophore selection" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:48 +msgid "" +"Fluorophores are molecules that are able to emit light upon absorption of" +" a photon, typically of shorter wavelength. The fluorophores relevant to " +"biomedical research can be small molecules organic dyes (FITC, Alexa " +"Fluor 488) that bind specific cell structure (e.g., DAPI, MitoTracker), " +"fluorescent analogues of small molecules (e.g., phalloidin, fluorescent " +"amino acids) or fluorescent proteins. Some of the important properties to" +" consider when choosing fluorophores are listed below:" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:50 +msgid "Excitation/emission spectra of each fluorophore" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:51 +msgid "Brightness (dyes tend to be brighter than proteins)" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:52 +msgid "Photostability" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:53 +msgid "Propensity to oligomerize (in the case of fluorescent proteins)" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:54 +msgid "Phototoxicity (when imaging in live samples)" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:56 +msgid "" +"Understanding fluorophores, microscope specifications (light source, " +"filters, detector), and analysis goals are key in selecting the " +"appropriate fluorophore(s) to address a scientific question. See the " +"section on [reproducibility](content/reproducibility) for more " +"information." +msgstr "" + +#: ../../01_Sample_preparation/Introduction.md:1 +msgid "Introduction" +msgstr "" + +#: ../../01_Sample_preparation/Introduction.md:3 +msgid "" +"A good image starts at the bench. The best performing instrument will not" +" produce rigorous, reproducible or high quality data unless sample " +"preparation has been optimized. To design a rigorous and reproducible " +"microscopy experiment, it is critical to identify the goal of the " +"experiment and understand the factors that impact the image. This " +"information informs researchers about how to prepare the sample, what " +"minimal controls and corrections are needed, how to choose the " +"appropriate instrumentation, optimize acquisition, analyze and present " +"microscopy data." +msgstr "" + +#: ../../01_Sample_preparation/Introduction.md:5 +msgid "" +"Here we will discuss some of the key choices you will make during sample " +"preparation, including selecting your sample type and fluorophore (if " +"you're performing fluorescence microscopy). We also discuss some minimal " +"controls necessary for interpreting your results." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:1 +msgid "Reproducibility" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:5 +msgid "" +"A number of factors are critical in designing a reproducible microscopy " +"experiment. A few critical factors are laid out here; see other works " +"such as {cite}`Jost2019-nx`" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:7 +msgid "Antibody validation" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:9 +msgid "" +"While in a perfect world, antibodies would always be specific to a " +"particular target, unfortunately, this cannot always be relied upon when " +"performing {term}`immunolabeling`. {cite}`Uhlen2016-wy` When possible, " +"one should perform knockout and/or knockdown controls to confirm antibody" +" specificity; where not, look for availability of another antibody to a " +"different part of the target molecule (sometimes called the _epitope_) " +"and confirm you get consistent localization." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:11 +msgid "" +"Optimizing your {term}`blocking` and {term}`permeabilization` conditions " +"for the particular antibody and protocol can reduce non-specific " +"background. No-primary-antibody controls should always be performed as " +"well, as they are essential for validating signal specificity." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:13 +msgid "Fluorescent protein localization validation" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:15 +#, python-format +msgid "" +"Expression of fluorescently-tagged proteins can make localization of a " +"molecule or structure possible, especially when no good antibody exist " +"for immunolabeling and/or it will be helpful to observe the molecule's " +"behavior in live cells. While a study comparing overlap between the same " +"molecular targets with fluorescent proteins vs antibodies found 80% " +"overlap, they also found that some considerations (such as whether the C-" +" or N- terminus of a protein is tagged) may cause changes in " +"localization. {cite}`Stadler2013`. A recent paper {cite}`Sittewelle2023` " +"surveys considerations for genetic tagging of molecules for live " +"microscopy." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:18 +msgid "Bleedthrough" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:20 +msgid "" +"When performing multicolor fluorescence microscopy, it is critical to " +"choose fluorophores with sufficiently distinct excitation and emission " +"spectra; online tools such as FPbase {cite}`Lambert2019-xl` can help with" +" such selections, especially if you know the various optical components " +"of the microscope on which you will be imaging your samples (these " +"configurations can be saved and shared on FPbase; ask the maintainer of " +"the microscope you plan to use if such a configuration file is already " +"online). Even if you believe your fluorophores are sufficiently " +"separated, it is critical to check single-color fluorescent controls " +"using the same imaging conditions (and preferably on the same day) as " +"your multicolor controls to be certain no bleedthrough is occurring; it " +"is _mandatory_ to do this if you are planning to measure " +"[colocalization](content/colocalization)." +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:8 +msgid "**Resource Name**" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:9 +msgid "**Link**" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:10 +msgid "**Brief description**" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:11 +msgid "๐ŸŒ Microforum" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:12 +msgid "[link](https://forum.microlist.org/)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:13 +msgid "" +"An online forum for discussing issues with and getting advice on sample " +"preparation and microscopy" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:14 +msgid "๐ŸŒ FPbase {cite}`Lambert2019-xl`" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:15 +msgid "[link](https://www.fpbase.org/)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:16 +msgid "" +"Database for identifying fluorophores by brightness, spectra and " +"assessing compatibility with other fluorophores and with microscope " +"filters" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:17 +msgid "๐ŸŒ Bio-protocol" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:18 +msgid "[link](https://bio-protocol.org/en/about )" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:19 +msgid "" +"Website to search for protocols across biological disciplines, including " +"protocols associated with work published elsewhere. All protocols are " +"available under an open access license (CC BY or CC BY-NC)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:20 +msgid "๐ŸŒ protocolos.io" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:21 +msgid "[link](https://www.protocols.io/)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:22 +msgid "A secure platform for developing and sharing reproducible methods" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:23 +msgid "" +"๐Ÿ“„ Designing a rigorous microscopy experiment: Validating methods and " +"avoiding bias {cite}`Jost2019-nx`" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:24 +msgid "" +"[link](https://rupress.org/jcb/article/218/5/1452/120908/Designing-a" +"-rigorous-microscopy-experiment)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:25 +msgid "" +"Review of aspects of designing a rigorous light microscopy experiment, " +"including validation of samples and imaging, identification and " +"correction of errors, and strategies to avoid biases" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:26 +msgid "" +"๐Ÿ“„ Tutorial: guidance for quantitative confocal microscopy " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:27 +msgid "[link](https://doi.org/10.1038/s41596-020-0313-9)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:28 +msgid "" +"Step-by-step guidance on practical considerations for sample preparation," +" acquisition, and image analysis; primarily though not exclusively aimed " +"at users of confocal microscopy" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/02_Sample_acquisition.po b/locale/de/LC_MESSAGES/02_Sample_acquisition.po new file mode 100644 index 000000000..eb47f76e8 --- /dev/null +++ b/locale/de/LC_MESSAGES/02_Sample_acquisition.po @@ -0,0 +1,439 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../02_Sample_acquisition/Introduction.md:1 +#: ../../02_Sample_acquisition/Picking.md:3 +#: ../../02_Sample_acquisition/_notinyet_Setting_up.md:3 +msgid "Introduction" +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:3 +msgid "" +"Microscopes are optical instruments, and as such, they are composed of " +"different optical components and devices. As a beginner, it is important " +"to recognize the experimental parameters that can affect the quality and " +"rigor of the imaging data, and by extension, its interpretation." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:5 +msgid "" +"A foundational concept is the โ€œlight path,โ€ which can be used to trace " +"out lightโ€™s trajectory from the light source to the detector. When " +"working with microscopes, whether it is a cell culture microscope or a " +"cutting-edge superresolution system, it is important to take the time to " +"trace out the different light paths in the system. By approaching the " +"system as a sum of its parts means that optimizing and troubleshooting " +"become systematic processes compared to when the system is treated as a " +"black box. This [interactive tutorial at " +"MicroscopyU](https://www.microscopyu.com/tutorials/tepaths) shows the " +"light paths in a standard inverted microscope; [this " +"view](https://www.microscopyu.com/microscopy-basics/components) gives " +"more detail about the various parts." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:7 +msgid "Types of microscopes" +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:9 +msgid "" +"While far from a comprehensive list of what is available, a few of the " +"most common types of microscopes are listed below." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:10 +msgid "" +"**Widefield**, sometimes called _epifluorescence_, microscopes that take " +"in all the light available to them in a single light path; this approach " +"requires the least complex hardware, and also is often advantageous when " +"imaging dim samples. {term}`Deconvolution` is sometimes performed after " +"imaging on a widefield microscope to remove blur." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:11 +msgid "" +"**Confocal** - microscopes that remove out-of-focus light in the light " +"path, typically using one or many pinholes to physically block this " +"light. Several variants of confocal microscopy exist; spinning-disk " +"confocal microscopes are often preferred for live-cell imaging " +"applications as they tend to minimize toxicity to the sample." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:12 +msgid "" +"**Multiphoton** microscopes utilize multiple pulses of longer-wavelength " +"(lower energy) light to penetrate deep into tissue, since tissues are " +"less likely to scatter these wavelengths; once there, multiple low-" +"engergy photons hitting the fluorphore at the same time will use their " +"combined energy to activate a fluorophore that each photon alone would be" +" too weak to do. Because the benefit of these systems is in their deeper " +"penetration, they are often used for performing live-animal imaging." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:13 +msgid "" +"**Superresolution** microscopes that are designed to allows the user to " +"bypass the minimum optical resolution limit (typically 200 nm, depending " +"on sample consideration) to resolve very small structures. Sometimes this" +" is achieved with specialized hardware (such as in STED and SIM) and " +"sometimes with specialized probes (such as in PALM and STORM)." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:14 +msgid "" +"**Light sheet** microscopes that illuminate the sample perpendicular to " +"the axis of imaging, often by a second, orthogonal set of objective " +"lenses. This allows for thin optical sectioning across large volumes, but" +" introduces more considerations around sample mounting. Many variations " +"on light sheet microscopes have emerged in recent years." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:17 +msgid "" +"No matter which kind of microscope you use, scientific microscopes are " +"complex instruments with many working parts, all of which typically must " +"be in good working order and calibrated/aligned properly for quantitative" +" imaging to take place. The maintainer of your microscope will typically " +"ensure this, but speak with them regularly about questions you may have " +"and about how changes to the microscope configuration may affect your " +"ability to accurately make certain measurements. Your microscope " +"maintainer may be maintaining a large number of microscopes with a large " +"number of independent users, so if something looks \"off\", make sure to " +"talk with them before proceeding!" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:1 +msgid "Choosing the right microscopy modality" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:5 +msgid "" +"Choosing the right microscope for your experiment will be a factor both " +"of what the experiment dictates and what the researcher can access. The " +"image below (from [Fundamentals of Microscopy by Jermey " +"Sanderson](http://dx.doi.org/10.1002/cpmo.76) {cite}`Sanderson2020-qz`) " +"gives a sense of the sorts of decisions one should consider when choosing" +" a microscope; a more thorough description of the pros and cons of " +"various kinds of microscopes can be found in [this " +"tutorial](https://doi.org/10.1038/s41596-020-0313-9){cite}`Jonkman2020-bo`." +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:14 +msgid "BBBC image montage" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:14 +msgid "" +"**Flow chart to help choose which type of microscope to use.** Figure by " +"Jeremy Sanderson. [Source](https://www.researchgate.net/figure/Flow-" +"chart-to-help-choose-which-type-of-microscope-to-use_fig5_341918746) " +"{cite}`Sanderson2020-qz`" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:17 +msgid "Opportunities for microscopy resource access" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:19 +msgid "" +"While some imaging facilities are open only to members of a single " +"institution, others allow outside visitors or even sponsor visitors to " +"travel to them." +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:21 +msgid "" +"**Advanced Imaging Center - Janelia Research Campus.** The AIC was " +"created to give access to the broad scientific community to new imaging " +"instruments that are not commercially available. Proposals can be " +"submitted during open calls at [their " +"website](https://www.aicjanelia.org/apply)." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:1 +msgid "Practical considerations" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:3 +msgid "Objective selection" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:5 +msgid "" +"Microscope objectives have a number of features that must be considered " +"when deciding which objective is right for your experiment" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:7 +msgid "" +"Magnification and resolution: the higher the numerical aperture (NA) of " +"the lens, the finer the resolution one can obtain in one's sample. The NA" +" is calculated as {math}`NA=RI * sin(ฮธ)`, relating both to the " +"{term}`refractive index` of the sample, glass, and {term}`immersion " +"media` as well as the range of angles of emitted light that can be " +"collected into the lens. Unless special techniques are used, the typical " +"limit of resultion is calculated as {math}`d = ฮป / 2NA`, meaning the " +"resolution is set both by the NA of the lens but also by the wavelength " +"of light used for imaging." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:16 +msgid "microtubules imaged at 488nm and 647nm" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:16 +msgid "" +"**Decreased resolution at longer wavelengths of light**. Microtubules " +"imaged at a shorter wavelength of light show higher resolution than those" +" imaged at longer wavelengths. Adapted from Jonkman J., Brown C.M., " +"Wright G.D _et al_. Tutorial: guidance for quantitative confocal " +"microscopy. _Nat Prot_ **15**, (2020) {cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:19 +msgid "" +"Color correction: When performing multicolor microscopy, it is important " +"to choose an objective lens that is labeled as `Apo` or `Super Apo`, as " +"such lenses are corrected to focus 3 to 6 colors in the same plane at the" +" same time. `Fluor` lenses will typically focus two colors at once." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:20 +msgid "" +"Working distance: The working distance (WD) gives the distance in " +"millimeters that the lens can focus into the sample. This distance " +"includes the coverslip and mounting media as well. If imaging a thick " +"sample, and/or if needing to image away from the surface of the sample, " +"it is important to ensure the lens has a sufficient working distance." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:22 +msgid "Filter sets" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:24 +msgid "" +"It is important to make sure that the microscope that you want to image " +"on has the correct filter sets for the fluorphores you wish to use. See " +"the [section on bleedthrough](content/bleedthrough) for more information." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:26 +msgid "Z sampling" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:28 +msgid "" +"If you wish to capture multiple z sections, the spacing of these setions " +"is important if you wish to be able to perform an accurate 3D " +"reconstruction. SVI has a [fuller mathematical explanation of " +"this](https://svi.nl/NyquistRate),as well as an easy-to-use [online " +"calculator](https://svi.nl/NyquistCalculator) that you can use to " +"calculate the optimal z section spacing for your imaging conditions." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:30 +msgid "Acquisition power/speed" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:32 +msgid "" +"The amount of signal captured from any fluorophore will be related not " +"just to the intrinsic brightness of the fluorophore, but also the amount " +"of excitation light it is exposed to (due to duration, power, or both) as" +" well as amount of time and signal multiplication that happens at the " +"detector (typically a camera or a photomultiplier tube (PMT)). An optimal" +" experiment is typically one that minimizes the amount of light hitting " +"the sample (to reduce photobleaching and/or phototoxicity) while " +"acheiving adequate fluorescent signal and in minimal time on the " +"equipment. How exactly to balance these competing factors will depend on " +"the exact biology being studied and the researcher's constraints." +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:7 +msgid "**Resource Name**" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:8 +msgid "**Link**" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:9 +msgid "**Brief description**" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:10 +msgid "๐ŸŒ Nikon MicroscopyU" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:11 +msgid "[link](https://www.microscopyu.com/microscopy-basics)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:12 +msgid "" +"Fundamentals of microscopy explained for beginners with lots of images " +"and plain language descriptions of terms used in microscopy" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:13 +msgid "" +"๐Ÿ“„ Seeing is believing? A beginners' guide to practical pitfalls in image " +"acquisition {cite}`North2006-sb`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:14 +msgid "[link](https://doi.org/10.1083/jcb.200507103)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:15 +msgid "" +"An overview of common concerns to check for during sample preparation and" +" image acquisition" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:16 +msgid "๐Ÿ“„ Fluorescence microscopy - avoiding the pitfalls {cite}`Brown2007-ou`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:17 +msgid "" +"[link](https://journals.biologists.com/jcs/article/120/10/1703/29404" +"/Fluorescence-microscopy-avoiding-the-pitfalls)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:18 +msgid "" +"Short overview of some of the most common pitfalls for beginners to " +"fluorescence microscopy" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:19 +msgid "" +"๐Ÿ“„ Tutorial: guidance for quantitative confocal microscopy " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:20 +msgid "[link](https://doi.org/10.1038/s41596-020-0313-9)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:21 +msgid "" +"Step-by-step guidance on practical considerations for sample preparation," +" acquisition, and image analysis; primarily though not exclusively aimed " +"at users of confocal microscopy" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:22 +msgid "" +"๐Ÿ“„ Best practices and tools for reporting reproducible fluorescence " +"microscopy methods {cite}`Montero_Llopis2021-nb`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:23 +msgid "[link](https://www.nature.com/articles/s41592-021-01156-w)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:24 +msgid "" +"Guidelines and resources for accurate reporting of the most common " +"fluorescence light microscopy techniques, emphasizing the impact of " +"accurate microscopy metadata on data interpretation.'" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:25 +msgid "๐ŸŽฅ iBiology Microscopy Short Course" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:26 +msgid "" +"[link](https://www.youtube.com/watch?v=4c5ILWQmqRY&list=PLQFc-" +"Dxlf4pSRaEk8Xi9BzS0r8-LYmwRQ)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:27 +msgid "" +"An 8 hour video series consisting of 14 videos introducting major " +"concepts in microscopy. A longer course with >70 videos is also " +"available." +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:28 +msgid "๐ŸŽฅ Microcourses" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:29 +msgid "[link](https://www.youtube.com/@Microcourses)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:30 +msgid "" +"Videos about microscopy from the microscopy cores at Harvard Medical " +"School" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:31 +msgid "๐ŸŒ Advanced Imaging Center" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:32 +msgid "[link](https://www.aicjanelia.org/apply)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:33 +msgid "Access to the state of the art microscopy instruments and imaging experts" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:34 +msgid "๐ŸŒ Africa Microscopy Initiative" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:35 +msgid "[link](https://www.microscopy.africa/ )" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:36 +msgid "" +"Access to advanced microscopes, molecular biology and cell culture " +"equipment for scientists in Africa" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:37 +msgid "๐ŸŒ Euro-Bioimaging" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:38 +msgid "[link](https://www.eurobioimaging.eu)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:39 +msgid "Access to microcopy instruments and training for scientists in Europe" +msgstr "" + +#: ../../02_Sample_acquisition/_notinyet_Setting_up.md:1 +msgid "Setting up your acquisition" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/03_Image_analysis.po b/locale/de/LC_MESSAGES/03_Image_analysis.po new file mode 100644 index 000000000..75a7e2be0 --- /dev/null +++ b/locale/de/LC_MESSAGES/03_Image_analysis.po @@ -0,0 +1,1587 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-15 11:57-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../03_Image_analysis/Classification.md:1 +msgid "Object classification" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:3 +msgid "What is classification?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:4 +msgid "" +"Simply put, phenotypic classification is about categorizing objects into " +"different groups based on their features (aka measurements)." +msgstr "" + +#: ../../03_Image_analysis/Classification.md +#: ../../03_Image_analysis/Colocalization.md +#: ../../03_Image_analysis/Intensity.md ../../03_Image_analysis/Shape.md +#: ../../03_Image_analysis/Tracking.md +msgid "๐Ÿ“ How do I measure it?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:10 +msgid "" +"Phenotypic classification can be performed a few different ways. One way " +"to break this down is by unsupervised vs. supervised classification." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:12 +msgid "" +"In **supervised classification**, a human also provides information on " +"what the different groups of objects should look like by providing " +"representative examples of each group in a training dataset. The computer" +" then learns how to assign objects to groups based on their measurements " +"by testing models against the ground truth training dataset." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:14 +msgid "" +"For example, you could classify cells based on a visual phenotype and " +"train a machine learning classifier to derive which measurement ranges " +"are associated with different classes. This is supervised classification " +"because a person is providing instruction of how many classes there " +"should be and examples of what each class should look like for the " +"computer to learn from. An example of this could be annotating a subset " +"of cells that are in different stages of mitosis and training a " +"classifier to use your labels to find other cells in those stages." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:16 +msgid "" +"In **unsupervised classification**, you group objects based on their " +"measurements, but without any top-down human-defined guidance into how " +"many groups there are or what the groups should look like." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:18 +msgid "" +"For example, you could measure hundreds or thousands of features of cells" +" from many treatments, as is typical in large-scale cell profiling " +"experiments. Next you could let the computer cluster the cells into some " +"number of different groups based on having similar measurements. This is " +"a form of unsupervised clustering, where you observe what groups emerge " +"from a computer considering their measurements only, and not class labels" +" we impose as researchers. These sorts of clustering experiments can " +"provide novel results but may also be harder to interpret; see this " +"protocol{cite}`GarciaFossaCruz2023` for more information." +msgstr "" + +#: ../../03_Image_analysis/Classification.md +#: ../../03_Image_analysis/Colocalization.md +#: ../../03_Image_analysis/Data_management.md +#: ../../03_Image_analysis/Intensity.md ../../03_Image_analysis/Shape.md +#: ../../03_Image_analysis/Tracking.md +msgid "โš ๏ธ Where can things go wrong?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:23 +msgid "" +"**Valid measurements are still important** Classification can be simple " +"or complex, but results always depend on the validity of your " +"measurements. For this reason, all the caveats of earlier measurement " +"sections also apply here." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:24 +msgid "" +"**Machines are lazy** Machine learning classifiers arenโ€™t necessarily " +"going to learn the biologically relevant features that distinguish " +"objects from distinct groups. Confounding features, or features that vary" +" with your phenotype but are not biologically related to it, can limit " +"the usefulness of your classifier and lead to incorrect conclusions. For " +"instance, if clinicians often put rulers next to malignant looking moles " +"and not next to benign moles and try to train a machine learning " +"classifier to distinguish malignant vs. benign, the model might learn to " +"classify images with rulers as malignant without tapping into any of the " +"relevant features of the moles. This is a [real " +"example](https://pubmed.ncbi.nlm.nih.gov/30244720/) {cite}`Narla2018-qh`." +" If possible, examining which features your model is relying on to " +"classify objects can be a way to check for this. Itโ€™s also important to " +"standardize how you capture images of your different classes of objects " +"and include a large enough training set with images with lots of " +"variation. You wouldnโ€™t want all your positive cells to come from samples" +" you imaged in March and all your negative cells from samples you imaged " +"in January, for example." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:25 +msgid "" +"**Violating model assumptions** If using a machine learning classifier, " +"different models come with different baked-in assumptions. If youโ€™re " +"starting out, it can be difficult to know which to pick. There are " +"interactive tools such as [CellProfiler " +"Analyst](https://academic.oup.com/bioinformatics/article/32/20/3210/2196630)" +" {cite}`Stirling2021-ov` and [Piximi](https://www.piximi.app/) that make " +"training a classifier easier, especially if you donโ€™t know how to code." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:26 +msgid "" +"**Messy boundaries** Most methods of supervised classification, where the" +" user assigns objects to a score or to a bin, ultimately treat each bin " +"as a totally separate entity; biology is rarely so neat. For example, a " +"supervised classifier for cell cycle phase must assign a cell to one " +"phase, but in fact progression through the cell cycle is not a perfectly " +"switch-like process, as can be visualized by measurements of individual " +"cells (colored by their class given by a human observer). More " +"sophisticated methods may be needed to classify more continuous " +"phenotypes" +msgstr "" + +#: ../../03_Image_analysis/Classification.md +msgid "a continuous distribution of cell cycle states" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:35 +msgid "" +"**Strict division into supervised classes can be tricky for continuous " +"biological processes**. Adapted from Eulenberg, P., Kรถhler, N., Blasi, T." +" _et al_. Reconstructing cell cycle and disease progression using deep " +"learning. _Nat Commun_ **8**, 463 (2017) {cite}`Eulenberg2017-ax`" +msgstr "" + +#: ../../03_Image_analysis/Classification.md +#: ../../03_Image_analysis/Colocalization.md +#: ../../03_Image_analysis/Data_management.md +#: ../../03_Image_analysis/Intensity.md ../../03_Image_analysis/Shape.md +#: ../../03_Image_analysis/Tracking.md +msgid "๐Ÿ“š๐Ÿคทโ€โ™€๏ธ Where can I learn more?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:41 +msgid "" +"๐Ÿ“„ [Data-analysis strategies for image-based cell " +"profiling](https://www.nature.com/articles/nmeth.4397) " +"{cite}`Caicedo2017-ks`" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:42 +msgid "" +"๐Ÿ“„ [Scoring diverse cellular morphologies in image-based screens with " +"iterative feedback and machine " +"learning](https://www.pnas.org/doi/10.1073/pnas.0808843106) " +"{cite}`Jones2009-zz`" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:43 +msgid "" +"๐ŸŽฅ [iBiology video series: Measurement and Phenotype " +"Classification](https://www.youtube.com/watch?v=Odi9pIerT7I)" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:44 +msgid "" +"๐Ÿ“„ [Interpreting Image-based Profiles using Similarity Clustering and " +"Single-Cell Visualization](https://doi.org/10.1002/cpz1.713) " +"{cite}`GarciaFossaCruz2023`" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:1 +msgid "Colocalization" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:4 +msgid "What is colocalization?" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:6 +msgid "" +"Colocalization is when two or more different labels (e.g., eGFP and " +"mCherry) spatially overlap in your image (also called co-occurrence). " +"Another component of colocalization is that the fluorescent labels often " +"correlate in intensity (i.e., pixels with brighter eGFP also have " +"brighter mCherry). It is very important to measure colocalization " +"quantitativelyโ€“**do not just trust your eyes!**" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:8 +msgid "" +"It is also important to recognize that co-ocurrence does not " +"_necessarily_ imply interaction." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:11 +msgid "" +"As an example, it is possible for two people to work in the same building" +" an never interact." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:21 +msgid "degrees of colocalization" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:21 +msgid "**Colocalization is about intensity and spatial overlap of labels**" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:28 +msgid "" +"There are two main branches for how to look at colocalization: Object-" +"based and correlation-based." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:30 +#, python-format +msgid "" +"**Object-based colocalization** is appropriate when you want to be able " +"to say something about a fraction of objects being positive for multiple " +"labels (e.g., 99% of eGFP+ cells were also mCherry+). Hereโ€™s a sample " +"workflow:" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:51 +msgid "" +"**Correlation-based colocalization** is more appropriate when the labels " +"youโ€™re measuring are not found in discrete objects or when you predict " +"that the signal in the labels should correlate. Correlation-based " +"colocalization is simpler to measure as it does not require any " +"{term}`segmentation` of objects. Pearson correlation coefficients are " +"readily measurable in most image analysis softwares (e.g., FIJI, " +"CellProfiler, etc.)." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:55 +msgid "" +"**Not having adequate controls** (e.g., single label controls where only " +"one fluorescent label is present). Noise, uneven illumination, and other " +"technical artifacts can cause correlation between two channels" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:56 +msgid "" +"**Not correcting for shift between channels** Itโ€™s common to have some " +"degree of shift between different imaging channels due to differences in " +"optics (e.g., different filter cubes). Not correcting for this shift " +"(e.g., by measuring it and applying the corresponding correction to the " +"channels) can limit your ability to detect colocalization." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:57 +msgid "" +"**Bleedthrough** Sometimes signal from one fluorescent channel bleeds " +"into another, which can falsely increase your detected colocalization. " +"This happens most commonly with fluorophores that are similar in spectra " +"(e.g., GFP and YFP). This is caused by fluorophore in one channel being " +"weakly excited by light used to excite a different fluorophore and the " +"resulting emitted fluorescence makes it through the emission filter " +"(e.g., your green objects show up in the yellow channel as well). Assess " +"this with single label controls." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:58 +msgid "" +"**Improper interpretation of your colocalization metric** The details of " +"the metric chosen here are very important - they vary widely in terms of " +"their inclusion of background pixels, their sensitivity to signal-to-" +"noise, etc. Consultation with an expert and the inclusion of proper " +"controls can help you be assured that your measurement is truly what you " +"think it is." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:63 +msgid "" +"๐Ÿ”ข [Theoretical background on " +"colocalization](https://svi.nl/ColocalizationTheory)" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:64 +msgid "" +"๐Ÿ“„ [Image co-localization - co-occurrence versus " +"correlation](https://journals.biologists.com/jcs/article/131/3/jcs211847/77151" +"/Image-co-localization-co-occurrence-versus) {cite}`Aaron2018-qi`" +msgstr "" + +#: ../../03_Image_analysis/Common_types_of_analysis.md:1 +msgid "Common types of analysis" +msgstr "" + +#: ../../03_Image_analysis/Common_types_of_analysis.md:3 +msgid "" +"In this section, we detail information and tips about some common, very " +"useful types of image analysis. We first describe two aspects of " +"morphological analysis. **Morphology** is the study of the appearance, " +"form, and structure of an object and morphological measurements include " +"those based on object **shape** (e.g. cell area) as well as **intensity**" +" (e.g. mean brightness of GFP). After describing shape-based and " +"intensity-based analyses, we also present tips for measuring " +"**colocalization**, **tracking objects**, and **classifying objects**." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:1 +msgid "Data management and sharing" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:3 +msgid "What is it?" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:5 +msgid "" +"Both journals and scientific funders have placed more emphasis in recent " +"years on the fact that it is critical to save both the raw data generated" +" during the course of scientific discovery as well as the workflows used " +"to process such data. While mandates to publicly deposit raw image data " +"have recently gone into place in several countries, it can be difficult " +"for researchers to know where to store images, code, and metadata " +"associated with their bioimaging experiments." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md +msgid "๐Ÿค” What are my options?" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:9 +msgid "" +"There are many options for storing image data in online repositories. " +"These services make it easy to share and reuse data. The best option will" +" depend on the size of the dataset, the budget for storage, whether there" +" is related non-image data, and how much metadata is available for the " +"dataset. Some options are summarized below:" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md +msgid "Comparison of various data respositories" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:18 +msgid "" +"**Options for storing bioimaging data** Figure by Beth Cimini (2023) " +"[Source](https://doi.org/10.5281/zenodo.7628604)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:24 +msgid "" +"**Not storing original versions of images**. It is critical that the raw " +"image data be saved and stored. It is very important that these files are" +" not compressed formats (e.g., '.jpeg') or modified from the original " +"files on which analysis was performed. If files are modified, " +"measurements will change and the analysis pipeline will not be " +"reproducible to anyone else." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:26 +msgid "" +"**Necessary imaging metadata is unavailable**. In order to properly " +"calibrate measurement data, it's critical that information like pixel " +"size (e.g., in microns), the microscope manufacturer and model, and " +"acquisition settings are included alongside the data. If this isn't " +"included, it will be very difficult to reproduce results or use the " +"combine the data with other datasets." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:32 +msgid "๐ŸŒ [Zenodo](https://zenodo.org/)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:33 +msgid "๐ŸŒ [Figshare](https://figshare.com)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:34 +msgid "๐ŸŒ [Dryad](https://datadryad.org)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:35 +msgid "" +"๐ŸŒ [Bioimage Archive](https://www.ebi.ac.uk/bioimage-archive/) " +"{cite}`Hartley2022-mt`" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:36 +msgid "" +"๐ŸŒ [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) " +"{cite}`Williams2017-yy`" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:37 +msgid "๐ŸŒ [BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr`" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:38 +msgid "" +"๐ŸŒ [Cell Painting Gallery](https://registry.opendata.aws/cellpainting-" +"gallery/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:1 +msgid "General Use Software" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:3 +msgid "" +"Tools on this page tend to be relatively multipurpose across a lot of " +"kinds of analyses and/or images. For tools that specialize in certain " +"analysis steps, see the [Specific Use Software](./SpecificUseSoftware.md)" +" page." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:6 +msgid "" +"\"logo\" ImageJ" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:9 +msgid "" +"[ImageJ](https://imagej.net/) " +"{cite}`Schneider2012-gs,Schindelin2012-kk,Rueden2017-ku` is an imaging " +"processing program that is capable of operating on a variety of images " +"including multichannel, 3D and time series. It provides a variety of " +"basic imaging processing operations, but it can be complemented with a " +"variety of plugins for more complex tasks." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md +#: ../../03_Image_analysis/SpecificUseSoftware.md +msgid "What are its disadvantages?" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:14 +msgid "" +"Imaging processing operations are done one at a time, while it has the " +"capability of batch processing and creating macros it does require some " +"understanding of coding." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:15 +msgid "" +"But while it can open large images, there is a size limit to the size it " +"can handle based on the available memory. And even if it can open large " +"images it can slow down performance." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md +#: ../../03_Image_analysis/SpecificUseSoftware.md +msgid "How to download/install and learn more?" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:20 +msgid "To download ImageJ or its โ€œbatteries-includedโ€ distribution Fiji go to" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:24 +msgid "๐ŸŒ [ImageJ download](https://imagej.net/downloads)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:26 +msgid "" +"For documentation and tutorials on how to use ImageJ as well as a list of" +" available plugins" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:30 +msgid "๐ŸŒ [ImageJ basics](https://imagej.net/learn/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:34 +msgid "" +"\"logo\" CellProfiler" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:36 +msgid "" +"[CellProfiler](https://cellprofiler.org/) {cite}`Stirling2021-sg` is a " +"software designed for biologists by biologists; it creates a bridge " +"between image analysis and scientist with no need of computational " +"expertise. It was designed with the idea of an image analysis pipeline in" +" mind: it allows you to take a series of interoperable modules to design " +"your own custom analysis pipeline that can be applied to one or thousands" +" of images, making it suitable for high throughput image analysis." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:42 +msgid "" +"CellProfiler canโ€™t handle large images, like whole tissue sections from " +"histology experiments. The image size is currently limited by the " +"available memory on your computer." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:43 +msgid "" +"While CellProfiler can perform analysis on 3D images the visualization is" +" limited to a one z-plane at a time via a slider on the viewing window." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:44 +msgid "Also several features of CellProfiler are only available for 2D images." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:49 +msgid "To download CellProfiler" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:53 +msgid "๐ŸŒ [CellProfiler download](https://cellprofiler.org/releases)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:55 +#: ../../03_Image_analysis/GeneralUseSoftware.md:84 +#: ../../03_Image_analysis/GeneralUseSoftware.md:113 +#: ../../03_Image_analysis/GeneralUseSoftware.md:142 +#: ../../03_Image_analysis/GeneralUseSoftware.md:172 +#: ../../03_Image_analysis/SpecificUseSoftware.md:59 +msgid "For documentation examples and tutorials." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:59 +msgid "" +"๐ŸŒ [CellProfiler user manual](https://cellprofiler-" +"manual.s3.amazonaws.com/CellProfiler-4.2.4/index.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:60 +msgid "๐ŸŒ [Examples](https://cellprofiler.org/examples)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:61 +msgid "๐ŸŒ [Tutorials](https://tutorials.cellprofiler.org/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:62 +msgid "" +"๐ŸŽฅ [Video tutorials and " +"workshops](https://www.youtube.com/playlist?list=PLXSm9cHbSZBBy7JkChB32_e3lURUcT3RL)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:66 +msgid "" +"\"logo\" QuPath" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:68 +msgid "" +"[QuPath](https://qupath.github.io/) {cite}`Bankhead2017-kz` offers a wide" +" set of image analysis tools that can be applied to whole slide images. " +"For that reason it is widely utilized with pathology images, but it can " +"be used with other images as well. QuPath also contains pixel " +"classification tools and can integrate with ImageJ (e.g., for sending " +"{term}`ROIs` between the programs, or for accessing ImageJ plugins)." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:73 +msgid "" +"To get the most out of QuPath (especially when analyzing many images), " +"some scripting and knowledge of coding (or adapting otherโ€™s code) is " +"necessary" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:78 +msgid "To download QuPath" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:82 +msgid "๐ŸŒ [QuPath download](https://qupath.github.io/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:88 +msgid "๐ŸŒ [QuPath user manual](https://qupath.readthedocs.io/en/stable/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:89 +msgid "๐ŸŽฅ [Video tutorials and workshops](https://www.youtube.com/c/qupath)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:93 +msgid "" +"\"logo\" Icy" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:95 +msgid "" +"[Icy](https://icy.bioimageanalysis.org/) {cite}`De_Chaumont2012-pe` is an" +" out of the box image analysis tools, it utilizes plugins to create " +"visual image analysis protocols that can be shared with other users." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:102 +msgid "Icy interoperability with other softwares is limited to ImageJ" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:107 +msgid "To download Icy" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:111 +msgid "๐ŸŒ [Icy download](https://icy.bioimageanalysis.org/download/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:117 +msgid "๐ŸŒ [Icy course and tutorial](https://icy.bioimageanalysis.org/trainings/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:118 +msgid "" +"๐ŸŽฅ [Bioimage analysis with Icy " +"](https://www.youtube.com/watch?v=myal9BD6J-k)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:122 +msgid "" +"\"logo\" MIB (Microscopy Image Browser)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:124 +msgid "" +"[MIB](http://mib.helsinki.fi/index.html) {cite}`Belevich2016-vi` is a " +"user-friendly software for image analysis of multidimensional datasets " +"for both light and electron microscopy. It allows you to use the whole " +"acquired data for its analysis and extraction of morphological features." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:131 +msgid "" +"It was created using MATLAB, a standalone packaged version exist, but " +"they do not use the most up-to-date MATLAB releases" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:136 +msgid "To download MIB" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:140 +msgid "๐ŸŒ [MIB download](http://mib.helsinki.fi/downloads.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:146 +msgid "" +"๐ŸŒ [MIB user " +"guide](http://mib.helsinki.fi/help/main2/im_browser_user_guide.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:147 +msgid "๐ŸŒ [Tutorials](http://mib.helsinki.fi/tutorials.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:148 +msgid "" +"๐ŸŽฅ [Video " +"tutorials](https://www.youtube.com/playlist?list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:152 +msgid "" +"\"logo\" napari" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:154 +msgid "" +"[napari](https://napari.org/) {cite}`Sofroniew2022-nd` is being developed" +" as a multi-dimensional image viewer that can be expanded via a variety " +"of plugins to perform basic and complex image analysis tasks." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:161 +msgid "" +"napari is still in the development stages, but it is a very popular " +"platform and already has a variety of plugins and use cases with " +"tutorials available." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:166 +msgid "To download napari" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:170 +msgid "" +"๐ŸŒ [napari bundled app download " +"](https://napari.org/stable/tutorials/fundamentals/installation.html" +"#install-as-a-bundled-app)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:176 +msgid "" +"๐ŸŒ [New to napari guide " +"](https://napari.org/stable/tutorials/fundamentals/getting_started.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:177 +msgid "๐ŸŒ [Tutorials](https://napari.org/stable/tutorials/index.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:178 +msgid "" +"๐ŸŒ [Bioimage Analysis with Napari - A FocalPlane blog " +"series](https://focalplane.biologists.com/category/blog-series/bio-image-" +"analysis-with-napari/)" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:1 +msgid "Intensity measurements" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:3 +msgid "What are intensity measurements?" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:4 +msgid "" +"Intensity refers to the brightness of signal for a fluorescent label. " +"Using intensity measurements, we can infer a relative amount of " +"fluorophore or stain. So for instance, if you have a protein tagged with " +"a fluorophore, you can measure the intensity of that fluorophore to get a" +" relative measure of how much protein is present in your sample. " +"Intensity measurements include the following (non-exhaustive) and can be " +"measured within an image, in a object like a cell, in subregions of an " +"object:" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:5 +msgid "**Mean intensity**: the average intensity across all pixels" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:6 +msgid "" +"**Integrated intensity**: the sum of pixel intensities, a proxy for the " +"total amount of that marker in an object" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:7 +msgid "**Texture measurements**: the smoothness of the intensities" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:13 +msgid "" +"Intensity is relatively straightforward to measure, but can be quite " +"tricky to do _correctly_ (see below). We strongly suggest you contact an " +"image analysis expert before proceeding with this type of analysis " +"because there are so many places things can go wrong. In general, you " +"want to measure on either raw images, or illumination-corrected images, " +"but in general with minimal {term}`image processing`. Illumination-" +"correction is a form of {term}`image processing` to compensate for the " +"uneven pattern of illumination produced by most light sources where the " +"middle of the field of illumination is brighter than the edges. Then " +"intensity measurements can be made in any standard image analysis " +"software, either across the whole image or in identified objects. See " +"below for an example workflow:" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:35 +msgid "" +"To understand saturation another way, imagine youโ€™re trying to measure " +"average male height with a 2 meter tape measure. If our sample contains " +"men that are taller than 2 meters, we canโ€™t tell _how much taller_ than 6" +" feet they are; theyโ€™re like saturated pixels that exceed the intensity " +"we can detect. This saturation of our measurement tool means we canโ€™t " +"accurately report average height." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:38 +msgid "" +"**Saturation** Saturated pixels are so bright their intensity values max " +"out our detector (camera). If you have saturated pixels in the cells " +"youโ€™re trying to measure, you really canโ€™t do most intensity " +"measurements. This is because for saturated pixels, you donโ€™t know how " +"bright they really are, just that theyโ€™re brighter than you can detect. " +"There are some intensity measurements that are robust to some saturation." +" For example, the median intensity of an image wonโ€™t be affected by " +"saturation unless you have >ยฝ the image saturated. But measurements like " +"mean intensity will be affected by saturation." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:40 +msgid "" +"**Inadequate controls** In most cases, the exact intensity measures you " +"get donโ€™t mean anything biologically in isolation. Itโ€™s only by " +"comparison of conditions that we can generate some biological insight. A " +"control condition is therefore **very** important to compare to your " +"experimental condition." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:42 +msgid "" +"**Not matching imaging conditions across experimental conditions** " +"Because intensity measures are affected by exposure time, light source " +"intensity, and other factors, itโ€™s very important to match imaging " +"settings across your samples. Relatedly, you should make sure you donโ€™t " +"separate imaging your experimental and control conditions to different " +"days if this can be in any way avoided. Fluorophores can become dimmer " +"over time in samples, which complicates interpretation if different " +"sample types were imaged on different days." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:48 +msgid "" +"๐ŸŽ“ [Neubias training resource on intensity " +"measures](https://neubias.github.io/training-" +"resources/measure_intensities/index.html)" +msgstr "" + +#: ../../03_Image_analysis/Introduction.md:1 +#: ../../03_Image_analysis/Software.md:3 +#: ../../03_Image_analysis/_notinyet_Image_processing.md:3 +#: ../../03_Image_analysis/_notinyet_Image_segmentation.md:3 +msgid "Introduction" +msgstr "" + +#: ../../03_Image_analysis/Introduction.md:3 +msgid "" +"Microscopy images are inherently quantitative, which makes them a very " +"powerful data source. As a biologist, image analysis allows you to " +"translate these numbers into insights that answer biological questions. " +"For our purposes, **image analysis** is the process of measuring aspects " +"of biological phenomena captured in microscopy images. Microscopy images " +"are already _inherently quantitative_ in that they are matrices (i.e., " +"grids) of numbers. However, image analysis is the process of turning " +"these raw numbers into biologically interpretable measurements. Image " +"analysis typically involves a series of steps that can be collected into " +"a pipeline or analysis workflow. A simple example workflow is shown " +"below:" +msgstr "" + +#: ../../03_Image_analysis/Introduction.md:26 +msgid "" +"The specifics of your workflow depend on your biological question. Below " +"we present a few common types of analysis for fluorescence microscopy " +"experiments. For each, weโ€™ll explain key ideas to understand before you " +"begin, common pitfalls, and links to a few key resources to learn more. " +"We encourage you to think about your analysis strategy even before " +"beginning sample preparation. While not always possible, speaking with an" +" image analysis expert in your local core facility or asking a question " +"on the [image.sc](https://image.sc) forum _before you begin_ can save you" +" a ton of time and headache when it comes to designing an image analysis " +"strategy." +msgstr "" + +#: ../../03_Image_analysis/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:7 +msgid "**Resource Name**" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:8 +msgid "**Link**" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:9 +msgid "**Brief description**" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:10 +msgid "๐ŸŒ Image.sc {cite}`Rueden2019-qp`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:11 +msgid "[link](https://forum.image.sc/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:12 +msgid "Discussion forum for bioimage analysis software" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:13 +msgid "๐ŸŒ Peter Bankheadโ€™s Intro to Bioimage Analysis" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:14 +msgid "[link](https://bioimagebook.github.io/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:15 +msgid "" +"Guide for absolute beginners to image analysis, including embedded " +"questions/answers, exercises with Python and ImageJ, and videos to check " +"understanding" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:16 +msgid "๐Ÿ“– Bioimage Data Analysis {cite}`Miura2016-wq`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:17 +msgid "[link](https://analyticalscience.wiley.com/do/10.1002/was.00050003/full/bioimagedataanalysis.pdf)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:18 +msgid "" +"A free online textbook introducing various topics by Bioimage Analysis " +"experts, edited by Kota Miura" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:19 +msgid "๐Ÿ“„ Reproducible image handling and analysis {cite}`Miura2021-mb`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:20 +msgid "[link](https://www.embopress.org/doi/full/10.15252/embj.2020105889)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:21 +msgid "" +"An article reviewing major pitfalls in image handling and how to avoid " +"them and create reproducible analysis workflows" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:22 +msgid "๐Ÿ“„ Made to measure: an introduction to quantification in microscopy data" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:23 +msgid "[link](https://arxiv.org/abs/2302.01657#) {cite}`Culley2023-dj`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:24 +msgid "" +"An article describing several common classes of measurements made in " +"microscopy data, as well as technical factors that may affect the results" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:25 +msgid "" +"๐Ÿ“„ A Hitchhiker's guide through the bio-image analysis software universe " +"{cite}`Haase2022-ad`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:26 +msgid "[link](https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:27 +msgid "" +"An article that gives guidance and a glossary of available image analysis" +" software and packages" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:28 +msgid "๐ŸŒ BioImage Informatics Index" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:29 +msgid "[link](https://biii.eu/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:30 +msgid "" +"Repository platform for searching bioimage analysis tools and workflows " +"based on the problem, method or software of choice" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:31 +msgid "๐ŸŽฅ iBiology Bioimage Analysis video series" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:32 +msgid "[link](https://youtu.be/1xo4vi6Ub4I)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:33 +msgid "" +"Video series that introduces Bioimage analysis, including overviews of " +"{term}`image processing`, {term}`segmentation`, tracking, making and " +"interpreting measurements, tips and pitfalls" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:34 +msgid "๐ŸŒ Bioimage ANalysis Desktop (BAND)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:35 +msgid "[link](https://band.embl.de)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:36 +msgid "" +"Access to virtual desktops allowing access to bioimage analysis software " +"from a browser" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:37 +msgid "๐ŸŒ Galaxy Imaging Node" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:38 +msgid "[link](https://imaging.usegalaxy.eu/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:39 +msgid "" +"A Galaxy node prepopulated with a number of open-source image analysis " +"tools and workflows, making it easy to create and share reproducible FAIR" +" workflows" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:40 +msgid "๐ŸŒ Image Analysis Training Resources" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:41 +msgid "[link](https://neubias.github.io/training-resources/index.html)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:42 +msgid "" +"Image analysis traning resources collected by NEUBIAS, styled based on " +"The Carpentries" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:43 +msgid "๐ŸŒ Bioimage Analysis AwesomeList" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:44 +msgid "[link](https://github.com/hallvaaw/awesome-biological-image-analysis)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:45 +msgid "" +"A curated [AwesomeList](https://github.com/sindresorhus/awesome) of " +"resources related to bioimage analysis" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:46 +msgid "๐ŸŒ Bioimage Analysis Notebooks" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:47 +msgid "[link](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:48 +msgid "" +"A collection of Python Jupyter notebooks for BioImageAnalysis, GPU-" +"accelerated image processing, bio-image data science and more" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:1 +msgid "Size and Shape measurements" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:3 +msgid "What are size measurements?" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:4 +msgid "" +"Size measurements describe the dimensions of objects in your image. " +"Common size measurements include:" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:6 +msgid "" +"**Area**: the 2D space an object takes up in the image or the 3D surface " +"area of an object" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:7 +msgid "**Volume**: the 3D space an object takes up in a 3D image" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:8 +msgid "**Perimeter**: the distance around the edge of an object" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:10 +msgid "What are shape measurements?" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:11 +msgid "" +"Shape measurements describe the 2D or 3D form of objects in our sample. " +"Common shape measurements include:" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:13 +msgid "" +"**Circularity**: How round vs. elongated an object is. Formally defined " +"as $circularity = 4pi*{area}/{perimeter}^2$ where 1 is a perfect circle " +"and circularity <1 is a more elongated polygon." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:14 +msgid "" +"**Solidity**: how dense vs. wispy/holey an object is. Formally defined as" +" $solidity = area/convex area$ where _convex area_ is akin to the area " +"inside a shape formed by stretching a rubber band around the object." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:20 +msgid "" +"After segmenting an image to locate the pixels belonging to different " +"objects, morphology can be measured readily in many image analysis " +"softwares, like FIJI and CellProfiler. For example, in {term}`Fiji`, " +"after identifying your objects as {term}`ROIs`, be sure to **Analyze > " +"Set Measurementsโ€ฆ** and select โ€œShape Descriptorsโ€ then simply measure " +"your {term}`ROIs` with **Analyze > Measure**. In CellProfiler, this is " +"accomplished using the module MeasureObjectSizeShape." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:25 +msgid "" +"**Not understanding the limitations of your images**. All biological " +"structures are 3D, but we often analyze 2D images. Often this is still " +"very useful! But the larger and more complex your objects (e.g., neurons " +"in a tissue section), the more limited a 2D view becomes." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:26 +msgid "" +"**Failing to use calibrated units**. Be sure to properly calibrate your " +"images and present final measurements in microns (or similar units). If " +"measuring 3D images, be sure to take into account the z-step, which is " +"likely larger than the xy pixel size." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:31 +msgid "" +"๐Ÿ“„ [Current Methods and Pipelines for Image-Based Quantitation of Nuclear " +"Shape and Nuclear Envelope " +"Abnormalities](https://www.mdpi.com/2073-4409/11/3/347/htm) " +"{cite}`Janssen2022-bm`" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:32 +msgid "" +"๐ŸŒ [Description of morphological measurements made by CellProfiler](https" +"://cellprofiler-" +"manual.s3.amazonaws.com/CellProfiler-4.2.4/modules/measurement.html#id20)" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:33 +msgid "" +"๐ŸŽ“ [Plain language description of various morphological measures by " +"Michael " +"Wirth](http://www.cyto.purdue.edu/cdroms/micro2/content/education/wirth10.pdf)" +msgstr "" + +#: ../../03_Image_analysis/Software.md:1 +msgid "Open source software" +msgstr "" + +#: ../../03_Image_analysis/Software.md:5 +msgid "" +"When it comes time to select a software program for your image analysis, " +"there are many options, some more general and others highly specialized " +"to specific image modalities or types of experiments. In general, a good " +"place to start exploring is by examining papers in your field and seeing " +"what others have used to analyze similar experiments to your own. Itโ€™s " +"important to note that there isnโ€™t one correct answer to \"Which program " +"should I use?\" Depending on your biological question, your images, and " +"your own comfort with coding, there are many options available." +msgstr "" + +#: ../../03_Image_analysis/Software.md:7 +msgid "" +"Below, we summarize the use-cases and limitations of some of the most " +"common, free and open-source software for image analysis, this is a small" +" list and more extensive ones exist like the [A Hitchhiker's guide " +"through the bio-image analysis software " +"universe](https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451)" +" {cite}`Haase2022-ad` and the [BioImage Informatics " +"Index](https://biii.eu) {cite}`Paul-Gilloteaux2021-vw`." +msgstr "" + +#: ../../03_Image_analysis/Software.md:9 +msgid "" +"Whatever software you choose, be sure to include a detailed description " +"of your analysis in your methods, with pipeline or workflow files if " +"possible, so others can reproduce your work. Also be sure to cite the " +"analysis software you use! This helps developers of the software get " +"grant funding and helps others find useful tools." +msgstr "" + +#: ../../03_Image_analysis/Software.md:17 +#: ../../03_Image_analysis/Software.md:26 +#: ../../03_Image_analysis/Software.md:35 +#: ../../03_Image_analysis/Software.md:44 +#: ../../03_Image_analysis/Software.md:53 +#: ../../03_Image_analysis/Software.md:62 +#: ../../03_Image_analysis/Software.md:71 +#: ../../03_Image_analysis/Software.md:80 +#: ../../03_Image_analysis/Software.md:89 +msgid "card-img-top" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "ImageJ" +msgstr "" + +#: ../../03_Image_analysis/Software.md:21 +msgid "" +"[ImageJ](https://imagej.net/) is an imaging processing program that is " +"capable of operating on a variety of images including multichannel, 3D " +"and time series. It provides basic imaging processing operations and has " +"a variety of plugins for more complex tasks. [Read " +"more...](content/imagej)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "CellProfiler" +msgstr "" + +#: ../../03_Image_analysis/Software.md:30 +msgid "" +"[CellProfiler](https://cellprofiler.org/) was designed with the idea of " +"an image analysis pipeline in mind; it allows you to take a series of " +"interoperable modules to design your own custom analysis pipeline that " +"can be applied to one or thousands of images, making it suitable for high" +" throughput image analysis. [Read more...](content/cellprofiler)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "QuPath" +msgstr "" + +#: ../../03_Image_analysis/Software.md:39 +msgid "" +"[QuPath](https://qupath.github.io/) offers a wide set of image analysis " +"tools that can be applied to whole slide images like pathology images, " +"but it can be used with other images as well. QuPath also contains pixel " +"classification tools and can integrate with ImageJ. [Read " +"more...](content/qupath)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "Icy" +msgstr "" + +#: ../../03_Image_analysis/Software.md:48 +msgid "" +"[Icy](https://icy.bioimageanalysis.org/) is an out of the box image " +"analysis tools, it utilizes plugins to create visual image analysis " +"protocols that can be shared with other users. [Read " +"more...](content/icy)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "MIB" +msgstr "" + +#: ../../03_Image_analysis/Software.md:57 +msgid "" +"[MIB](http://mib.helsinki.fi/index.html) is a user-friendly software for " +"image analysis of multidimensional datasets for both light and electron " +"microscopy. It allows you to use the whole acquired data for its analysis" +" and extraction of morphological features. [Read more...](content/mib)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "napari" +msgstr "" + +#: ../../03_Image_analysis/Software.md:66 +msgid "" +"[napari](https://napari.org/) is being developed as a multi-dimensional " +"image viewer that can be expanded via a variety of plugins to perform " +"basic and complex image analysis tasks. [Read more...](content/napari)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "Cellpose" +msgstr "" + +#: ../../03_Image_analysis/Software.md:75 +msgid "" +"[Cellpose](https://www.cellpose.org/) is a {term}`segmentation` " +"algorithm, it provides a graphical user interface that allows users to " +"use trained models or train their own using their images and annotations." +" [Read more...](content/cellpose)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "ilastik" +msgstr "" + +#: ../../03_Image_analysis/Software.md:84 +msgid "" +"[ilastik](https://www.ilastik.org/) is a tool for interactive image " +"classification, {term}`segmentation` and analysis. It leverages machine-" +"learning algorithms to perform pixel and object-level classification. " +"Using it requires no experience in {term}`image processing`. [Read " +"more...](content/ilastik)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "Piximi" +msgstr "" + +#: ../../03_Image_analysis/Software.md:93 +msgid "" +"[Piximi](https://www.piximi.app/) is an application for annotation and " +"classification that runs entirely from your browser and requires no " +"installation and minimal setup. [Read more...](content/piximi)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:1 +msgid "Specific Use Software" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:3 +msgid "" +"Tools on this page tend to be extremely good at certain tasks, but are " +"less intended for a wide range of use cases. For tools with broader areas" +" of focus, see the [General Use Software](./GeneralUseSoftware.md) page." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:6 +msgid "" +" Cellpose" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:8 +msgid "" +"[Cellpose](https://www.cellpose.org/) {cite}`Stringer2021-uq` is a " +"{term}`segmentation` algorithm, it provides a graphical user interface " +"that allows users to use trained models or train their own using their " +"images and annotations." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md +msgid "What type of image analysis problem is it best at?" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:13 +msgid "" +"Object {term}`segmentation`, most trained models are for cell " +"{term}`segmentation` but could be applied to segment other similar " +"objects" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:20 +msgid "Its use requires some computational knowledge." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:21 +msgid "" +"Training a new model requires manual annotation correction that can be " +"time consuming, but is likely less time consuming than other methods of " +"training models." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:28 +msgid "" +"๐ŸŒ [Installation " +"instructions](https://cellpose.readthedocs.io/en/latest/installation.html)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:29 +msgid "๐ŸŽฅ [How to use tutorial](https://www.youtube.com/watch?v=5qANHWoubZU)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:33 +msgid "" +"\"logo\" ilastik" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:35 +msgid "" +"[ilastik](https://www.ilastik.org/) {cite}`Berg2019-no` is a tool for " +"interactive image classification, {term}`segmentation` and analysis. It " +"leverages machine-learning algorithms to perform pixel and object-level " +"classification. Using it requires no experience in {term}`image " +"processing`." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:40 +msgid "" +"It can be used for both instance {term}`segmentation` and semantic " +"{term}`segmentation`. It does also perform {term}`segmentation` and " +"tracking, though with somewhat fewer tunable parameters than some other " +"tools offer." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:47 +msgid "" +"Sometimes loading or exporting images can require a bit of " +"troubleshooting to get the dimensions correct." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:48 +msgid "" +"ilastik is limited by your computerโ€™s RAM so training a model with lots " +"of features or working with very large images is likely to slow you down." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:53 +msgid "To download ilastik:" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:57 +msgid "๐ŸŒ [ilastik download ](https://www.ilastik.org/download.html)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:63 +msgid "" +"๐ŸŒ [User guide](https://www.ilastik.org/documentation/index.html#user-" +"documentation)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:67 +msgid "" +"\"logo\" Piximi" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:70 +msgid "" +"[Piximi](https://www.piximi.app/) is an application for annotation and " +"classification that runs entirely from your browser and requires no " +"installation and minimal setup." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:75 +msgid "Piximi can do image classification using machine learning" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:82 +msgid "" +"It is still in the developing phases and some of its proposed features " +"are not available yet" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:89 +msgid "๐ŸŒ [Piximi website ](https://www.piximi.app/)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:90 +msgid "๐ŸŒ [Piximi user guide ](https://documentation.piximi.app/intro.html)" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:1 +msgid "Object tracking" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:3 +msgid "What is tracking?" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:4 +msgid "" +"Tracking, or _object tracking_, refers to the ability to estimate the " +"location of objects in motion from one frame of video to the next. " +"Practically, object tracking in microscopy involves identifying your " +"objects in each frame of your video, then relating objects from frame to " +"frame to be able to identify the same cell as it moves in space." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:10 +msgid "" +"There are several options for tracking objects, like the " +"[TrackMate](https://imagej.net/plugins/trackmate/) {cite}`Tinevez2017-fb`" +" plugin in Fiji, but tracking is somewhat more complex to setup than the " +"previous analyses. In addition to just identifying objects in the " +"movie/time series, tracking also allows you to identify splitting (e.g. " +"mitosis) and merging events. There are many measurements that come out of" +" tracking, including spatial measures like where the objects move to, " +"speed measurements, distance traveled (length of track), and rate of " +"splitting events (e.g., mitotic events) and merging events." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:15 +msgid "" +"**Poor {term}`segmentation`** If objects are dropping out from frame to " +"frame, this makes it more difficult to track them over time. Accurate " +"{term}`segmentation` is the foundation of good tracking results. This can" +" become more difficult if your objects are also changing in shape or " +"intensity (due to things such as bleaching) over the course of the video." +" Itโ€™s important to find a {term}`segmentation` strategy that can work " +"well across your frames." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:16 +msgid "" +"**Inadequate frame rate** If objects are highly dynamic but the images " +"were not taken at a high frequency, tracking can be difficult because " +"objects might have moved too much for the algorithm to relate them from " +"one frame to the next. It is important to match the image acquisition " +"frequency to how dynamic your cells or objects are." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:22 +msgid "" +"๐Ÿ“„ [Computerized Cell " +"Tracking](https://www.sciencedirect.com/science/article/pii/S2468502X20300711)" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:23 +msgid "" +"๐ŸŒ [TrackMate Manual](https://imagej.net/media/plugins/trackmate" +"/trackmate-manual.pdf)" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:1 +msgid "Common pitfalls" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:3 +msgid "" +"In addition to the mistakes we summarize for common image analysis tasks," +" here we present a general list of common mistakes for beginners to image" +" analysis. For each, we explain why this is a problem and make " +"suggestions for how to avoid these issues." +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:5 +msgid "Changing your image bit depth" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:7 +msgid "" +"Let's say you've opened your image in {term}`Fiji` and you want to " +"process it in some way (e.g., maximum intensity projection, splitting " +"channels, etc.) before saving it out to measure somewhere else. You go to" +" `Image` > `Type` > `RGB (Color)` since you want a color image to import " +"into your next analysis software and then save the resulting image. " +"What's the problem with this? By making this change, even if the image " +"looks exactly the same to your eyes, you've actually inadvertently " +"changed the intensity values quite a bit! Let's take a look at an " +"example. In Fiji there are several built-in example images. Let's open " +"neuron.tif (you can follow along by going to `File` > `Open Samples...` >" +" `Neuron (5 channels)`." +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:9 +msgid "" +"Here's how the image opens. There are 5 channels, but let's just look at " +"the first one: ![image](https://user-" +"images.githubusercontent.com/28116530/206793825-364998d4-6043-4b1d-8438-0a5b37b97232.png)" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:9 +msgid "image" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Image_processing.md:1 +msgid "Image Processing" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Image_segmentation.md:1 +msgid "Image Segmentation" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/04_Data_presentation.po b/locale/de/LC_MESSAGES/04_Data_presentation.po new file mode 100644 index 000000000..39caf56eb --- /dev/null +++ b/locale/de/LC_MESSAGES/04_Data_presentation.po @@ -0,0 +1,618 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-28 07:29-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../04_Data_presentation/Introduction.md:1 +#: ../../04_Data_presentation/Statistics.md:3 +#: ../../04_Data_presentation/_notinyet_Presentation_graphs.md:3 +msgid "Introduction" +msgstr "" + +#: ../../04_Data_presentation/Introduction.md:3 +msgid "" +"When presenting microscopy image data in biology and biomedicine, it's " +"important to consider the quality of the images, the labeling and " +"annotation of important features, and the overall visual appeal. This " +"also applies to diagrams and plots which convey numerical data derived " +"from microscopy images. Chart types must in addition be suitable for the " +"specific data that is being conveyed to not mislead audiences. This " +"applies to image data in scientific posters, talk-slides, or " +"publications." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:1 +msgid "Presentation of microscopy images" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:3 +#: ../../04_Data_presentation/Statistics.md:9 +#: ../../04_Data_presentation/Statistics.md:34 +#: ../../04_Data_presentation/Statistics.md:57 +msgid "What is it?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:5 +msgid "" +"Microscopy images are often shown in scientific papers to illustrate a " +"particular conclusion. While qualitative conclusions are not a subsitute " +"for quantitative comparisons (see next section), images can certainly " +"guide our reasoning and our conclusions. Following a few consistent best " +"practices ensures that these conclusions are correct and robust." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:14 +msgid "10 tips for image presentation" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:14 +msgid "" +"**A brief visual summary of image presentation tips.** Figure by Helena " +"Jambor. [Source](https://doi.org/10.5281/zenodo.7750259)" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Adjust the image crop, orientation, and size." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:18 +msgid "" +"For any adjustments, work with an image copy and do not alter the " +"original file. Note, do not use adjusted images for quantitative image " +"data analyses Adjustments to effectively communicate the image content " +"may include removing uninformative image regions (crop), changing the " +"image orientation, and adjusting the size. Note that rotation and re-" +"sizing may change the image data when pixel information is redistributed." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:17 +msgid "rotation" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "๐Ÿค” How do I do it?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:25 +#: ../../04_Data_presentation/Presentation_images.md:43 +#: ../../04_Data_presentation/Presentation_images.md:62 +#: ../../04_Data_presentation/Presentation_images.md:82 +#: ../../04_Data_presentation/Presentation_images.md:98 +msgid "See the [cheat-sheet below](image-cheat-sheet) for more information." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +#: ../../04_Data_presentation/Statistics.md +msgid "โš ๏ธ Where can things go wrong?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:28 +msgid "Any adjustments that alter the conclusions are not permitted." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +#: ../../04_Data_presentation/Statistics.md +msgid "๐Ÿ“š๐Ÿคทโ€โ™€๏ธ Where can I learn more?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:31 +msgid "" +"๐Ÿ“„ [Reproducible image handling and " +"analysis](https://doi.org/10.15252/embj.2020105889) {cite}`Miura2021-mb`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:32 +#: ../../04_Data_presentation/Presentation_images.md:49 +#, python-format +msgid "" +"๐Ÿ“„ [Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use " +"and Manipulation of Scientific Digital " +"Images](https://doi.org/10.1007%2Fs11948-010-9201-y) " +"{cite}`Cromey2010-jr`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Enhance visibility of image content" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:37 +msgid "" +"Images often do not have regular spaced intensity values. To still " +"display the data visible on a screen/in a figure, adjustments of " +"brightness and contrast are usually necessary." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:36 +msgid "image adjustment" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:46 +msgid "" +"Any adjustments that result in the disappearance of image details are " +"considered misleading {cite}`Cromey2010-jr`. Note that many nonlinear " +"transformations of brightness and contrast are available in image " +"processing software, before using these users should ensure that they " +"faithfully represent the data to avoid accidentally misleading audiences " +"and disclose them as annotations." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Use accessible colors" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:54 +msgid "" +"Fluorescent microscope images are often composed of data from multiple " +"wavelengths/color channels. To best visualize molecular structures, " +"individual channels can be shown in separate grayscale images. When " +"colors are chosen to represent the illumination wavelength (blue, green, " +"red, far-red), for example Green-Fluorescent Protein is shown in green " +"color, be reminded that intensity values on a black background reduces " +"the level of detail." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:56 +msgid "" +"When channels are over-laid in โ€˜compositeโ€™ images, authors should ensure " +"that structures are visible, i.e., that the overlay does not obstruct " +"features and that the colors used are clearly distinguishable." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:53 +msgid "multicolor image composition" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:65 +msgid "" +"For composite images consider if color combinations are accessible to " +"color-blind audiences (e.g. not combine red with green, but rather " +"magenta and green, see reference below for examples) and possibly " +"additionally show individual channels in grayscale for maximizing " +"accessibility and detail. Tools for color blindness simulation of the " +"images exist in image processing software (ImageJ/Fiji) and visibility of" +" colors in final image figures can be tested with applications such as " +"ColorOracle." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:69 +msgid "" +"๐Ÿ“„ [Creating clear and informative image-based figures for scientific " +"publications](https://doi.org/10.1371/journal.pbio.3001161) " +"{cite}`Jambor2021-qe`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Annotate key image features" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:74 +msgid "" +"Each image needs a reference to its physical dimensions. This is " +"typically achieved by including a scale bar with dimensions annotated in " +"the image or the figure legend." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:76 +msgid "" +"In addition, authors should remember to annotate the colors used, any " +"symbols and arrows used to guide readers, and, if used, the origin of any" +" zoom/inset. If specialized images are shown (time-lapse, volumes, " +"reconstructions) authors are encouraged to consider annotating important " +"information in the figures." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:73 +msgid "speech bubbles" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:85 +msgid "" +"Lack of details and missing of key explanations will make it impossible " +"for audiences to interpret image data in figures. To unambiguously " +"reference probes consider using terms from the ISAC Probe Tag Dictionary," +" a standardized nomenclature for probers used in cytometry and " +"microscopy." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:89 +msgid "" +"๐Ÿ“„ [ISAC Probe Tag Dictionary: Standardized Nomenclature for Detection and" +" Visualization Labels Used in Cytometry and Microscopy Imaging " +"](https://doi.org/10.1002/cyto.a.24224) {cite}`Blenman2021-ki`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Explain the image" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:95 +msgid "" +"To rapidly orient audiences, a minimal explanatory text should be " +"presented along with images. This includes the figure legend and the " +"methods section in scientific papers or the title of figures in posters " +"and slides. Consider using a controlled vocabulary to reduce ambiguity " +"and increase machine-readability of the descriptions of specimens, " +"tissues, cell lines, and proteins etc. A useful tool is the [RRID " +"(Reseach Resource Identifying " +"Data)index](https://scicrunch.org/resources) , which provides indices for" +" commonly used biological reagents and resources, e.g., plasmids, cell " +"lines and antibodies ." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:101 +msgid "" +"Missing explanations of image details/methods may result in non-" +"reproducible data and limits the insights from the data." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:104 +msgid "" +"๐Ÿ“„ [Replication Study: Biomechanical remodeling of the microenvironment by" +" stromal caveolin-1 favors tumor invasion and " +"metastasis](https://doi.org/10.7554/eLife.45120) {cite}`Sheen2019-bg`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:105 +msgid "" +"๐Ÿ“„ [Imaging methods are vastly underreported in biomedical " +"research](https://doi.org/10.7554/eLife.55133) {cite}`Marques2020-nx`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:106 +msgid "" +"๐Ÿ“„ [Are figure legends sufficient? Evaluating the contribution of " +"associated text to biomedical figure " +"comprehension.](https://doi.org/10.1186/1747-5333-4-1) {cite}`Yu2009-ip`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:110 +msgid "Where can I learn more?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:112 +msgid "" +"Check out _Creating clear and informative image-based figures for " +"scientific publications_{cite}`Jambor2021-qe` and _Community-developed " +"checklists for publishing images and image " +"analysis_{cite}`Schmied2023-ad` for more tips and best practices for " +"making image figures." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:114 +msgid "" +"A cheat sheet on how to do basic image preparation with open source " +"software:" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:124 +msgid "Instructions for common image processing operations in Fiji" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:124 +msgid "" +"**How to correctly perform various image manipulations in Fiji.** Figure " +"by Christopher Schmied and Helena Jambor. " +"[Source](https://doi.org/10.12688/f1000research.27140.2)" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:8 +msgid "**Resource Name**" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:9 +msgid "**Link**" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:10 +msgid "**Brief description**" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:11 +msgid "" +"๐Ÿ“„ Creating clear and informative image-based figures for scientific " +"publications {cite}`Jambor2021-qe`" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:12 +msgid "" +"[link](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001161" +" )" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:13 +msgid "" +"Review article on how to create accessible, fair scientific figures, " +"including guidelines for microscopy images" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:14 +msgid "" +"๐Ÿ“„ Community-developed checklists for publishing images and image analysis" +" {cite}`Schmied2023-ad`" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:15 +msgid "[link](https://arxiv.org/abs/2302.07005)" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:16 +msgid "" +"A paper recommending checklists and best practices for publishing image " +"data" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:17 +msgid "๐Ÿ“– Modern Statistics for Modern Biology {cite}`Holmes2019-no`" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:18 +msgid "[link](https://www.huber.embl.de/msmb/)" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:19 +msgid "Online statistics for biologists textbook with code examples (in R)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:1 +msgid "Statistics" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:5 +msgid "" +"Quantitative data is often summarized and analysed with statistical " +"methods and visualized with plots/graphs/diagrams. Statistical methods " +"reveal quantitative trends, patterns, and outliers in data, while plots " +"and graphs help to convey them to audiences. Carrying out a suitable " +"statistical analysis and choosing a suitable chart type for your data, " +"identifying their potential pitfalls, and faithfully realising the " +"analysis or generating the chart with suitable software are essential to " +"back up experimental conclusions with data and reach communication goals." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:7 +msgid "Dimensionality reduction" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:10 +msgid "" +"Dimensionality reduction (also called dimension reduction) aims at " +"mapping high-dimensional data onto a lower-dimensional space in order to " +"better reveal trends and patterns. Algorithms performing this task " +"attempt to retain as much information as possible when reducing the " +"dimensionality of the data: this is achieved by assigning importance " +"scores to individual features, removing redundancies, and identifying " +"uninformative (for instance constant) features. Dimensionality reduction " +"is an important step in quantitative analysis as it makes data more " +"manageable and easier to visualize. It is also an important preprocessing" +" step in many downstream analysis algorithms, such as machine learning " +"classifiers." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md +msgid "๐Ÿ“ How do I do it?" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:13 +msgid "" +"The most traditional dimensionality reduction technique is principal " +"component analysis (PCA){cite}`Lever2017-pca`. In a nutshell, PCA " +"recovers a linear transformation of the input data into a new coordinate " +"system (the principal components) that concentrates variation into its " +"first axes. This is achieved by relying on classical linear algebra, by " +"computing an eigendecomposition of the covariance matrix of the data. As " +"a result, the first 2 or 3 principal components provide a low-dimensional" +" version of the data distribution that is faithful to the variance that " +"was originally present. More advanced dimensionality reduction methods " +"that are popular in biology include t-distributed stochastic neighbor " +"embedding (t-SNE) and Uniform Manifold Approximation and Projection " +"(UMAP). In contrast to PCA, these methods are non-linear and can " +"therefore exploit more complex relationships between features when " +"building the lower-dimensional representation. This however comes at a " +"cost: both t-SNE and UMAP are stochastic, meaning that the results they " +"produce are highly dependent on the choice of hyperparameters and can " +"differ across different runs." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:18 +msgid "" +"Although reducing dimensionality can be very useful for data exploration " +"and analysis, it may also wipe information or structure that is relevant " +"to the problem being studied. This is famously well illustrated by the " +"[Datasaurus " +"dataset](https://cran.r-project.org/web/packages/datasauRus/vignettes/Datasaurus.html)," +" which demonstrates how very differently-looking sets of measurements can" +" become indistinguishable when described by a small set of summary " +"statistics. The best way to minimize this risk is to start by visually " +"exploring the data whenever possible, and carefully checking any " +"underlying assumptions of the dimensionality reduction method being used " +"to ensure that they hold for the considered data. Dimensionality " +"reduction may also enhance and reveal patterns that are not biologically " +"relevant, due to noise or systematic artifacts in the original data (see " +"Batch effect correction section below). In addition to applying " +"normalization and batch correction to the data prior to reducing " +"dimensionality, some dimensionality reduction methods also offer so-" +"called regularization strategies to mitigate this. In the end, any " +"pattern identified in dimension-reduced data should be considered while " +"keeping in mind the biological context of the data in order to interpret " +"the results appropriately." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:26 +msgid "" +"๐Ÿ“– [Dimension Reduction: A Guided " +"Tour](https://www.researchgate.net/publication/220416606_Dimension_Reduction_A_Guided_Tour)" +" {cite}`Burges2010-fi`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:27 +msgid "" +"๐Ÿ’ป [UMAP introduction and Python implementation](https://umap-" +"learn.readthedocs.io/en/latest/index.html)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:28 +msgid "" +"๐Ÿ’ป [t-SNE Python implementation](https://scikit-" +"learn.org/stable/modules/generated/sklearn.manifold.TSNE.html)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:32 +msgid "Batch correction" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:35 +msgid "" +"Batch effects are systematic variations across samples correlated with " +"experimental conditions (such as different times of the day, different " +"days of the week, or different experimental tools) that are not related " +"to the biological process of interest. Batch effects must be mitigated " +"prior to making comparisons across several datasets as they impact the " +"reproducibility and reliability of computational analysis and can " +"dramatically bias conclusions. Algorithms for batch effect correction " +"address this by identifying and quantifying sources of technical " +"variation, and adjusting the data so that these are minimized while the " +"biological signal is preserved. Most batch effect correction methods were" +" originally developed for microarray data and sequencing data, but can be" +" adapted to feature vectors extracted from images." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:38 +msgid "" +"Two of the most used methods for batch effect correction are ComBat and " +"Surrogate Variable Analysis (SVA), depending on whether the sources of " +"batch effects are known a priori or not. In a nutshell, ComBat involves " +"three steps: 1) dividing the data into known batches, 2) estimating batch" +" effect by fitting a linear model that includes the batch as a covariate " +"and 3) adjusting the data by removing the estimated effect of the batch " +"from each data point. In contrast, SVA aims at identifying \"surrogate " +"variables\" that capture unknown sources of variability in the data. The " +"surrogate variables can be estimated relying on linear algebra methods " +"(such as singular value decomposition) or through a Bayesian factor " +"analysis model. SVA has been demonstrated to reduce unobserved sources of" +" variability and is therefore of particular help when identifying " +"possible causes of batch effects is challenging, but comes at a higher " +"computational cost than ComBat." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:41 +msgid "" +"As important as it is for analysis, batch effect correction can go wrong " +"when too much or too little of it is done. Both over- and under-" +"correction can happen when methods are not used properly or when their " +"underlying assumptions are not met. As a result, either biological " +"signals can be removed (in the case of over-correction) or irrelevant " +"sources of variation can remain (in the case of under-correction) - both " +"potentially leading to inaccurate conclusions. Batch effect correction " +"can be particularly tricky when the biological variation of interest is " +"suspected to confound with the batch. In this case in particular " +"(although always a good approach), the first lines of fight against batch" +" effects should be thought-through experimental design and careful " +"quality control, as well as visual exploration of the " +"data{cite}`Lord2020-sp`. Plotting data batch-by-batch before applying any" +" correction can help confirm (or infirm) that the observed trends are " +"similar across batches." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:49 +msgid "" +"๐Ÿ“„ [Why Batch Effects Matter in Omics Data, and How to Avoid " +"Them](https://doi.org/10.1016/j.tibtech.2017.02.012) {cite}`Goh2017-kd`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:50 +msgid "" +"๐Ÿ’ป [pyComBat (ComBat Python " +"implementation)](https://epigenelabs.github.io/pyComBat/)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:51 +msgid "" +"๐Ÿ“„ [The sva package for removing batch effects and other unwanted " +"variation in high-throughput " +"experiments](https://doi.org/10.1093/bioinformatics/bts034) " +"{cite}`Leek2012-rv`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:55 +msgid "Normality testing" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:58 +msgid "" +"Normality testing is about assessing whether data follow a Gaussian (or " +"nomal) distribution. Because the Gaussian distribution is frequently " +"found in nature and has important mathematical properties, normality is a" +" core assumption in many widely-used statistical tests. When this " +"assumption is violated, their conclusions may not hold or be flawed. " +"Normality testing is therefore an important step of the data analysis " +"pipeline prior to any sort of statistical testing." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:61 +msgid "" +"Normality of a data distribution can be qualitatively assessed through " +"plotting, for instance relying on a histogram. For a more quantitative " +"readout, statistical methods such as the Kolmogorov-Smirnov (KS) and " +"Shapiro-Wilk tests (among many others) report how much the observed data " +"distribution deviates from a Gaussian. These tests usually return and a " +"p-value linked to the hypothesis that the data are sampled from a " +"Gaussian distribution. A high p-value indicates that the data are not " +"inconsistent with a normal distribution, but is not sufficient to prove " +"that they indeed follow a Gaussian. A p-values smaller than a pre-defined" +" significance threshold (usually 0.05) indicates that the data are not " +"sampled from a normal distribution." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:65 +msgid "" +"Although lots of the โ€œstandardโ€ statistical methods have been designed " +"with a normnality assumption, alternative approaches exist for non-" +"normally-ditributed data. Many biological processes result in multimodal " +"โ€œstatesโ€ (for instance differentiation) that are inherently not Gaussian." +" Normality testing should therefore not be mistaken for a quality " +"assessment of the data: it merely informs on the types of tools that are " +"appropriate to use when analyzing them." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:68 +msgid "" +"๐Ÿ“– [Modern statistics for modern biology](https://www.huber.embl.de/msmb/)" +" {cite}`Holmes2019-no`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:69 +msgid "" +"๐Ÿ’ป [To get started with statistical analysis: " +"R](https://www.r-project.org/)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:70 +msgid "" +"๐Ÿ’ป [To do statistics in Python: " +"scipy.stats](https://docs.scipy.org/doc/scipy/reference/stats.html)" +msgstr "" + +#: ../../04_Data_presentation/_notinyet_Presentation_graphs.md:1 +msgid "Presentation of graphs" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/Glossary.po b/locale/de/LC_MESSAGES/Glossary.po new file mode 100644 index 000000000..7ca060bb3 --- /dev/null +++ b/locale/de/LC_MESSAGES/Glossary.po @@ -0,0 +1,317 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-19 07:07-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../Glossary.md:1 +msgid "Glossary" +msgstr "" + +#: ../../Glossary.md +msgid "Blocking" +msgstr "" + +#: ../../Glossary.md:5 +msgid "" +"During the immunostaining procedure, it is important to minimize " +"nonspecific binding of the primary or secondary antibodies. In most " +"cases, this is achieved by blocking, which typically involves adding " +"substances such as normal sera, gelatin, or albumin before immunostaining" +" in order to \"occupy\" all the non-specific binding sites in the sample." +msgstr "" + +#: ../../Glossary.md:3 +msgid "Deconvolution" +msgstr "" + +#: ../../Glossary.md:8 +msgid "" +"The process of computationally removing blur from microscopy images by " +"using the known optical properties of the light path to \"reassign\" " +"pixel intensity away from where it hit the camera and back onto the " +"structure that emitted the light." +msgstr "" + +#: ../../Glossary.md:6 +msgid "Ex-Vivo imaging" +msgstr "" + +#: ../../Glossary.md:11 +#, python-format +msgid "" +"Refers to imaging performed on live animal tissue in an external " +"controllable environment (e.g., tissue explant on a petri dish). It " +"enables high-resolution imaging of live tissue that may be otherwise " +"inaccessible within the animal. The tissue is maintained alive on the " +"imaging system through perfusion of oxygenated (95% oxygen and 5% CO2), " +"temperature-controlled media using peristaltic pumps and microfluidics." +msgstr "" + +#: ../../Glossary.md:9 +msgid "Fiji" +msgstr "" + +#: ../../Glossary.md:14 +msgid "" +"[Fiji](https://imagej.net/software/fiji/) Is Just ImageJ. ImageJ2 plus a " +"lot of common plugins." +msgstr "" + +#: ../../Glossary.md:12 +msgid "Fixation" +msgstr "" + +#: ../../Glossary.md:17 +msgid "" +"Fixation of a specimen refers to the stabilization of the " +"cellular/molecular components within the sample while at the same time " +"stopping any biological function in that sample. The fixative used (e.g.," +" paraformaldehyde, glutaraldehyde, methanol), concentration and " +"conditions (e.g., buffer, temperature) determine the extent of " +"preservation of the cellular and/or molecular structures within a sample," +" and needs to be optimized depending on the sample or structure that is " +"being imaged." +msgstr "" + +#: ../../Glossary.md:15 +msgid "Image processing" +msgstr "" + +#: ../../Glossary.md:20 +msgid "" +"Is an operation that can be performed on an image, resulting in another " +"image. Image processing operations can be simple (e.g. resizing or " +"rotating) or more advanced (e.g. enhancing particular features of an " +"image like circles or lines)." +msgstr "" + +#: ../../Glossary.md:18 +msgid "Immersion media" +msgstr "" + +#: ../../Glossary.md:23 +msgid "" +"The immersion media is the medium that fills the gap between your " +"objective lens and the glass coverslip or sample. It impacts the " +"numerical aperture of the objective lens {math}`NA=RI * sin(ฮธ)`, thus " +"impacting lateral and axial resolution. It is critical to match the RI of" +" the immersion media with that of the mounting media to minimize " +"aberrations and improve image quality. Immersion media can be air, water," +" silicone oil, glycerol or oil." +msgstr "" + +#: ../../Glossary.md:21 +msgid "Immunolabeling" +msgstr "" + +#: ../../Glossary.md:26 +msgid "" +"Immunolabeling is one of the most common labeling techniques for fixed " +"samples. You can use fluorescently conjugated primary antibodies to " +"detect the protein of interest or a two-step labeling with a primary " +"antibody and a fluorescently conjugated secondary antibody. Primary-" +"secondary labeling tends to result in signal amplification. The main " +"issue with immunolabeling is the size of the antibodies, which require " +"extensive permeabilization. Another good option is to use nano-bodies, " +"which only have the heavy-chain and are significantly smaller than " +"regular antibodies." +msgstr "" + +#: ../../Glossary.md:24 +msgid "Intravital imaging" +msgstr "" + +#: ../../Glossary.md:29 +msgid "" +"It refers to the imaging of cellular structures or biological processes " +"inside a live animal in real time, without extracting the organs or " +"fixing the sample. In general, it requires specific instrumentation or " +"modalities with improved light penetration, such as multiphoton " +"microscopy and is limited to the ability to access the specific organ, " +"often through optical windows. Intravital imaging is overseen by " +"bioethical committees and needs to be approved by IACUC and/or other " +"institutional committees." +msgstr "" + +#: ../../Glossary.md:27 +msgid "Mounting media" +msgstr "" + +#: ../../Glossary.md:32 +msgid "" +"Is the solution in which your specimen is placed in (mounted). Its " +"purpose is to preserve the sample, including the fluorophores in it, and" +" enhance the imaging quality during acquisition, by buffering the pH, " +"matching the refractive index throughout the sample (ideally matching it " +"to that of glass) and minimizing photobleaching (depending on the " +"medium). Mounting media prevents the sample from drying out allowing " +"long-term storage." +msgstr "" + +#: ../../Glossary.md:30 +msgid "Object detection" +msgstr "" + +#: ../../Glossary.md:35 +msgid "" +"Is the image processing technique to detect objects within an image. It " +"would not give you a mask of the objects but it could give you a bounding" +" box, or and x,y position." +msgstr "" + +#: ../../Glossary.md:33 +msgid "Oxygen scavengers" +msgstr "" + +#: ../../Glossary.md:38 +msgid "" +"Oxygen tends to induce photobleaching of organic dyes and other " +"fluorophores. Addition of oxygen scavengers to the imaging media such as " +"glucose oxidase or pyranose 2-oxidase can significantly reduce " +"photobleaching of the fluorophores present in the sample. It is important" +" to understand that the use of oxygen scavengers may affect live cell " +"imaging, as these scavengers can affect the ATP and oxygen levels within " +"the sample, compromising its health and therefore biological function." +msgstr "" + +#: ../../Glossary.md:36 +msgid "Permeabilization" +msgstr "" + +#: ../../Glossary.md:41 +msgid "" +"In order for the antibodies used during immunostaining or other " +"fluorophores to penetrate and bind to their antigen within a cell or " +"tissue, the membrane integrity (holes) needs to be challenged with a mild" +" detergent. The permeabilization step needs to be carefully optimized " +"depending on the antigen of interest, as it can result in a loss of " +"cytoplasm or a degradation of the signal." +msgstr "" + +#: ../../Glossary.md:39 +msgid "Refractive index" +msgstr "" + +#: ../../Glossary.md:44 +msgid "" +"It's a measure of how light travels through a specific medium. It is an " +"important value when calculating the numerical aperture of an objective, " +"Ideally, a mismatch in refractive index between the sample (mounting " +"medium), the coverslip and immersion media should be minimized in order " +"to enhance the image quality. [See an interactive demo of refactive index" +" at MicroscopyU](https://www.microscopyu.com/microscopy-basics" +"/refractive-index-index-of-refraction)" +msgstr "" + +#: ../../Glossary.md:42 +msgid "ROIs" +msgstr "" + +#: ../../Glossary.md:47 +msgid "" +"Regions Of Interest. Pixels in your image that you care about (e.g., a " +"region in tissue, a cell, a tumor, etc.)" +msgstr "" + +#: ../../Glossary.md:45 +msgid "Segmentation" +msgstr "" + +#: ../../Glossary.md:50 +msgid "" +"Method of dividing an image into multiple parts or regions. There are " +"three different types of segmentation." +msgstr "" + +#: ../../Glossary.md:51 +msgid "" +"Semantic segmentation, where all parts of an image are part of a class, " +"common in cell biology will be detecting cells and background on an " +"image." +msgstr "" + +#: ../../Glossary.md:52 +msgid "" +"Instance segmentation, the segmentation is object based, not just " +"detecting were the cells are but diving each cell as a separate object." +msgstr "" + +#: ../../Glossary.md:53 +msgid "" +"Panoptic Segmentation, it can be defined as a combination of the prior " +"two, because it identifies the object but also classifies them. An " +"example in biology might be detecting all the cells on an image and " +"classifying them as dividing vs not." +msgstr "" + +#: ../../Glossary.md:51 +msgid "Thresholding" +msgstr "" + +#: ../../Glossary.md:56 +msgid "" +"The easiest form of image segmentation, it divides the image into two " +"part the background and the foreground (or signal). It creates a binary " +"image where usually the background pixels would be change to a 0 value " +"and the foreground pixels values would be 1." +msgstr "" + +#: ../../Glossary.md:54 +msgid "Tissue clearing" +msgstr "" + +#: ../../Glossary.md:59 +msgid "" +"Fluorescence imaging of the whole thickness of a piece of tissue is very " +"challenging due to light absorption and scattering induced by the " +"inhomogeneities in refractive indexes within the tissue itself, resulting" +" in poor light penetration. Additionally, light coming from different " +"parts of the sample contribute to fluorescence blur, drastically reducing" +" contrast and resolution in any given plane. As a result, researchers " +"tend to use tissue sectioning techniques to extract information about " +"cellular components and their spatial distribution or relationships from " +"a thin two-dimensional volume. However, most components in any complex " +"biological system such as an organ are not contained within this two-" +"dimensional volume, and therefore, this approach compromises the " +"understanding of the spatial relationships among cellular components. " +"Tissue clearing focused on reducing the inhomogeneities in the tissue by " +"equilibrating the refractive index throughout the sample. This allows " +"light to pass through the tissue and therefore enables high resolution, " +"volumetric imaging of whole organs and tissues using conventional " +"microscopy techniques such as confocal microscopy without the need to " +"physically section the sample." +msgstr "" + +#: ../../Glossary.md:57 +msgid "Tissue sectioning" +msgstr "" + +#: ../../Glossary.md:62 +msgid "" +"Light penetration and fluorescence imaging is negatively impacted by " +"light scattering within a thick specimen. This scattering is due to the " +"different refractive indexes present within a tissue. To facilitate " +"imaging of tissues, researchers often cut thick tissues into slices of " +"different thicknesses. This process is called tissue sectioning. In most " +"cases the samples are fixed and embedded in paraffin or frozen in tissue " +"freezing medium and later cut into thin slices by a machine like a " +"cryostat, microtome, or vibratome and sections collected into a tube or " +"onto a slide." +msgstr "" + diff --git a/locale/de/LC_MESSAGES/QuantitativeBioimaging.po b/locale/de/LC_MESSAGES/QuantitativeBioimaging.po new file mode 100644 index 000000000..701c569f5 --- /dev/null +++ b/locale/de/LC_MESSAGES/QuantitativeBioimaging.po @@ -0,0 +1,99 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-28 07:29-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../QuantitativeBioimaging.md:1 +msgid "Quantitative Bioimaging" +msgstr "" + +#: ../../QuantitativeBioimaging.md:3 +msgid "What do we mean by quantitative bioimaging?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:5 +msgid "" +"While microscopy was by necessity a qualitative science for most of its " +"history, we now live in an era where microscope images can be used to " +"precisely quantify observable phenotypes." +msgstr "" + +#: ../../QuantitativeBioimaging.md:7 +msgid "" +"The ability to draw accurate quantitative answers from these experiments " +"relies on certain best practices being followed. If one can confidently " +"say \"Yes\" to each of the following 4 questions, one is likely to be " +"able to quantify their sample." +msgstr "" + +#: ../../QuantitativeBioimaging.md:9 +msgid "" +"Have I prepared my sample in a way that minimizes technical artifacts and" +" lets me understand exactly which molecule(s) I am observing?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:10 +msgid "" +"Have I conducted my microscopy so that I minimize technical artifacts and" +" am in the quantitative range of the detector attached to my microscope?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:11 +msgid "" +"Have I selected analysis metric(s) that truly answer my biological " +"question and measured them in a way that minimizes technical artifacts?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:12 +msgid "" +"Have I chosen appropriate statistical comparisons and data presentation " +"approaches so that the distribution of my metric(s) can be fairly " +"compared across samples, answering my biolgical question?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:14 +msgid "" +"Answering each of these questions requires thought, expertise, and often " +"a fair amount of trial and error; it can feel overwhelming to grapple " +"with all the technical aspects and caveats present in a bioimaging " +"experiment. These questions **_can_** be answered, however, though often " +"not in a single pass - [continuous optimization through multiple rounds " +"of answering these questions](qb-decision-cycle) is typically needed for " +"best results." +msgstr "" + +#: ../../QuantitativeBioimaging.md:16 +msgid "" +"The resources linked in this guide are designed to help a reader develop " +"skills in each or all of these areas, helping them get the most from " +"their microscopy data." +msgstr "" + +#: ../../QuantitativeBioimaging.md:25 +msgid "cycle" +msgstr "" + +#: ../../QuantitativeBioimaging.md:25 +msgid "" +"**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " +"Reproduced from Senft and Diaz-Rohrer et al, [**_A biologistโ€™s guide to " +"planning and performing quantitative bioimaging " +"experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." +msgstr "" + diff --git a/locale/de/LC_MESSAGES/README.po b/locale/de/LC_MESSAGES/README.po new file mode 100644 index 000000000..f417647dc --- /dev/null +++ b/locale/de/LC_MESSAGES/README.po @@ -0,0 +1,37 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-30 07:32-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../README.md:1 +msgid "Microscopy For Beginners Reference Guide" +msgstr "" + +#: ../../README.md:2 +msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" +msgstr "" + +#: ../../README.md:4 +msgid "" +"A Beginner's guide to microscopy, from sample prep to acquisition, image " +"analysis, and data interpretation. See the paper " +"[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" +" (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/bibliography.po b/locale/de/LC_MESSAGES/bibliography.po new file mode 100644 index 000000000..c4407e990 --- /dev/null +++ b/locale/de/LC_MESSAGES/bibliography.po @@ -0,0 +1,25 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../bibliography.md:1 +msgid "Bibliography" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/community_resources.po b/locale/de/LC_MESSAGES/community_resources.po new file mode 100644 index 000000000..38ad67740 --- /dev/null +++ b/locale/de/LC_MESSAGES/community_resources.po @@ -0,0 +1,173 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../community_resources.md:1 +msgid "Community resources" +msgstr "" + +#: ../../community_resources.md:3 +msgid "Below are globally and locally available community resources" +msgstr "" + +#: ../../community_resources.md:5 +msgid "Global and online resources" +msgstr "" + +#: ../../community_resources.md:12 ../../community_resources.md:35 +msgid "**Resource Name**" +msgstr "" + +#: ../../community_resources.md:13 ../../community_resources.md:36 +msgid "**Link**" +msgstr "" + +#: ../../community_resources.md:14 +msgid "**Brief description**" +msgstr "" + +#: ../../community_resources.md:15 +msgid "Global BioImaging" +msgstr "" + +#: ../../community_resources.md:16 +msgid "[link](https://globalbioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:17 +msgid "" +"Training resources, working groups, recommendations for standardization " +"and research reproducibility for global bioimaging efforts" +msgstr "" + +#: ../../community_resources.md:18 +msgid "Microforum" +msgstr "" + +#: ../../community_resources.md:19 +msgid "[link](https://forum.microlist.org/)" +msgstr "" + +#: ../../community_resources.md:20 +msgid "Discussion forum for bioimaging sample preparation and acquisition" +msgstr "" + +#: ../../community_resources.md:21 +msgid "Scientific Community Image Forum (Image . sc)" +msgstr "" + +#: ../../community_resources.md:22 +msgid "[link](https://forum.image.sc/)" +msgstr "" + +#: ../../community_resources.md:23 +msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" +msgstr "" + +#: ../../community_resources.md:24 +msgid "HMS Nikon Imaging Center \"Favorite References\"" +msgstr "" + +#: ../../community_resources.md:25 +msgid "[link](https://nic.med.harvard.edu/fav_references/)" +msgstr "" + +#: ../../community_resources.md:26 +msgid "" +"A curated list of references related to many aspects of microscopy and " +"image analysis" +msgstr "" + +#: ../../community_resources.md:29 +msgid "Local resources" +msgstr "" + +#: ../../community_resources.md:37 +msgid "BioImaging North America (BINA)" +msgstr "" + +#: ../../community_resources.md:38 +msgid "[link](https://www.bioimagingnorthamerica.org/)" +msgstr "" + +#: ../../community_resources.md:39 +msgid "Latin America BioImaging" +msgstr "" + +#: ../../community_resources.md:40 +msgid "[link](https://www.latambioimaging.org/ )" +msgstr "" + +#: ../../community_resources.md:41 +msgid "African BioImaging Consortium" +msgstr "" + +#: ../../community_resources.md:42 +msgid "[link](https://www.africanbioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:43 +msgid "South Africa BioImaging" +msgstr "" + +#: ../../community_resources.md:44 +msgid "[link](https://www.sabioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:45 +msgid "Euro-bioimaging" +msgstr "" + +#: ../../community_resources.md:46 +msgid "[link](https://www.eurobioimaging.eu/)" +msgstr "" + +#: ../../community_resources.md:47 +msgid "Advanced BioImaging support (Japan)" +msgstr "" + +#: ../../community_resources.md:48 +msgid "[link](https://www.nibb.ac.jp/abis/)" +msgstr "" + +#: ../../community_resources.md:49 +msgid "Microscopy Australia" +msgstr "" + +#: ../../community_resources.md:50 +msgid "[link](https://micro.org.au/)" +msgstr "" + +#: ../../community_resources.md:51 +msgid "Canada BioImaging" +msgstr "" + +#: ../../community_resources.md:52 +msgid "[link](https://www.canadabioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:53 +msgid "Singapore Microscopy Infrastructure Network" +msgstr "" + +#: ../../community_resources.md:54 +msgid "[link](https://www.singascope.sg/)" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/contributors.po b/locale/de/LC_MESSAGES/contributors.po new file mode 100644 index 000000000..6d9f14ca9 --- /dev/null +++ b/locale/de/LC_MESSAGES/contributors.po @@ -0,0 +1,90 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-30 07:32-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../contributors.md:1 +msgid "Contributing to this guide" +msgstr "" + +#: ../../contributors.md:3 +msgid "Contributors" +msgstr "" + +#: ../../contributors.md:5 +msgid "" +"The original material for this book was created as part of the paper " +"\"[**_A biologistโ€™s guide to planning and performing quantitative " +"bioimaging " +"experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " +"{cite}`Senft2023-zy`. by Rebecca A. Senft*, Barbara Diaz-Rohrer*, Pina " +"Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig " +"Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew" +" Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W Eliceiri and Beth" +" A. Cimini." +msgstr "" + +#: ../../contributors.md:7 +msgid "" +"Since this guide has become available, we gratefully acknowledge " +"contributions from the following members of the microscopy and bioimage " +"analysis community!" +msgstr "" + +#: ../../contributors.md:8 +msgid "William Giang" +msgstr "" + +#: ../../contributors.md:9 +msgid "Robert Haase" +msgstr "" + +#: ../../contributors.md:11 +msgid "How can I become a contributor?" +msgstr "" + +#: ../../contributors.md:13 +msgid "" +"Please feel free to open an " +"[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" +" or pull request to contribute! We hope for this to be a living document " +"reflecting the best practices and resources available." +msgstr "" + +#: ../../contributors.md:15 +msgid "" +"We currently also offer a [Google " +"Form](https://docs.google.com/forms/d/e/1FAIpQLScWQbemviI2OkvVkeTKUOozAzKNndcZpXIB_nE0qFMl72lqvQ/viewform)" +" for contributions, though note these may be responded to more slowly " +"than direct contributions to the GitHub repository." +msgstr "" + +#: ../../contributors.md:18 +msgid "Translation" +msgstr "" + +#: ../../contributors.md:20 +msgid "" +"Work is underway to translate this guide into other languages - " +"translation is planned or has begun in French, Spanish, Portuguese, " +"Czech, and Polish. To help translate into one of these languages, or " +"another language not listed here, please contact bcimini AT " +"broadinstitute DOT org." +msgstr "" + diff --git a/locale/de/LC_MESSAGES/genindex.po b/locale/de/LC_MESSAGES/genindex.po new file mode 100644 index 000000000..19df54cbb --- /dev/null +++ b/locale/de/LC_MESSAGES/genindex.po @@ -0,0 +1,25 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../genindex.md:1 +msgid "Index" +msgstr "" + diff --git a/locale/de/LC_MESSAGES/welcome.po b/locale/de/LC_MESSAGES/welcome.po new file mode 100644 index 000000000..afc9a2869 --- /dev/null +++ b/locale/de/LC_MESSAGES/welcome.po @@ -0,0 +1,167 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-28 07:29-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: de\n" +"Language-Team: de \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../welcome.md:1 +msgid "Sample Preparation" +msgstr "" + +#: ../../welcome.md:1 +msgid "Sample Acquisition" +msgstr "" + +#: ../../welcome.md:1 +msgid "Image Analysis and Data Handling" +msgstr "" + +#: ../../welcome.md:1 +msgid "Data Interpretation" +msgstr "" + +#: ../../welcome.md:1 +msgid "Additional Resources" +msgstr "" + +#: ../../welcome.md:1 +msgid "Welcome" +msgstr "" + +#: ../../welcome.md:3 +msgid "Welcome to the world of bioimaging and bioimage analysis! ๐ŸŽ‰" +msgstr "" + +#: ../../welcome.md:11 +msgid "BBBC image montage" +msgstr "" + +#: ../../welcome.md:11 +msgid "" +"**Montage of fluorescence microscopy images from " +"[BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` (Broad " +"Institute).** Images shown are from experiments BBBC007, BBBC008, " +"BBBC034, BBBC038, BBBC039, and BBBC020 from left to right, top to bottom." +msgstr "" + +#: ../../welcome.md:13 +msgid "What is this book?" +msgstr "" + +#: ../../welcome.md:15 +msgid "" +"This book is a companion website to our paper \"[**_A biologistโ€™s guide " +"to planning and performing quantitative bioimaging " +"experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " +"{cite}`Senft2023-zy`. Our goal is to provide recommendations and a " +"curated set of resources for biologists looking to understand the factors" +" that impact their fluorescence microscopy experiments." +msgstr "" + +#: ../../welcome.md:17 +msgid "" +"This book is a collaborative effort from experts in biology, imaging, " +"image analysis, and data management, interpretation, and presentation. " +"Our tips and recommendations come from real experiences training and " +"working with biologists who are beginners to bioimaging and bioimage " +"analysis. When starting out in a new field, you often don't know what you" +" don't know. Here we provide context, tips for avoiding common beginner " +"errors, and a focused list of high-quality, open source resources (full " +"list available [here](bibliography)). We use icons to indicate the type " +"of resource:" +msgstr "" + +#: ../../welcome.md:39 +msgid "What **isn't** this book?" +msgstr "" + +#: ../../welcome.md:41 +msgid "" +"This book is **not** meant to be an exhaustive list of all resources. " +"Many others have curated excellent such resources(see " +"[here](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) " +"{cite}`Haase2022-ad` and [here](https://www.bioimagingnorthamerica.org" +"/training-education-resources/) and [here](https://biii.eu/) {cite}`Paul-" +"Gilloteaux2021-vw`). Our goal is to create a more streamlined, beginner-" +"accessible guide." +msgstr "" + +#: ../../welcome.md:42 +msgid "" +"This book is **not** a protocol or step by step guide, though certain " +"resources we link to might be. Each subsection from sample prep to data " +"interpretation are massive topics that we can't exhaustively cover in a " +"guide for beginners." +msgstr "" + +#: ../../welcome.md:45 +msgid "How to use this book:" +msgstr "" + +#: ../../welcome.md:46 +msgid "" +"Please select a section using the navigation panel on the left to get " +"started or begin with sample preparation by clicking the \"Next\" button " +"below โ†˜๏ธ." +msgstr "" + +#: ../../welcome.md:48 +msgid "" +"Most sections will guide you through individual subtopics using some or " +"all of the following list of questions:" +msgstr "" + +#: ../../welcome.md:49 +msgid "What is it?" +msgstr "" + +#: ../../welcome.md:50 +msgid "What are my options?" +msgstr "" + +#: ../../welcome.md:51 +msgid "How do I do it?" +msgstr "" + +#: ../../welcome.md:52 +msgid "Where can things go wrong?" +msgstr "" + +#: ../../welcome.md:53 +msgid "Where can I learn more? (links to resources)" +msgstr "" + +#: ../../welcome.md:55 +msgid "" +"Which questions are used and the exact phrasing may vary by section, but " +"we hope this structure helps guide users to a deeper understanding of " +"each subtopic." +msgstr "" + +#: ../../welcome.md:57 +msgid "What if my resource/topic is not included?" +msgstr "" + +#: ../../welcome.md:58 +msgid "" +"Please feel free to open an " +"[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" +" or pull request to contribute! We hope for this to be a living document " +"reflecting the best practices and resources available." +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/01_Sample_preparation.po b/locale/fi/LC_MESSAGES/01_Sample_preparation.po new file mode 100644 index 000000000..d23464254 --- /dev/null +++ b/locale/fi/LC_MESSAGES/01_Sample_preparation.po @@ -0,0 +1,708 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-19 07:07-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../01_Sample_preparation/Considerations.md:1 +msgid "Considerations for different sample types" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:3 +msgid "" +"There are many different options for types of samples to image, and " +"advances in sample preparation techniques and imaging modalities are " +"continually enabling the imaging of more diverse and complex biological " +"specimens. As with many other aspects of experimental design, sample type" +" selection comes with tradeoffs. Samples that are amenable to simple " +"preparation and imaging tend to be small, thin, and relatively clear, " +"like a monolayer of cultured cells. Such samples have obvious advantages " +"and can be imaged in a high-throughput manner, but they're not suitable " +"for every biological question. Sometimes a thicker specimen, like an " +"organoid, or whole or sectioned tissue is needed, especially when the " +"biological question involves interactions between different types of " +"cells. Carefully consider what biological context is appropriate for your" +" question and what measurements you'd ultimately like to be able to make." +" Below, we summarize some common sample types" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md +msgid "๐Ÿค” What are my options?" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:7 +msgid "" +"Here we present some major categories for sample types. Note that there " +"are not hard boundaries between these different categories (e.g., both " +"cells and organoids can be cultured in 3D, many of these specimens can be" +" imaged live or after {term}`fixation`), but some general advantages and " +"disadvantages are summarized below." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:11 +msgid "**Cultured cells**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:13 +msgid "" +"Many different types of cells can be cultured, or grown in a dish. Cells " +"can be grown in a monoculture, with only one cell type, or in a co-" +"culture with multiple cell types." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:15 +#: ../../01_Sample_preparation/Considerations.md:31 +#: ../../01_Sample_preparation/Considerations.md:49 +#: ../../01_Sample_preparation/Considerations.md:67 +msgid "_Advantages_" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:17 +msgid "" +"Cultured cells tend to be relatively simple to image and for many " +"questions can be imaged with widefield microscopy (see " +"[Acquisition](content/microscope_selection)), which is faster and more " +"accessible than confocal or superresolution methods. Additionally, high-" +"throughput microscopes integrated with robotics can enable automation of " +"experiments and imaging with cultured cells." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:19 +msgid "" +"Cells can be frozen, thawed, and grown much faster than work with more " +"complex specimens like organoids or whole organisms, compressing the " +"timeline to perform an experiment" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:21 +#: ../../01_Sample_preparation/Considerations.md:37 +#: ../../01_Sample_preparation/Considerations.md:55 +#: ../../01_Sample_preparation/Considerations.md:71 +msgid "_Disadvantages_" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:23 +msgid "" +"Most applications in microscopy require imaging through a glass coverslip" +" of a specific thickness and tolerance. However, many cell types do not " +"survive or cannot grow on glass and require additional coatings and " +"manipulations of the coverslip to ensure the health of the sample. As an " +"alternative some companies manufacture imaging chambers (multi well " +"plates, 35 mm dishesโ€ฆ) with proprietary polymers that have similar " +"properties to glass (optical polymers), thus enabling high resolution " +"imaging. It is imperative to understand whether the immersion oil used " +"during imaging affects the integrity of these polymers, as the solvents " +"in some immersion media can crack or dissolve the polymer layer." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:27 +msgid "**Organoids**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:29 +msgid "" +"Organoids are cultured cells that are grown in 3D to mimic the structure " +"and sometimes functions of organs. Organoids are typically grown from " +"stem cells that self-organize into a more complex structure, including " +"differentiating into different cell types. Organoids are well suited to " +"questions of development, modeling disease, and for understanding tissue " +"and organ regeneration." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:33 +msgid "" +"Because organoids contain multiple cell types and reflect some structure " +"and cell relationships seen in organs _in vivo_, they are well-suited to " +"more complex questions about disease and cell-cell interactions. They can" +" also be used to model processes and structures that are necessarily 3D " +"and not recapitulated well in a flat layer of cells, like many " +"developmental processes." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:35 +msgid "" +"Organoids can be made from induced pluripotent stem cells (iPSCs) from " +"human or animal samples, and thus can model disease processes specific to" +" a given human donor." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:39 +msgid "" +"Organoids can take more complex resources and protocols to grow and can " +"take more time than just growing cultured cells on glass or plastic." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:41 +msgid "" +"Because organoids are 3D structures, they often are not amenable to " +"widefield imaging and may require spinning disk or point-scanning " +"confocal microscopy." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:45 +msgid "**Tissue**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:47 +msgid "" +"Tissues are formed when cells act together to perform a specific " +"function. Tissues can be cultured by taking a piece of an animal or plant" +" and allowing it to continue to survive and grow in a dish. Tissues can " +"also be harvested from plants or animals and stained for the presence of " +"different molecules. Tissues are typically cut into pieces (aka " +"{term}`tissue sectioning`), and can be fixed, fresh, or frozen, or even " +"alive in {term}`ex-vivo imaging`." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:51 +msgid "" +"Tissues have more intact cell-cell interactions that are generally more " +"representative of what happens _in vivo_ than in cell culture." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:53 +msgid "" +"Repositories of donated human tissues enable biomedical research to study" +" a diverse sample of patients with a particular disease." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:57 +msgid "" +"Primary cells and tissues tend to be sensitive to environment than " +"immortalized cell lines and can be more difficult to grow and may require" +" specialized protocols depending on cell type." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:59 +msgid "" +"Tissues harvested from a whole animal or plant require time for the " +"development and growth of that specimen before harvesting." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:63 +msgid "**Whole organism / embryo**" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:65 +msgid "" +"Some whole organisms are thin and transparent enough to image. Some " +"animals also have near-transparent embryonic stages, like the zebrafish. " +"Additionally, {term}`intravital imaging` is the imaging of cellular " +"structures or biological processes inside a live animal in real time, " +"without extracting the organs or fixing the sample. In general, it " +"requires specific instrumentation or modalities with improved light " +"penetration, such as multiphoton microscopy and is limited to the ability" +" to access the specific organ, often through optical windows." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:69 +msgid "" +"Imaging whole organisms or embyros provides the most possible intact " +"biological context when studying a particular process or structure." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:73 +msgid "" +"Imaging of thicker specimens may require processing ({term}`tissue " +"clearing`) of the sample to make its {term}`refractive index` match that " +"of the imaging media and reduce absorption and scattering of light." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:75 +msgid "" +"Intravital imaging often requires specific surgical techniques and is " +"overseen by bioethical committees and needs to be approved by IACUC " +"and/or other institutional committees." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md +msgid "โš ๏ธ Where can things go wrong?" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:80 +msgid "" +"**Photobleaching and phototoxicity** - Photobleaching can be defined as " +"the irreversible destruction of a fluorophore in its excited state, " +"meaning, that fluorophore will not be able to emit more light and the " +"fluorescence signal will therefore degrade over time, affecting signal to" +" noise ratio and intensity measurements. In order to minimize " +"photobleaching during acquisition, there are a number of photobleaching " +"reagent agents that can be added to the media. These agents minimize " +"photobleaching of fluorophores to a different extent, and therefore it is" +" important to contact the manufacturer to ensure they are optimal for the" +" specific fluorophore. For example addition of oxygen scavengers to the " +"imaging media such as glucose oxidase or pyranose 2-oxidase can " +"significantly reduce photobleaching. It is important to understand that " +"the use of {term}`oxygen scavengers` may affect live cell imaging, as " +"these scavengers can affect the ATP and oxygen levels within the sample, " +"compromising its health and therefore biological function." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:82 +msgid "" +"**Cells are dying** - Fluorescent light induces DNA damage and oxidation " +"of cellular components (phototoxicity). In addition, fluorophore " +"photobleaching can further induce phototoxicity by creating reactive " +"oxygen species (ROS). The addition of antioxidants and removal of certain" +" molecules (e.g., riboflavin) from the imaging media can reduce the ROS " +"produced during imaging, improving the health of the " +"sample.{cite}`Stockley2017`" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:85 +msgid "" +"**My fixed cells don't looked as expected** - Fixation can change the " +"localization and fluorescence of different proteins. Where possible, " +"always compare the distribution of a protein or molecule of interest with" +" and without fixation. Also consider whether a different {term}`fixation`" +" method may be more appropriate for your specimen." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:88 +msgid "" +"**My sample is too opaque** - Thicker specimens, like thick tissue " +"sections, pigmented cells, or whole organisms can be challenging to image" +" due to light absorption and scattering induced by the inhomogeneities in" +" {term}`refractive index` within the tissue itself, resulting in poor " +"light penetration. To facilitate imaging of tissues, researchers often " +"cut thick tissues into slices of different thicknesses. This process is " +"called tissue sectioning. In most cases the samples are fixed and " +"embedded in paraffin or frozen in tissue freezing medium and later cut " +"into thin slices by a machine like a cryostat, microtome, or vibratome " +"and sections collected into a tube or onto a slide. Alternatively, most " +"components in any complex biological system such as an organ are not " +"contained within this two-dimensional volume, and therefore, this " +"approach compromises the understanding of the spatial relationships among" +" cellular components. Tissue clearing focused on reducing the " +"inhomogeneities in the tissue by equilibrating the {term}`refractive " +"index` throughout the sample. This allows light to pass through the " +"tissue and therefore enables high resolution, volumetric imaging of whole" +" organs and tissues using conventional microscopy techniques such as " +"confocal microscopy without the need to physically section the sample." +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md +msgid "๐Ÿ“š๐Ÿคทโ€โ™€๏ธ Where can I learn more?" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:94 +#, python-format +msgid "" +"๐Ÿ“„ [Organoids " +"Primer](https://www.nature.com/articles/s43586-022-00174-y#:~:text=An%20organoid%20is%20a%20self,%2C9%2C10%2C11.)" +" {cite}`Zhao2022-rm`" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:95 +msgid "" +"๐Ÿ“„ [Tutorial: guidance for quantitative confocal " +"microscopy](https://doi.org/10.1038/s41596-020-0313-9) " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../01_Sample_preparation/Considerations.md:96 +msgid "" +"๐Ÿ“„ [Hypothesis-driven quantitative fluorescence microscopy - the " +"importance of reverse-thinking in experimental " +"design](https://pubmed.ncbi.nlm.nih.gov/33154172/) {cite}`Wait2020-gq`" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:1 +msgid "Experimental design decisions" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:3 +msgid "" +"A number of critical decisions must be made when designing a quantitative" +" bioimaging experiment. Many of these decisions will be deeply dependent " +"on what is possible given the biology you wish to study, for example:" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:4 +msgid "" +"You will always prefer live imaging to fixed imaging if it is important " +"to assess the dynamics of a given process" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:5 +msgid "" +"You may need to perform special processes such as tissue clearing if it " +"is important to image deep into a relatively opaque specimen" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:6 +msgid "" +"You cannot rely on genetic tagging with fluorescent proteins if your " +"model system is not genetically tractable to such manipulations" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:7 +msgid "" +"You have to image at a particularly high resolution to confidently assess" +" interactions between two molecules imaged in the same system" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:9 +msgid "" +"It is therefore _**extremely**_ important to think through all of the " +"aspects of your biological question before ever picking up a pipette or a" +" slide. Many sample preparation decisions are deeply entwined with the " +"availability and suitability of particular microscopes; see [that " +"section](content/microscope_selection) for more information." +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:11 +msgid "Mounting" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:13 +msgid "Glass coverslips" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:15 +msgid "" +"Many imaging applications involve mounting on glass coverslips, either " +"directly or using a coverslip mounted into a dish. While there is a wide " +"range of coverslip sizes and shapes, the most important attribute is the " +"coverslip thickness. Coverslip grade dictates the expected thickness and " +"tolerance. These factors are important because most microscope " +"manufacturers assume a specific coverslip thickness (0.17mm) in the " +"design of objective lenses to minimize aberrations. These aberrations " +"tend to affect the brightness and axial resolution, reducing signal to " +"noise ratio, sharpness, and resolution. The tolerance of the coverslip " +"(to minimize the variability in thickness) is essential for super-" +"resolution techniques or intensity measurements in images collected with " +"high numerical aperture objectives. Other applications do not require the" +" mounting of samples onto glass or plastic but instead have the sample " +"and the objective lens immersed in the same medium." +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:17 +msgid "Comparison of coverslip grades" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:21 +msgid "Grade" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:22 +msgid "Nominal thickness [mm]" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:23 +msgid "Thickness range [mm]" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:24 +msgid "#1.5" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:25 +#: ../../01_Sample_preparation/Experimental_design.md:28 +msgid "0.17" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:26 +msgid "0.16 - 0.19" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:27 +msgid "#1.5H" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:29 +msgid "0.165 - 0.175" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:32 +msgid "Mounting media" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:34 +msgid "" +"The {term}`refractive index` the sample is placed in, as well as the " +"refractive index of the glass and the medium between the objective and " +"the sample are all critical to determining the achievable resolution. The" +" {term}`mounting media` can have other important optical and/or " +"experimental properties; it is important to use the correct mounting " +"media for experiment planned." +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:43 +msgid "effects of mounting media" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:43 +msgid "" +"**Effects of mounting media on staining with various fluorophores**. " +"Adapted from Jonkman J., Brown C.M., Wright G.D _et al_. Tutorial: " +"guidance for quantitative confocal microscopy. _Nat Prot_ **15**, (2020) " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:46 +msgid "Fluorophore selection" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:48 +msgid "" +"Fluorophores are molecules that are able to emit light upon absorption of" +" a photon, typically of shorter wavelength. The fluorophores relevant to " +"biomedical research can be small molecules organic dyes (FITC, Alexa " +"Fluor 488) that bind specific cell structure (e.g., DAPI, MitoTracker), " +"fluorescent analogues of small molecules (e.g., phalloidin, fluorescent " +"amino acids) or fluorescent proteins. Some of the important properties to" +" consider when choosing fluorophores are listed below:" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:50 +msgid "Excitation/emission spectra of each fluorophore" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:51 +msgid "Brightness (dyes tend to be brighter than proteins)" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:52 +msgid "Photostability" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:53 +msgid "Propensity to oligomerize (in the case of fluorescent proteins)" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:54 +msgid "Phototoxicity (when imaging in live samples)" +msgstr "" + +#: ../../01_Sample_preparation/Experimental_design.md:56 +msgid "" +"Understanding fluorophores, microscope specifications (light source, " +"filters, detector), and analysis goals are key in selecting the " +"appropriate fluorophore(s) to address a scientific question. See the " +"section on [reproducibility](content/reproducibility) for more " +"information." +msgstr "" + +#: ../../01_Sample_preparation/Introduction.md:1 +msgid "Introduction" +msgstr "" + +#: ../../01_Sample_preparation/Introduction.md:3 +msgid "" +"A good image starts at the bench. The best performing instrument will not" +" produce rigorous, reproducible or high quality data unless sample " +"preparation has been optimized. To design a rigorous and reproducible " +"microscopy experiment, it is critical to identify the goal of the " +"experiment and understand the factors that impact the image. This " +"information informs researchers about how to prepare the sample, what " +"minimal controls and corrections are needed, how to choose the " +"appropriate instrumentation, optimize acquisition, analyze and present " +"microscopy data." +msgstr "" + +#: ../../01_Sample_preparation/Introduction.md:5 +msgid "" +"Here we will discuss some of the key choices you will make during sample " +"preparation, including selecting your sample type and fluorophore (if " +"you're performing fluorescence microscopy). We also discuss some minimal " +"controls necessary for interpreting your results." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:1 +msgid "Reproducibility" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:5 +msgid "" +"A number of factors are critical in designing a reproducible microscopy " +"experiment. A few critical factors are laid out here; see other works " +"such as {cite}`Jost2019-nx`" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:7 +msgid "Antibody validation" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:9 +msgid "" +"While in a perfect world, antibodies would always be specific to a " +"particular target, unfortunately, this cannot always be relied upon when " +"performing {term}`immunolabeling`. {cite}`Uhlen2016-wy` When possible, " +"one should perform knockout and/or knockdown controls to confirm antibody" +" specificity; where not, look for availability of another antibody to a " +"different part of the target molecule (sometimes called the _epitope_) " +"and confirm you get consistent localization." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:11 +msgid "" +"Optimizing your {term}`blocking` and {term}`permeabilization` conditions " +"for the particular antibody and protocol can reduce non-specific " +"background. No-primary-antibody controls should always be performed as " +"well, as they are essential for validating signal specificity." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:13 +msgid "Fluorescent protein localization validation" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:15 +#, python-format +msgid "" +"Expression of fluorescently-tagged proteins can make localization of a " +"molecule or structure possible, especially when no good antibody exist " +"for immunolabeling and/or it will be helpful to observe the molecule's " +"behavior in live cells. While a study comparing overlap between the same " +"molecular targets with fluorescent proteins vs antibodies found 80% " +"overlap, they also found that some considerations (such as whether the C-" +" or N- terminus of a protein is tagged) may cause changes in " +"localization. {cite}`Stadler2013`. A recent paper {cite}`Sittewelle2023` " +"surveys considerations for genetic tagging of molecules for live " +"microscopy." +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:18 +msgid "Bleedthrough" +msgstr "" + +#: ../../01_Sample_preparation/Reproducibility.md:20 +msgid "" +"When performing multicolor fluorescence microscopy, it is critical to " +"choose fluorophores with sufficiently distinct excitation and emission " +"spectra; online tools such as FPbase {cite}`Lambert2019-xl` can help with" +" such selections, especially if you know the various optical components " +"of the microscope on which you will be imaging your samples (these " +"configurations can be saved and shared on FPbase; ask the maintainer of " +"the microscope you plan to use if such a configuration file is already " +"online). Even if you believe your fluorophores are sufficiently " +"separated, it is critical to check single-color fluorescent controls " +"using the same imaging conditions (and preferably on the same day) as " +"your multicolor controls to be certain no bleedthrough is occurring; it " +"is _mandatory_ to do this if you are planning to measure " +"[colocalization](content/colocalization)." +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:8 +msgid "**Resource Name**" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:9 +msgid "**Link**" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:10 +msgid "**Brief description**" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:11 +msgid "๐ŸŒ Microforum" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:12 +msgid "[link](https://forum.microlist.org/)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:13 +msgid "" +"An online forum for discussing issues with and getting advice on sample " +"preparation and microscopy" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:14 +msgid "๐ŸŒ FPbase {cite}`Lambert2019-xl`" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:15 +msgid "[link](https://www.fpbase.org/)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:16 +msgid "" +"Database for identifying fluorophores by brightness, spectra and " +"assessing compatibility with other fluorophores and with microscope " +"filters" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:17 +msgid "๐ŸŒ Bio-protocol" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:18 +msgid "[link](https://bio-protocol.org/en/about )" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:19 +msgid "" +"Website to search for protocols across biological disciplines, including " +"protocols associated with work published elsewhere. All protocols are " +"available under an open access license (CC BY or CC BY-NC)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:20 +msgid "๐ŸŒ protocolos.io" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:21 +msgid "[link](https://www.protocols.io/)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:22 +msgid "A secure platform for developing and sharing reproducible methods" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:23 +msgid "" +"๐Ÿ“„ Designing a rigorous microscopy experiment: Validating methods and " +"avoiding bias {cite}`Jost2019-nx`" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:24 +msgid "" +"[link](https://rupress.org/jcb/article/218/5/1452/120908/Designing-a" +"-rigorous-microscopy-experiment)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:25 +msgid "" +"Review of aspects of designing a rigorous light microscopy experiment, " +"including validation of samples and imaging, identification and " +"correction of errors, and strategies to avoid biases" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:26 +msgid "" +"๐Ÿ“„ Tutorial: guidance for quantitative confocal microscopy " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:27 +msgid "[link](https://doi.org/10.1038/s41596-020-0313-9)" +msgstr "" + +#: ../../01_Sample_preparation/Resources.md:28 +msgid "" +"Step-by-step guidance on practical considerations for sample preparation," +" acquisition, and image analysis; primarily though not exclusively aimed " +"at users of confocal microscopy" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/02_Sample_acquisition.po b/locale/fi/LC_MESSAGES/02_Sample_acquisition.po new file mode 100644 index 000000000..249a736e0 --- /dev/null +++ b/locale/fi/LC_MESSAGES/02_Sample_acquisition.po @@ -0,0 +1,439 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../02_Sample_acquisition/Introduction.md:1 +#: ../../02_Sample_acquisition/Picking.md:3 +#: ../../02_Sample_acquisition/_notinyet_Setting_up.md:3 +msgid "Introduction" +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:3 +msgid "" +"Microscopes are optical instruments, and as such, they are composed of " +"different optical components and devices. As a beginner, it is important " +"to recognize the experimental parameters that can affect the quality and " +"rigor of the imaging data, and by extension, its interpretation." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:5 +msgid "" +"A foundational concept is the โ€œlight path,โ€ which can be used to trace " +"out lightโ€™s trajectory from the light source to the detector. When " +"working with microscopes, whether it is a cell culture microscope or a " +"cutting-edge superresolution system, it is important to take the time to " +"trace out the different light paths in the system. By approaching the " +"system as a sum of its parts means that optimizing and troubleshooting " +"become systematic processes compared to when the system is treated as a " +"black box. This [interactive tutorial at " +"MicroscopyU](https://www.microscopyu.com/tutorials/tepaths) shows the " +"light paths in a standard inverted microscope; [this " +"view](https://www.microscopyu.com/microscopy-basics/components) gives " +"more detail about the various parts." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:7 +msgid "Types of microscopes" +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:9 +msgid "" +"While far from a comprehensive list of what is available, a few of the " +"most common types of microscopes are listed below." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:10 +msgid "" +"**Widefield**, sometimes called _epifluorescence_, microscopes that take " +"in all the light available to them in a single light path; this approach " +"requires the least complex hardware, and also is often advantageous when " +"imaging dim samples. {term}`Deconvolution` is sometimes performed after " +"imaging on a widefield microscope to remove blur." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:11 +msgid "" +"**Confocal** - microscopes that remove out-of-focus light in the light " +"path, typically using one or many pinholes to physically block this " +"light. Several variants of confocal microscopy exist; spinning-disk " +"confocal microscopes are often preferred for live-cell imaging " +"applications as they tend to minimize toxicity to the sample." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:12 +msgid "" +"**Multiphoton** microscopes utilize multiple pulses of longer-wavelength " +"(lower energy) light to penetrate deep into tissue, since tissues are " +"less likely to scatter these wavelengths; once there, multiple low-" +"engergy photons hitting the fluorphore at the same time will use their " +"combined energy to activate a fluorophore that each photon alone would be" +" too weak to do. Because the benefit of these systems is in their deeper " +"penetration, they are often used for performing live-animal imaging." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:13 +msgid "" +"**Superresolution** microscopes that are designed to allows the user to " +"bypass the minimum optical resolution limit (typically 200 nm, depending " +"on sample consideration) to resolve very small structures. Sometimes this" +" is achieved with specialized hardware (such as in STED and SIM) and " +"sometimes with specialized probes (such as in PALM and STORM)." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:14 +msgid "" +"**Light sheet** microscopes that illuminate the sample perpendicular to " +"the axis of imaging, often by a second, orthogonal set of objective " +"lenses. This allows for thin optical sectioning across large volumes, but" +" introduces more considerations around sample mounting. Many variations " +"on light sheet microscopes have emerged in recent years." +msgstr "" + +#: ../../02_Sample_acquisition/Introduction.md:17 +msgid "" +"No matter which kind of microscope you use, scientific microscopes are " +"complex instruments with many working parts, all of which typically must " +"be in good working order and calibrated/aligned properly for quantitative" +" imaging to take place. The maintainer of your microscope will typically " +"ensure this, but speak with them regularly about questions you may have " +"and about how changes to the microscope configuration may affect your " +"ability to accurately make certain measurements. Your microscope " +"maintainer may be maintaining a large number of microscopes with a large " +"number of independent users, so if something looks \"off\", make sure to " +"talk with them before proceeding!" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:1 +msgid "Choosing the right microscopy modality" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:5 +msgid "" +"Choosing the right microscope for your experiment will be a factor both " +"of what the experiment dictates and what the researcher can access. The " +"image below (from [Fundamentals of Microscopy by Jermey " +"Sanderson](http://dx.doi.org/10.1002/cpmo.76) {cite}`Sanderson2020-qz`) " +"gives a sense of the sorts of decisions one should consider when choosing" +" a microscope; a more thorough description of the pros and cons of " +"various kinds of microscopes can be found in [this " +"tutorial](https://doi.org/10.1038/s41596-020-0313-9){cite}`Jonkman2020-bo`." +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:14 +msgid "BBBC image montage" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:14 +msgid "" +"**Flow chart to help choose which type of microscope to use.** Figure by " +"Jeremy Sanderson. [Source](https://www.researchgate.net/figure/Flow-" +"chart-to-help-choose-which-type-of-microscope-to-use_fig5_341918746) " +"{cite}`Sanderson2020-qz`" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:17 +msgid "Opportunities for microscopy resource access" +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:19 +msgid "" +"While some imaging facilities are open only to members of a single " +"institution, others allow outside visitors or even sponsor visitors to " +"travel to them." +msgstr "" + +#: ../../02_Sample_acquisition/Picking.md:21 +msgid "" +"**Advanced Imaging Center - Janelia Research Campus.** The AIC was " +"created to give access to the broad scientific community to new imaging " +"instruments that are not commercially available. Proposals can be " +"submitted during open calls at [their " +"website](https://www.aicjanelia.org/apply)." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:1 +msgid "Practical considerations" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:3 +msgid "Objective selection" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:5 +msgid "" +"Microscope objectives have a number of features that must be considered " +"when deciding which objective is right for your experiment" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:7 +msgid "" +"Magnification and resolution: the higher the numerical aperture (NA) of " +"the lens, the finer the resolution one can obtain in one's sample. The NA" +" is calculated as {math}`NA=RI * sin(ฮธ)`, relating both to the " +"{term}`refractive index` of the sample, glass, and {term}`immersion " +"media` as well as the range of angles of emitted light that can be " +"collected into the lens. Unless special techniques are used, the typical " +"limit of resultion is calculated as {math}`d = ฮป / 2NA`, meaning the " +"resolution is set both by the NA of the lens but also by the wavelength " +"of light used for imaging." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:16 +msgid "microtubules imaged at 488nm and 647nm" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:16 +msgid "" +"**Decreased resolution at longer wavelengths of light**. Microtubules " +"imaged at a shorter wavelength of light show higher resolution than those" +" imaged at longer wavelengths. Adapted from Jonkman J., Brown C.M., " +"Wright G.D _et al_. Tutorial: guidance for quantitative confocal " +"microscopy. _Nat Prot_ **15**, (2020) {cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:19 +msgid "" +"Color correction: When performing multicolor microscopy, it is important " +"to choose an objective lens that is labeled as `Apo` or `Super Apo`, as " +"such lenses are corrected to focus 3 to 6 colors in the same plane at the" +" same time. `Fluor` lenses will typically focus two colors at once." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:20 +msgid "" +"Working distance: The working distance (WD) gives the distance in " +"millimeters that the lens can focus into the sample. This distance " +"includes the coverslip and mounting media as well. If imaging a thick " +"sample, and/or if needing to image away from the surface of the sample, " +"it is important to ensure the lens has a sufficient working distance." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:22 +msgid "Filter sets" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:24 +msgid "" +"It is important to make sure that the microscope that you want to image " +"on has the correct filter sets for the fluorphores you wish to use. See " +"the [section on bleedthrough](content/bleedthrough) for more information." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:26 +msgid "Z sampling" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:28 +msgid "" +"If you wish to capture multiple z sections, the spacing of these setions " +"is important if you wish to be able to perform an accurate 3D " +"reconstruction. SVI has a [fuller mathematical explanation of " +"this](https://svi.nl/NyquistRate),as well as an easy-to-use [online " +"calculator](https://svi.nl/NyquistCalculator) that you can use to " +"calculate the optimal z section spacing for your imaging conditions." +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:30 +msgid "Acquisition power/speed" +msgstr "" + +#: ../../02_Sample_acquisition/Practical_considerations.md:32 +msgid "" +"The amount of signal captured from any fluorophore will be related not " +"just to the intrinsic brightness of the fluorophore, but also the amount " +"of excitation light it is exposed to (due to duration, power, or both) as" +" well as amount of time and signal multiplication that happens at the " +"detector (typically a camera or a photomultiplier tube (PMT)). An optimal" +" experiment is typically one that minimizes the amount of light hitting " +"the sample (to reduce photobleaching and/or phototoxicity) while " +"acheiving adequate fluorescent signal and in minimal time on the " +"equipment. How exactly to balance these competing factors will depend on " +"the exact biology being studied and the researcher's constraints." +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:7 +msgid "**Resource Name**" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:8 +msgid "**Link**" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:9 +msgid "**Brief description**" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:10 +msgid "๐ŸŒ Nikon MicroscopyU" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:11 +msgid "[link](https://www.microscopyu.com/microscopy-basics)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:12 +msgid "" +"Fundamentals of microscopy explained for beginners with lots of images " +"and plain language descriptions of terms used in microscopy" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:13 +msgid "" +"๐Ÿ“„ Seeing is believing? A beginners' guide to practical pitfalls in image " +"acquisition {cite}`North2006-sb`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:14 +msgid "[link](https://doi.org/10.1083/jcb.200507103)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:15 +msgid "" +"An overview of common concerns to check for during sample preparation and" +" image acquisition" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:16 +msgid "๐Ÿ“„ Fluorescence microscopy - avoiding the pitfalls {cite}`Brown2007-ou`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:17 +msgid "" +"[link](https://journals.biologists.com/jcs/article/120/10/1703/29404" +"/Fluorescence-microscopy-avoiding-the-pitfalls)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:18 +msgid "" +"Short overview of some of the most common pitfalls for beginners to " +"fluorescence microscopy" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:19 +msgid "" +"๐Ÿ“„ Tutorial: guidance for quantitative confocal microscopy " +"{cite}`Jonkman2020-bo`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:20 +msgid "[link](https://doi.org/10.1038/s41596-020-0313-9)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:21 +msgid "" +"Step-by-step guidance on practical considerations for sample preparation," +" acquisition, and image analysis; primarily though not exclusively aimed " +"at users of confocal microscopy" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:22 +msgid "" +"๐Ÿ“„ Best practices and tools for reporting reproducible fluorescence " +"microscopy methods {cite}`Montero_Llopis2021-nb`" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:23 +msgid "[link](https://www.nature.com/articles/s41592-021-01156-w)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:24 +msgid "" +"Guidelines and resources for accurate reporting of the most common " +"fluorescence light microscopy techniques, emphasizing the impact of " +"accurate microscopy metadata on data interpretation.'" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:25 +msgid "๐ŸŽฅ iBiology Microscopy Short Course" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:26 +msgid "" +"[link](https://www.youtube.com/watch?v=4c5ILWQmqRY&list=PLQFc-" +"Dxlf4pSRaEk8Xi9BzS0r8-LYmwRQ)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:27 +msgid "" +"An 8 hour video series consisting of 14 videos introducting major " +"concepts in microscopy. A longer course with >70 videos is also " +"available." +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:28 +msgid "๐ŸŽฅ Microcourses" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:29 +msgid "[link](https://www.youtube.com/@Microcourses)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:30 +msgid "" +"Videos about microscopy from the microscopy cores at Harvard Medical " +"School" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:31 +msgid "๐ŸŒ Advanced Imaging Center" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:32 +msgid "[link](https://www.aicjanelia.org/apply)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:33 +msgid "Access to the state of the art microscopy instruments and imaging experts" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:34 +msgid "๐ŸŒ Africa Microscopy Initiative" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:35 +msgid "[link](https://www.microscopy.africa/ )" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:36 +msgid "" +"Access to advanced microscopes, molecular biology and cell culture " +"equipment for scientists in Africa" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:37 +msgid "๐ŸŒ Euro-Bioimaging" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:38 +msgid "[link](https://www.eurobioimaging.eu)" +msgstr "" + +#: ../../02_Sample_acquisition/Resources.md:39 +msgid "Access to microcopy instruments and training for scientists in Europe" +msgstr "" + +#: ../../02_Sample_acquisition/_notinyet_Setting_up.md:1 +msgid "Setting up your acquisition" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/03_Image_analysis.po b/locale/fi/LC_MESSAGES/03_Image_analysis.po new file mode 100644 index 000000000..0d41c3257 --- /dev/null +++ b/locale/fi/LC_MESSAGES/03_Image_analysis.po @@ -0,0 +1,1587 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-15 11:57-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../03_Image_analysis/Classification.md:1 +msgid "Object classification" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:3 +msgid "What is classification?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:4 +msgid "" +"Simply put, phenotypic classification is about categorizing objects into " +"different groups based on their features (aka measurements)." +msgstr "" + +#: ../../03_Image_analysis/Classification.md +#: ../../03_Image_analysis/Colocalization.md +#: ../../03_Image_analysis/Intensity.md ../../03_Image_analysis/Shape.md +#: ../../03_Image_analysis/Tracking.md +msgid "๐Ÿ“ How do I measure it?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:10 +msgid "" +"Phenotypic classification can be performed a few different ways. One way " +"to break this down is by unsupervised vs. supervised classification." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:12 +msgid "" +"In **supervised classification**, a human also provides information on " +"what the different groups of objects should look like by providing " +"representative examples of each group in a training dataset. The computer" +" then learns how to assign objects to groups based on their measurements " +"by testing models against the ground truth training dataset." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:14 +msgid "" +"For example, you could classify cells based on a visual phenotype and " +"train a machine learning classifier to derive which measurement ranges " +"are associated with different classes. This is supervised classification " +"because a person is providing instruction of how many classes there " +"should be and examples of what each class should look like for the " +"computer to learn from. An example of this could be annotating a subset " +"of cells that are in different stages of mitosis and training a " +"classifier to use your labels to find other cells in those stages." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:16 +msgid "" +"In **unsupervised classification**, you group objects based on their " +"measurements, but without any top-down human-defined guidance into how " +"many groups there are or what the groups should look like." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:18 +msgid "" +"For example, you could measure hundreds or thousands of features of cells" +" from many treatments, as is typical in large-scale cell profiling " +"experiments. Next you could let the computer cluster the cells into some " +"number of different groups based on having similar measurements. This is " +"a form of unsupervised clustering, where you observe what groups emerge " +"from a computer considering their measurements only, and not class labels" +" we impose as researchers. These sorts of clustering experiments can " +"provide novel results but may also be harder to interpret; see this " +"protocol{cite}`GarciaFossaCruz2023` for more information." +msgstr "" + +#: ../../03_Image_analysis/Classification.md +#: ../../03_Image_analysis/Colocalization.md +#: ../../03_Image_analysis/Data_management.md +#: ../../03_Image_analysis/Intensity.md ../../03_Image_analysis/Shape.md +#: ../../03_Image_analysis/Tracking.md +msgid "โš ๏ธ Where can things go wrong?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:23 +msgid "" +"**Valid measurements are still important** Classification can be simple " +"or complex, but results always depend on the validity of your " +"measurements. For this reason, all the caveats of earlier measurement " +"sections also apply here." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:24 +msgid "" +"**Machines are lazy** Machine learning classifiers arenโ€™t necessarily " +"going to learn the biologically relevant features that distinguish " +"objects from distinct groups. Confounding features, or features that vary" +" with your phenotype but are not biologically related to it, can limit " +"the usefulness of your classifier and lead to incorrect conclusions. For " +"instance, if clinicians often put rulers next to malignant looking moles " +"and not next to benign moles and try to train a machine learning " +"classifier to distinguish malignant vs. benign, the model might learn to " +"classify images with rulers as malignant without tapping into any of the " +"relevant features of the moles. This is a [real " +"example](https://pubmed.ncbi.nlm.nih.gov/30244720/) {cite}`Narla2018-qh`." +" If possible, examining which features your model is relying on to " +"classify objects can be a way to check for this. Itโ€™s also important to " +"standardize how you capture images of your different classes of objects " +"and include a large enough training set with images with lots of " +"variation. You wouldnโ€™t want all your positive cells to come from samples" +" you imaged in March and all your negative cells from samples you imaged " +"in January, for example." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:25 +msgid "" +"**Violating model assumptions** If using a machine learning classifier, " +"different models come with different baked-in assumptions. If youโ€™re " +"starting out, it can be difficult to know which to pick. There are " +"interactive tools such as [CellProfiler " +"Analyst](https://academic.oup.com/bioinformatics/article/32/20/3210/2196630)" +" {cite}`Stirling2021-ov` and [Piximi](https://www.piximi.app/) that make " +"training a classifier easier, especially if you donโ€™t know how to code." +msgstr "" + +#: ../../03_Image_analysis/Classification.md:26 +msgid "" +"**Messy boundaries** Most methods of supervised classification, where the" +" user assigns objects to a score or to a bin, ultimately treat each bin " +"as a totally separate entity; biology is rarely so neat. For example, a " +"supervised classifier for cell cycle phase must assign a cell to one " +"phase, but in fact progression through the cell cycle is not a perfectly " +"switch-like process, as can be visualized by measurements of individual " +"cells (colored by their class given by a human observer). More " +"sophisticated methods may be needed to classify more continuous " +"phenotypes" +msgstr "" + +#: ../../03_Image_analysis/Classification.md +msgid "a continuous distribution of cell cycle states" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:35 +msgid "" +"**Strict division into supervised classes can be tricky for continuous " +"biological processes**. Adapted from Eulenberg, P., Kรถhler, N., Blasi, T." +" _et al_. Reconstructing cell cycle and disease progression using deep " +"learning. _Nat Commun_ **8**, 463 (2017) {cite}`Eulenberg2017-ax`" +msgstr "" + +#: ../../03_Image_analysis/Classification.md +#: ../../03_Image_analysis/Colocalization.md +#: ../../03_Image_analysis/Data_management.md +#: ../../03_Image_analysis/Intensity.md ../../03_Image_analysis/Shape.md +#: ../../03_Image_analysis/Tracking.md +msgid "๐Ÿ“š๐Ÿคทโ€โ™€๏ธ Where can I learn more?" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:41 +msgid "" +"๐Ÿ“„ [Data-analysis strategies for image-based cell " +"profiling](https://www.nature.com/articles/nmeth.4397) " +"{cite}`Caicedo2017-ks`" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:42 +msgid "" +"๐Ÿ“„ [Scoring diverse cellular morphologies in image-based screens with " +"iterative feedback and machine " +"learning](https://www.pnas.org/doi/10.1073/pnas.0808843106) " +"{cite}`Jones2009-zz`" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:43 +msgid "" +"๐ŸŽฅ [iBiology video series: Measurement and Phenotype " +"Classification](https://www.youtube.com/watch?v=Odi9pIerT7I)" +msgstr "" + +#: ../../03_Image_analysis/Classification.md:44 +msgid "" +"๐Ÿ“„ [Interpreting Image-based Profiles using Similarity Clustering and " +"Single-Cell Visualization](https://doi.org/10.1002/cpz1.713) " +"{cite}`GarciaFossaCruz2023`" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:1 +msgid "Colocalization" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:4 +msgid "What is colocalization?" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:6 +msgid "" +"Colocalization is when two or more different labels (e.g., eGFP and " +"mCherry) spatially overlap in your image (also called co-occurrence). " +"Another component of colocalization is that the fluorescent labels often " +"correlate in intensity (i.e., pixels with brighter eGFP also have " +"brighter mCherry). It is very important to measure colocalization " +"quantitativelyโ€“**do not just trust your eyes!**" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:8 +msgid "" +"It is also important to recognize that co-ocurrence does not " +"_necessarily_ imply interaction." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:11 +msgid "" +"As an example, it is possible for two people to work in the same building" +" an never interact." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:21 +msgid "degrees of colocalization" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:21 +msgid "**Colocalization is about intensity and spatial overlap of labels**" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:28 +msgid "" +"There are two main branches for how to look at colocalization: Object-" +"based and correlation-based." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:30 +#, python-format +msgid "" +"**Object-based colocalization** is appropriate when you want to be able " +"to say something about a fraction of objects being positive for multiple " +"labels (e.g., 99% of eGFP+ cells were also mCherry+). Hereโ€™s a sample " +"workflow:" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:51 +msgid "" +"**Correlation-based colocalization** is more appropriate when the labels " +"youโ€™re measuring are not found in discrete objects or when you predict " +"that the signal in the labels should correlate. Correlation-based " +"colocalization is simpler to measure as it does not require any " +"{term}`segmentation` of objects. Pearson correlation coefficients are " +"readily measurable in most image analysis softwares (e.g., FIJI, " +"CellProfiler, etc.)." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:55 +msgid "" +"**Not having adequate controls** (e.g., single label controls where only " +"one fluorescent label is present). Noise, uneven illumination, and other " +"technical artifacts can cause correlation between two channels" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:56 +msgid "" +"**Not correcting for shift between channels** Itโ€™s common to have some " +"degree of shift between different imaging channels due to differences in " +"optics (e.g., different filter cubes). Not correcting for this shift " +"(e.g., by measuring it and applying the corresponding correction to the " +"channels) can limit your ability to detect colocalization." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:57 +msgid "" +"**Bleedthrough** Sometimes signal from one fluorescent channel bleeds " +"into another, which can falsely increase your detected colocalization. " +"This happens most commonly with fluorophores that are similar in spectra " +"(e.g., GFP and YFP). This is caused by fluorophore in one channel being " +"weakly excited by light used to excite a different fluorophore and the " +"resulting emitted fluorescence makes it through the emission filter " +"(e.g., your green objects show up in the yellow channel as well). Assess " +"this with single label controls." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:58 +msgid "" +"**Improper interpretation of your colocalization metric** The details of " +"the metric chosen here are very important - they vary widely in terms of " +"their inclusion of background pixels, their sensitivity to signal-to-" +"noise, etc. Consultation with an expert and the inclusion of proper " +"controls can help you be assured that your measurement is truly what you " +"think it is." +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:63 +msgid "" +"๐Ÿ”ข [Theoretical background on " +"colocalization](https://svi.nl/ColocalizationTheory)" +msgstr "" + +#: ../../03_Image_analysis/Colocalization.md:64 +msgid "" +"๐Ÿ“„ [Image co-localization - co-occurrence versus " +"correlation](https://journals.biologists.com/jcs/article/131/3/jcs211847/77151" +"/Image-co-localization-co-occurrence-versus) {cite}`Aaron2018-qi`" +msgstr "" + +#: ../../03_Image_analysis/Common_types_of_analysis.md:1 +msgid "Common types of analysis" +msgstr "" + +#: ../../03_Image_analysis/Common_types_of_analysis.md:3 +msgid "" +"In this section, we detail information and tips about some common, very " +"useful types of image analysis. We first describe two aspects of " +"morphological analysis. **Morphology** is the study of the appearance, " +"form, and structure of an object and morphological measurements include " +"those based on object **shape** (e.g. cell area) as well as **intensity**" +" (e.g. mean brightness of GFP). After describing shape-based and " +"intensity-based analyses, we also present tips for measuring " +"**colocalization**, **tracking objects**, and **classifying objects**." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:1 +msgid "Data management and sharing" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:3 +msgid "What is it?" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:5 +msgid "" +"Both journals and scientific funders have placed more emphasis in recent " +"years on the fact that it is critical to save both the raw data generated" +" during the course of scientific discovery as well as the workflows used " +"to process such data. While mandates to publicly deposit raw image data " +"have recently gone into place in several countries, it can be difficult " +"for researchers to know where to store images, code, and metadata " +"associated with their bioimaging experiments." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md +msgid "๐Ÿค” What are my options?" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:9 +msgid "" +"There are many options for storing image data in online repositories. " +"These services make it easy to share and reuse data. The best option will" +" depend on the size of the dataset, the budget for storage, whether there" +" is related non-image data, and how much metadata is available for the " +"dataset. Some options are summarized below:" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md +msgid "Comparison of various data respositories" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:18 +msgid "" +"**Options for storing bioimaging data** Figure by Beth Cimini (2023) " +"[Source](https://doi.org/10.5281/zenodo.7628604)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:24 +msgid "" +"**Not storing original versions of images**. It is critical that the raw " +"image data be saved and stored. It is very important that these files are" +" not compressed formats (e.g., '.jpeg') or modified from the original " +"files on which analysis was performed. If files are modified, " +"measurements will change and the analysis pipeline will not be " +"reproducible to anyone else." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:26 +msgid "" +"**Necessary imaging metadata is unavailable**. In order to properly " +"calibrate measurement data, it's critical that information like pixel " +"size (e.g., in microns), the microscope manufacturer and model, and " +"acquisition settings are included alongside the data. If this isn't " +"included, it will be very difficult to reproduce results or use the " +"combine the data with other datasets." +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:32 +msgid "๐ŸŒ [Zenodo](https://zenodo.org/)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:33 +msgid "๐ŸŒ [Figshare](https://figshare.com)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:34 +msgid "๐ŸŒ [Dryad](https://datadryad.org)" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:35 +msgid "" +"๐ŸŒ [Bioimage Archive](https://www.ebi.ac.uk/bioimage-archive/) " +"{cite}`Hartley2022-mt`" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:36 +msgid "" +"๐ŸŒ [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) " +"{cite}`Williams2017-yy`" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:37 +msgid "๐ŸŒ [BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr`" +msgstr "" + +#: ../../03_Image_analysis/Data_management.md:38 +msgid "" +"๐ŸŒ [Cell Painting Gallery](https://registry.opendata.aws/cellpainting-" +"gallery/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:1 +msgid "General Use Software" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:3 +msgid "" +"Tools on this page tend to be relatively multipurpose across a lot of " +"kinds of analyses and/or images. For tools that specialize in certain " +"analysis steps, see the [Specific Use Software](./SpecificUseSoftware.md)" +" page." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:6 +msgid "" +"\"logo\" ImageJ" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:9 +msgid "" +"[ImageJ](https://imagej.net/) " +"{cite}`Schneider2012-gs,Schindelin2012-kk,Rueden2017-ku` is an imaging " +"processing program that is capable of operating on a variety of images " +"including multichannel, 3D and time series. It provides a variety of " +"basic imaging processing operations, but it can be complemented with a " +"variety of plugins for more complex tasks." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md +#: ../../03_Image_analysis/SpecificUseSoftware.md +msgid "What are its disadvantages?" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:14 +msgid "" +"Imaging processing operations are done one at a time, while it has the " +"capability of batch processing and creating macros it does require some " +"understanding of coding." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:15 +msgid "" +"But while it can open large images, there is a size limit to the size it " +"can handle based on the available memory. And even if it can open large " +"images it can slow down performance." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md +#: ../../03_Image_analysis/SpecificUseSoftware.md +msgid "How to download/install and learn more?" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:20 +msgid "To download ImageJ or its โ€œbatteries-includedโ€ distribution Fiji go to" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:24 +msgid "๐ŸŒ [ImageJ download](https://imagej.net/downloads)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:26 +msgid "" +"For documentation and tutorials on how to use ImageJ as well as a list of" +" available plugins" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:30 +msgid "๐ŸŒ [ImageJ basics](https://imagej.net/learn/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:34 +msgid "" +"\"logo\" CellProfiler" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:36 +msgid "" +"[CellProfiler](https://cellprofiler.org/) {cite}`Stirling2021-sg` is a " +"software designed for biologists by biologists; it creates a bridge " +"between image analysis and scientist with no need of computational " +"expertise. It was designed with the idea of an image analysis pipeline in" +" mind: it allows you to take a series of interoperable modules to design " +"your own custom analysis pipeline that can be applied to one or thousands" +" of images, making it suitable for high throughput image analysis." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:42 +msgid "" +"CellProfiler canโ€™t handle large images, like whole tissue sections from " +"histology experiments. The image size is currently limited by the " +"available memory on your computer." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:43 +msgid "" +"While CellProfiler can perform analysis on 3D images the visualization is" +" limited to a one z-plane at a time via a slider on the viewing window." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:44 +msgid "Also several features of CellProfiler are only available for 2D images." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:49 +msgid "To download CellProfiler" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:53 +msgid "๐ŸŒ [CellProfiler download](https://cellprofiler.org/releases)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:55 +#: ../../03_Image_analysis/GeneralUseSoftware.md:84 +#: ../../03_Image_analysis/GeneralUseSoftware.md:113 +#: ../../03_Image_analysis/GeneralUseSoftware.md:142 +#: ../../03_Image_analysis/GeneralUseSoftware.md:172 +#: ../../03_Image_analysis/SpecificUseSoftware.md:59 +msgid "For documentation examples and tutorials." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:59 +msgid "" +"๐ŸŒ [CellProfiler user manual](https://cellprofiler-" +"manual.s3.amazonaws.com/CellProfiler-4.2.4/index.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:60 +msgid "๐ŸŒ [Examples](https://cellprofiler.org/examples)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:61 +msgid "๐ŸŒ [Tutorials](https://tutorials.cellprofiler.org/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:62 +msgid "" +"๐ŸŽฅ [Video tutorials and " +"workshops](https://www.youtube.com/playlist?list=PLXSm9cHbSZBBy7JkChB32_e3lURUcT3RL)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:66 +msgid "" +"\"logo\" QuPath" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:68 +msgid "" +"[QuPath](https://qupath.github.io/) {cite}`Bankhead2017-kz` offers a wide" +" set of image analysis tools that can be applied to whole slide images. " +"For that reason it is widely utilized with pathology images, but it can " +"be used with other images as well. QuPath also contains pixel " +"classification tools and can integrate with ImageJ (e.g., for sending " +"{term}`ROIs` between the programs, or for accessing ImageJ plugins)." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:73 +msgid "" +"To get the most out of QuPath (especially when analyzing many images), " +"some scripting and knowledge of coding (or adapting otherโ€™s code) is " +"necessary" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:78 +msgid "To download QuPath" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:82 +msgid "๐ŸŒ [QuPath download](https://qupath.github.io/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:88 +msgid "๐ŸŒ [QuPath user manual](https://qupath.readthedocs.io/en/stable/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:89 +msgid "๐ŸŽฅ [Video tutorials and workshops](https://www.youtube.com/c/qupath)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:93 +msgid "" +"\"logo\" Icy" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:95 +msgid "" +"[Icy](https://icy.bioimageanalysis.org/) {cite}`De_Chaumont2012-pe` is an" +" out of the box image analysis tools, it utilizes plugins to create " +"visual image analysis protocols that can be shared with other users." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:102 +msgid "Icy interoperability with other softwares is limited to ImageJ" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:107 +msgid "To download Icy" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:111 +msgid "๐ŸŒ [Icy download](https://icy.bioimageanalysis.org/download/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:117 +msgid "๐ŸŒ [Icy course and tutorial](https://icy.bioimageanalysis.org/trainings/)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:118 +msgid "" +"๐ŸŽฅ [Bioimage analysis with Icy " +"](https://www.youtube.com/watch?v=myal9BD6J-k)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:122 +msgid "" +"\"logo\" MIB (Microscopy Image Browser)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:124 +msgid "" +"[MIB](http://mib.helsinki.fi/index.html) {cite}`Belevich2016-vi` is a " +"user-friendly software for image analysis of multidimensional datasets " +"for both light and electron microscopy. It allows you to use the whole " +"acquired data for its analysis and extraction of morphological features." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:131 +msgid "" +"It was created using MATLAB, a standalone packaged version exist, but " +"they do not use the most up-to-date MATLAB releases" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:136 +msgid "To download MIB" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:140 +msgid "๐ŸŒ [MIB download](http://mib.helsinki.fi/downloads.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:146 +msgid "" +"๐ŸŒ [MIB user " +"guide](http://mib.helsinki.fi/help/main2/im_browser_user_guide.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:147 +msgid "๐ŸŒ [Tutorials](http://mib.helsinki.fi/tutorials.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:148 +msgid "" +"๐ŸŽฅ [Video " +"tutorials](https://www.youtube.com/playlist?list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:152 +msgid "" +"\"logo\" napari" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:154 +msgid "" +"[napari](https://napari.org/) {cite}`Sofroniew2022-nd` is being developed" +" as a multi-dimensional image viewer that can be expanded via a variety " +"of plugins to perform basic and complex image analysis tasks." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:161 +msgid "" +"napari is still in the development stages, but it is a very popular " +"platform and already has a variety of plugins and use cases with " +"tutorials available." +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:166 +msgid "To download napari" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:170 +msgid "" +"๐ŸŒ [napari bundled app download " +"](https://napari.org/stable/tutorials/fundamentals/installation.html" +"#install-as-a-bundled-app)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:176 +msgid "" +"๐ŸŒ [New to napari guide " +"](https://napari.org/stable/tutorials/fundamentals/getting_started.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:177 +msgid "๐ŸŒ [Tutorials](https://napari.org/stable/tutorials/index.html)" +msgstr "" + +#: ../../03_Image_analysis/GeneralUseSoftware.md:178 +msgid "" +"๐ŸŒ [Bioimage Analysis with Napari - A FocalPlane blog " +"series](https://focalplane.biologists.com/category/blog-series/bio-image-" +"analysis-with-napari/)" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:1 +msgid "Intensity measurements" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:3 +msgid "What are intensity measurements?" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:4 +msgid "" +"Intensity refers to the brightness of signal for a fluorescent label. " +"Using intensity measurements, we can infer a relative amount of " +"fluorophore or stain. So for instance, if you have a protein tagged with " +"a fluorophore, you can measure the intensity of that fluorophore to get a" +" relative measure of how much protein is present in your sample. " +"Intensity measurements include the following (non-exhaustive) and can be " +"measured within an image, in a object like a cell, in subregions of an " +"object:" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:5 +msgid "**Mean intensity**: the average intensity across all pixels" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:6 +msgid "" +"**Integrated intensity**: the sum of pixel intensities, a proxy for the " +"total amount of that marker in an object" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:7 +msgid "**Texture measurements**: the smoothness of the intensities" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:13 +msgid "" +"Intensity is relatively straightforward to measure, but can be quite " +"tricky to do _correctly_ (see below). We strongly suggest you contact an " +"image analysis expert before proceeding with this type of analysis " +"because there are so many places things can go wrong. In general, you " +"want to measure on either raw images, or illumination-corrected images, " +"but in general with minimal {term}`image processing`. Illumination-" +"correction is a form of {term}`image processing` to compensate for the " +"uneven pattern of illumination produced by most light sources where the " +"middle of the field of illumination is brighter than the edges. Then " +"intensity measurements can be made in any standard image analysis " +"software, either across the whole image or in identified objects. See " +"below for an example workflow:" +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:35 +msgid "" +"To understand saturation another way, imagine youโ€™re trying to measure " +"average male height with a 2 meter tape measure. If our sample contains " +"men that are taller than 2 meters, we canโ€™t tell _how much taller_ than 6" +" feet they are; theyโ€™re like saturated pixels that exceed the intensity " +"we can detect. This saturation of our measurement tool means we canโ€™t " +"accurately report average height." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:38 +msgid "" +"**Saturation** Saturated pixels are so bright their intensity values max " +"out our detector (camera). If you have saturated pixels in the cells " +"youโ€™re trying to measure, you really canโ€™t do most intensity " +"measurements. This is because for saturated pixels, you donโ€™t know how " +"bright they really are, just that theyโ€™re brighter than you can detect. " +"There are some intensity measurements that are robust to some saturation." +" For example, the median intensity of an image wonโ€™t be affected by " +"saturation unless you have >ยฝ the image saturated. But measurements like " +"mean intensity will be affected by saturation." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:40 +msgid "" +"**Inadequate controls** In most cases, the exact intensity measures you " +"get donโ€™t mean anything biologically in isolation. Itโ€™s only by " +"comparison of conditions that we can generate some biological insight. A " +"control condition is therefore **very** important to compare to your " +"experimental condition." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:42 +msgid "" +"**Not matching imaging conditions across experimental conditions** " +"Because intensity measures are affected by exposure time, light source " +"intensity, and other factors, itโ€™s very important to match imaging " +"settings across your samples. Relatedly, you should make sure you donโ€™t " +"separate imaging your experimental and control conditions to different " +"days if this can be in any way avoided. Fluorophores can become dimmer " +"over time in samples, which complicates interpretation if different " +"sample types were imaged on different days." +msgstr "" + +#: ../../03_Image_analysis/Intensity.md:48 +msgid "" +"๐ŸŽ“ [Neubias training resource on intensity " +"measures](https://neubias.github.io/training-" +"resources/measure_intensities/index.html)" +msgstr "" + +#: ../../03_Image_analysis/Introduction.md:1 +#: ../../03_Image_analysis/Software.md:3 +#: ../../03_Image_analysis/_notinyet_Image_processing.md:3 +#: ../../03_Image_analysis/_notinyet_Image_segmentation.md:3 +msgid "Introduction" +msgstr "" + +#: ../../03_Image_analysis/Introduction.md:3 +msgid "" +"Microscopy images are inherently quantitative, which makes them a very " +"powerful data source. As a biologist, image analysis allows you to " +"translate these numbers into insights that answer biological questions. " +"For our purposes, **image analysis** is the process of measuring aspects " +"of biological phenomena captured in microscopy images. Microscopy images " +"are already _inherently quantitative_ in that they are matrices (i.e., " +"grids) of numbers. However, image analysis is the process of turning " +"these raw numbers into biologically interpretable measurements. Image " +"analysis typically involves a series of steps that can be collected into " +"a pipeline or analysis workflow. A simple example workflow is shown " +"below:" +msgstr "" + +#: ../../03_Image_analysis/Introduction.md:26 +msgid "" +"The specifics of your workflow depend on your biological question. Below " +"we present a few common types of analysis for fluorescence microscopy " +"experiments. For each, weโ€™ll explain key ideas to understand before you " +"begin, common pitfalls, and links to a few key resources to learn more. " +"We encourage you to think about your analysis strategy even before " +"beginning sample preparation. While not always possible, speaking with an" +" image analysis expert in your local core facility or asking a question " +"on the [image.sc](https://image.sc) forum _before you begin_ can save you" +" a ton of time and headache when it comes to designing an image analysis " +"strategy." +msgstr "" + +#: ../../03_Image_analysis/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:7 +msgid "**Resource Name**" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:8 +msgid "**Link**" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:9 +msgid "**Brief description**" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:10 +msgid "๐ŸŒ Image.sc {cite}`Rueden2019-qp`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:11 +msgid "[link](https://forum.image.sc/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:12 +msgid "Discussion forum for bioimage analysis software" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:13 +msgid "๐ŸŒ Peter Bankheadโ€™s Intro to Bioimage Analysis" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:14 +msgid "[link](https://bioimagebook.github.io/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:15 +msgid "" +"Guide for absolute beginners to image analysis, including embedded " +"questions/answers, exercises with Python and ImageJ, and videos to check " +"understanding" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:16 +msgid "๐Ÿ“– Bioimage Data Analysis {cite}`Miura2016-wq`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:17 +msgid "[link](https://analyticalscience.wiley.com/do/10.1002/was.00050003/full/bioimagedataanalysis.pdf)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:18 +msgid "" +"A free online textbook introducing various topics by Bioimage Analysis " +"experts, edited by Kota Miura" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:19 +msgid "๐Ÿ“„ Reproducible image handling and analysis {cite}`Miura2021-mb`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:20 +msgid "[link](https://www.embopress.org/doi/full/10.15252/embj.2020105889)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:21 +msgid "" +"An article reviewing major pitfalls in image handling and how to avoid " +"them and create reproducible analysis workflows" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:22 +msgid "๐Ÿ“„ Made to measure: an introduction to quantification in microscopy data" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:23 +msgid "[link](https://arxiv.org/abs/2302.01657#) {cite}`Culley2023-dj`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:24 +msgid "" +"An article describing several common classes of measurements made in " +"microscopy data, as well as technical factors that may affect the results" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:25 +msgid "" +"๐Ÿ“„ A Hitchhiker's guide through the bio-image analysis software universe " +"{cite}`Haase2022-ad`" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:26 +msgid "[link](https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:27 +msgid "" +"An article that gives guidance and a glossary of available image analysis" +" software and packages" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:28 +msgid "๐ŸŒ BioImage Informatics Index" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:29 +msgid "[link](https://biii.eu/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:30 +msgid "" +"Repository platform for searching bioimage analysis tools and workflows " +"based on the problem, method or software of choice" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:31 +msgid "๐ŸŽฅ iBiology Bioimage Analysis video series" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:32 +msgid "[link](https://youtu.be/1xo4vi6Ub4I)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:33 +msgid "" +"Video series that introduces Bioimage analysis, including overviews of " +"{term}`image processing`, {term}`segmentation`, tracking, making and " +"interpreting measurements, tips and pitfalls" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:34 +msgid "๐ŸŒ Bioimage ANalysis Desktop (BAND)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:35 +msgid "[link](https://band.embl.de)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:36 +msgid "" +"Access to virtual desktops allowing access to bioimage analysis software " +"from a browser" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:37 +msgid "๐ŸŒ Galaxy Imaging Node" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:38 +msgid "[link](https://imaging.usegalaxy.eu/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:39 +msgid "" +"A Galaxy node prepopulated with a number of open-source image analysis " +"tools and workflows, making it easy to create and share reproducible FAIR" +" workflows" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:40 +msgid "๐ŸŒ Image Analysis Training Resources" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:41 +msgid "[link](https://neubias.github.io/training-resources/index.html)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:42 +msgid "" +"Image analysis traning resources collected by NEUBIAS, styled based on " +"The Carpentries" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:43 +msgid "๐ŸŒ Bioimage Analysis AwesomeList" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:44 +msgid "[link](https://github.com/hallvaaw/awesome-biological-image-analysis)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:45 +msgid "" +"A curated [AwesomeList](https://github.com/sindresorhus/awesome) of " +"resources related to bioimage analysis" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:46 +msgid "๐ŸŒ Bioimage Analysis Notebooks" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:47 +msgid "[link](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/)" +msgstr "" + +#: ../../03_Image_analysis/Resources.md:48 +msgid "" +"A collection of Python Jupyter notebooks for BioImageAnalysis, GPU-" +"accelerated image processing, bio-image data science and more" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:1 +msgid "Size and Shape measurements" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:3 +msgid "What are size measurements?" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:4 +msgid "" +"Size measurements describe the dimensions of objects in your image. " +"Common size measurements include:" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:6 +msgid "" +"**Area**: the 2D space an object takes up in the image or the 3D surface " +"area of an object" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:7 +msgid "**Volume**: the 3D space an object takes up in a 3D image" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:8 +msgid "**Perimeter**: the distance around the edge of an object" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:10 +msgid "What are shape measurements?" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:11 +msgid "" +"Shape measurements describe the 2D or 3D form of objects in our sample. " +"Common shape measurements include:" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:13 +msgid "" +"**Circularity**: How round vs. elongated an object is. Formally defined " +"as $circularity = 4pi*{area}/{perimeter}^2$ where 1 is a perfect circle " +"and circularity <1 is a more elongated polygon." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:14 +msgid "" +"**Solidity**: how dense vs. wispy/holey an object is. Formally defined as" +" $solidity = area/convex area$ where _convex area_ is akin to the area " +"inside a shape formed by stretching a rubber band around the object." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:20 +msgid "" +"After segmenting an image to locate the pixels belonging to different " +"objects, morphology can be measured readily in many image analysis " +"softwares, like FIJI and CellProfiler. For example, in {term}`Fiji`, " +"after identifying your objects as {term}`ROIs`, be sure to **Analyze > " +"Set Measurementsโ€ฆ** and select โ€œShape Descriptorsโ€ then simply measure " +"your {term}`ROIs` with **Analyze > Measure**. In CellProfiler, this is " +"accomplished using the module MeasureObjectSizeShape." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:25 +msgid "" +"**Not understanding the limitations of your images**. All biological " +"structures are 3D, but we often analyze 2D images. Often this is still " +"very useful! But the larger and more complex your objects (e.g., neurons " +"in a tissue section), the more limited a 2D view becomes." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:26 +msgid "" +"**Failing to use calibrated units**. Be sure to properly calibrate your " +"images and present final measurements in microns (or similar units). If " +"measuring 3D images, be sure to take into account the z-step, which is " +"likely larger than the xy pixel size." +msgstr "" + +#: ../../03_Image_analysis/Shape.md:31 +msgid "" +"๐Ÿ“„ [Current Methods and Pipelines for Image-Based Quantitation of Nuclear " +"Shape and Nuclear Envelope " +"Abnormalities](https://www.mdpi.com/2073-4409/11/3/347/htm) " +"{cite}`Janssen2022-bm`" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:32 +msgid "" +"๐ŸŒ [Description of morphological measurements made by CellProfiler](https" +"://cellprofiler-" +"manual.s3.amazonaws.com/CellProfiler-4.2.4/modules/measurement.html#id20)" +msgstr "" + +#: ../../03_Image_analysis/Shape.md:33 +msgid "" +"๐ŸŽ“ [Plain language description of various morphological measures by " +"Michael " +"Wirth](http://www.cyto.purdue.edu/cdroms/micro2/content/education/wirth10.pdf)" +msgstr "" + +#: ../../03_Image_analysis/Software.md:1 +msgid "Open source software" +msgstr "" + +#: ../../03_Image_analysis/Software.md:5 +msgid "" +"When it comes time to select a software program for your image analysis, " +"there are many options, some more general and others highly specialized " +"to specific image modalities or types of experiments. In general, a good " +"place to start exploring is by examining papers in your field and seeing " +"what others have used to analyze similar experiments to your own. Itโ€™s " +"important to note that there isnโ€™t one correct answer to \"Which program " +"should I use?\" Depending on your biological question, your images, and " +"your own comfort with coding, there are many options available." +msgstr "" + +#: ../../03_Image_analysis/Software.md:7 +msgid "" +"Below, we summarize the use-cases and limitations of some of the most " +"common, free and open-source software for image analysis, this is a small" +" list and more extensive ones exist like the [A Hitchhiker's guide " +"through the bio-image analysis software " +"universe](https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451)" +" {cite}`Haase2022-ad` and the [BioImage Informatics " +"Index](https://biii.eu) {cite}`Paul-Gilloteaux2021-vw`." +msgstr "" + +#: ../../03_Image_analysis/Software.md:9 +msgid "" +"Whatever software you choose, be sure to include a detailed description " +"of your analysis in your methods, with pipeline or workflow files if " +"possible, so others can reproduce your work. Also be sure to cite the " +"analysis software you use! This helps developers of the software get " +"grant funding and helps others find useful tools." +msgstr "" + +#: ../../03_Image_analysis/Software.md:17 +#: ../../03_Image_analysis/Software.md:26 +#: ../../03_Image_analysis/Software.md:35 +#: ../../03_Image_analysis/Software.md:44 +#: ../../03_Image_analysis/Software.md:53 +#: ../../03_Image_analysis/Software.md:62 +#: ../../03_Image_analysis/Software.md:71 +#: ../../03_Image_analysis/Software.md:80 +#: ../../03_Image_analysis/Software.md:89 +msgid "card-img-top" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "ImageJ" +msgstr "" + +#: ../../03_Image_analysis/Software.md:21 +msgid "" +"[ImageJ](https://imagej.net/) is an imaging processing program that is " +"capable of operating on a variety of images including multichannel, 3D " +"and time series. It provides basic imaging processing operations and has " +"a variety of plugins for more complex tasks. [Read " +"more...](content/imagej)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "CellProfiler" +msgstr "" + +#: ../../03_Image_analysis/Software.md:30 +msgid "" +"[CellProfiler](https://cellprofiler.org/) was designed with the idea of " +"an image analysis pipeline in mind; it allows you to take a series of " +"interoperable modules to design your own custom analysis pipeline that " +"can be applied to one or thousands of images, making it suitable for high" +" throughput image analysis. [Read more...](content/cellprofiler)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "QuPath" +msgstr "" + +#: ../../03_Image_analysis/Software.md:39 +msgid "" +"[QuPath](https://qupath.github.io/) offers a wide set of image analysis " +"tools that can be applied to whole slide images like pathology images, " +"but it can be used with other images as well. QuPath also contains pixel " +"classification tools and can integrate with ImageJ. [Read " +"more...](content/qupath)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "Icy" +msgstr "" + +#: ../../03_Image_analysis/Software.md:48 +msgid "" +"[Icy](https://icy.bioimageanalysis.org/) is an out of the box image " +"analysis tools, it utilizes plugins to create visual image analysis " +"protocols that can be shared with other users. [Read " +"more...](content/icy)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "MIB" +msgstr "" + +#: ../../03_Image_analysis/Software.md:57 +msgid "" +"[MIB](http://mib.helsinki.fi/index.html) is a user-friendly software for " +"image analysis of multidimensional datasets for both light and electron " +"microscopy. It allows you to use the whole acquired data for its analysis" +" and extraction of morphological features. [Read more...](content/mib)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "napari" +msgstr "" + +#: ../../03_Image_analysis/Software.md:66 +msgid "" +"[napari](https://napari.org/) is being developed as a multi-dimensional " +"image viewer that can be expanded via a variety of plugins to perform " +"basic and complex image analysis tasks. [Read more...](content/napari)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "Cellpose" +msgstr "" + +#: ../../03_Image_analysis/Software.md:75 +msgid "" +"[Cellpose](https://www.cellpose.org/) is a {term}`segmentation` " +"algorithm, it provides a graphical user interface that allows users to " +"use trained models or train their own using their images and annotations." +" [Read more...](content/cellpose)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "ilastik" +msgstr "" + +#: ../../03_Image_analysis/Software.md:84 +msgid "" +"[ilastik](https://www.ilastik.org/) is a tool for interactive image " +"classification, {term}`segmentation` and analysis. It leverages machine-" +"learning algorithms to perform pixel and object-level classification. " +"Using it requires no experience in {term}`image processing`. [Read " +"more...](content/ilastik)" +msgstr "" + +#: ../../03_Image_analysis/Software.md +msgid "Piximi" +msgstr "" + +#: ../../03_Image_analysis/Software.md:93 +msgid "" +"[Piximi](https://www.piximi.app/) is an application for annotation and " +"classification that runs entirely from your browser and requires no " +"installation and minimal setup. [Read more...](content/piximi)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:1 +msgid "Specific Use Software" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:3 +msgid "" +"Tools on this page tend to be extremely good at certain tasks, but are " +"less intended for a wide range of use cases. For tools with broader areas" +" of focus, see the [General Use Software](./GeneralUseSoftware.md) page." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:6 +msgid "" +" Cellpose" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:8 +msgid "" +"[Cellpose](https://www.cellpose.org/) {cite}`Stringer2021-uq` is a " +"{term}`segmentation` algorithm, it provides a graphical user interface " +"that allows users to use trained models or train their own using their " +"images and annotations." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md +msgid "What type of image analysis problem is it best at?" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:13 +msgid "" +"Object {term}`segmentation`, most trained models are for cell " +"{term}`segmentation` but could be applied to segment other similar " +"objects" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:20 +msgid "Its use requires some computational knowledge." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:21 +msgid "" +"Training a new model requires manual annotation correction that can be " +"time consuming, but is likely less time consuming than other methods of " +"training models." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:28 +msgid "" +"๐ŸŒ [Installation " +"instructions](https://cellpose.readthedocs.io/en/latest/installation.html)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:29 +msgid "๐ŸŽฅ [How to use tutorial](https://www.youtube.com/watch?v=5qANHWoubZU)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:33 +msgid "" +"\"logo\" ilastik" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:35 +msgid "" +"[ilastik](https://www.ilastik.org/) {cite}`Berg2019-no` is a tool for " +"interactive image classification, {term}`segmentation` and analysis. It " +"leverages machine-learning algorithms to perform pixel and object-level " +"classification. Using it requires no experience in {term}`image " +"processing`." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:40 +msgid "" +"It can be used for both instance {term}`segmentation` and semantic " +"{term}`segmentation`. It does also perform {term}`segmentation` and " +"tracking, though with somewhat fewer tunable parameters than some other " +"tools offer." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:47 +msgid "" +"Sometimes loading or exporting images can require a bit of " +"troubleshooting to get the dimensions correct." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:48 +msgid "" +"ilastik is limited by your computerโ€™s RAM so training a model with lots " +"of features or working with very large images is likely to slow you down." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:53 +msgid "To download ilastik:" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:57 +msgid "๐ŸŒ [ilastik download ](https://www.ilastik.org/download.html)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:63 +msgid "" +"๐ŸŒ [User guide](https://www.ilastik.org/documentation/index.html#user-" +"documentation)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:67 +msgid "" +"\"logo\" Piximi" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:70 +msgid "" +"[Piximi](https://www.piximi.app/) is an application for annotation and " +"classification that runs entirely from your browser and requires no " +"installation and minimal setup." +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:75 +msgid "Piximi can do image classification using machine learning" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:82 +msgid "" +"It is still in the developing phases and some of its proposed features " +"are not available yet" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:89 +msgid "๐ŸŒ [Piximi website ](https://www.piximi.app/)" +msgstr "" + +#: ../../03_Image_analysis/SpecificUseSoftware.md:90 +msgid "๐ŸŒ [Piximi user guide ](https://documentation.piximi.app/intro.html)" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:1 +msgid "Object tracking" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:3 +msgid "What is tracking?" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:4 +msgid "" +"Tracking, or _object tracking_, refers to the ability to estimate the " +"location of objects in motion from one frame of video to the next. " +"Practically, object tracking in microscopy involves identifying your " +"objects in each frame of your video, then relating objects from frame to " +"frame to be able to identify the same cell as it moves in space." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:10 +msgid "" +"There are several options for tracking objects, like the " +"[TrackMate](https://imagej.net/plugins/trackmate/) {cite}`Tinevez2017-fb`" +" plugin in Fiji, but tracking is somewhat more complex to setup than the " +"previous analyses. In addition to just identifying objects in the " +"movie/time series, tracking also allows you to identify splitting (e.g. " +"mitosis) and merging events. There are many measurements that come out of" +" tracking, including spatial measures like where the objects move to, " +"speed measurements, distance traveled (length of track), and rate of " +"splitting events (e.g., mitotic events) and merging events." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:15 +msgid "" +"**Poor {term}`segmentation`** If objects are dropping out from frame to " +"frame, this makes it more difficult to track them over time. Accurate " +"{term}`segmentation` is the foundation of good tracking results. This can" +" become more difficult if your objects are also changing in shape or " +"intensity (due to things such as bleaching) over the course of the video." +" Itโ€™s important to find a {term}`segmentation` strategy that can work " +"well across your frames." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:16 +msgid "" +"**Inadequate frame rate** If objects are highly dynamic but the images " +"were not taken at a high frequency, tracking can be difficult because " +"objects might have moved too much for the algorithm to relate them from " +"one frame to the next. It is important to match the image acquisition " +"frequency to how dynamic your cells or objects are." +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:22 +msgid "" +"๐Ÿ“„ [Computerized Cell " +"Tracking](https://www.sciencedirect.com/science/article/pii/S2468502X20300711)" +msgstr "" + +#: ../../03_Image_analysis/Tracking.md:23 +msgid "" +"๐ŸŒ [TrackMate Manual](https://imagej.net/media/plugins/trackmate" +"/trackmate-manual.pdf)" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:1 +msgid "Common pitfalls" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:3 +msgid "" +"In addition to the mistakes we summarize for common image analysis tasks," +" here we present a general list of common mistakes for beginners to image" +" analysis. For each, we explain why this is a problem and make " +"suggestions for how to avoid these issues." +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:5 +msgid "Changing your image bit depth" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:7 +msgid "" +"Let's say you've opened your image in {term}`Fiji` and you want to " +"process it in some way (e.g., maximum intensity projection, splitting " +"channels, etc.) before saving it out to measure somewhere else. You go to" +" `Image` > `Type` > `RGB (Color)` since you want a color image to import " +"into your next analysis software and then save the resulting image. " +"What's the problem with this? By making this change, even if the image " +"looks exactly the same to your eyes, you've actually inadvertently " +"changed the intensity values quite a bit! Let's take a look at an " +"example. In Fiji there are several built-in example images. Let's open " +"neuron.tif (you can follow along by going to `File` > `Open Samples...` >" +" `Neuron (5 channels)`." +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:9 +msgid "" +"Here's how the image opens. There are 5 channels, but let's just look at " +"the first one: ![image](https://user-" +"images.githubusercontent.com/28116530/206793825-364998d4-6043-4b1d-8438-0a5b37b97232.png)" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Common_pitfalls.md:9 +msgid "image" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Image_processing.md:1 +msgid "Image Processing" +msgstr "" + +#: ../../03_Image_analysis/_notinyet_Image_segmentation.md:1 +msgid "Image Segmentation" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/04_Data_presentation.po b/locale/fi/LC_MESSAGES/04_Data_presentation.po new file mode 100644 index 000000000..9f505437f --- /dev/null +++ b/locale/fi/LC_MESSAGES/04_Data_presentation.po @@ -0,0 +1,618 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-28 07:29-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../04_Data_presentation/Introduction.md:1 +#: ../../04_Data_presentation/Statistics.md:3 +#: ../../04_Data_presentation/_notinyet_Presentation_graphs.md:3 +msgid "Introduction" +msgstr "" + +#: ../../04_Data_presentation/Introduction.md:3 +msgid "" +"When presenting microscopy image data in biology and biomedicine, it's " +"important to consider the quality of the images, the labeling and " +"annotation of important features, and the overall visual appeal. This " +"also applies to diagrams and plots which convey numerical data derived " +"from microscopy images. Chart types must in addition be suitable for the " +"specific data that is being conveyed to not mislead audiences. This " +"applies to image data in scientific posters, talk-slides, or " +"publications." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:1 +msgid "Presentation of microscopy images" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:3 +#: ../../04_Data_presentation/Statistics.md:9 +#: ../../04_Data_presentation/Statistics.md:34 +#: ../../04_Data_presentation/Statistics.md:57 +msgid "What is it?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:5 +msgid "" +"Microscopy images are often shown in scientific papers to illustrate a " +"particular conclusion. While qualitative conclusions are not a subsitute " +"for quantitative comparisons (see next section), images can certainly " +"guide our reasoning and our conclusions. Following a few consistent best " +"practices ensures that these conclusions are correct and robust." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:14 +msgid "10 tips for image presentation" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:14 +msgid "" +"**A brief visual summary of image presentation tips.** Figure by Helena " +"Jambor. [Source](https://doi.org/10.5281/zenodo.7750259)" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Adjust the image crop, orientation, and size." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:18 +msgid "" +"For any adjustments, work with an image copy and do not alter the " +"original file. Note, do not use adjusted images for quantitative image " +"data analyses Adjustments to effectively communicate the image content " +"may include removing uninformative image regions (crop), changing the " +"image orientation, and adjusting the size. Note that rotation and re-" +"sizing may change the image data when pixel information is redistributed." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:17 +msgid "rotation" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "๐Ÿค” How do I do it?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:25 +#: ../../04_Data_presentation/Presentation_images.md:43 +#: ../../04_Data_presentation/Presentation_images.md:62 +#: ../../04_Data_presentation/Presentation_images.md:82 +#: ../../04_Data_presentation/Presentation_images.md:98 +msgid "See the [cheat-sheet below](image-cheat-sheet) for more information." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +#: ../../04_Data_presentation/Statistics.md +msgid "โš ๏ธ Where can things go wrong?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:28 +msgid "Any adjustments that alter the conclusions are not permitted." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +#: ../../04_Data_presentation/Statistics.md +msgid "๐Ÿ“š๐Ÿคทโ€โ™€๏ธ Where can I learn more?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:31 +msgid "" +"๐Ÿ“„ [Reproducible image handling and " +"analysis](https://doi.org/10.15252/embj.2020105889) {cite}`Miura2021-mb`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:32 +#: ../../04_Data_presentation/Presentation_images.md:49 +#, python-format +msgid "" +"๐Ÿ“„ [Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use " +"and Manipulation of Scientific Digital " +"Images](https://doi.org/10.1007%2Fs11948-010-9201-y) " +"{cite}`Cromey2010-jr`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Enhance visibility of image content" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:37 +msgid "" +"Images often do not have regular spaced intensity values. To still " +"display the data visible on a screen/in a figure, adjustments of " +"brightness and contrast are usually necessary." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:36 +msgid "image adjustment" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:46 +msgid "" +"Any adjustments that result in the disappearance of image details are " +"considered misleading {cite}`Cromey2010-jr`. Note that many nonlinear " +"transformations of brightness and contrast are available in image " +"processing software, before using these users should ensure that they " +"faithfully represent the data to avoid accidentally misleading audiences " +"and disclose them as annotations." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Use accessible colors" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:54 +msgid "" +"Fluorescent microscope images are often composed of data from multiple " +"wavelengths/color channels. To best visualize molecular structures, " +"individual channels can be shown in separate grayscale images. When " +"colors are chosen to represent the illumination wavelength (blue, green, " +"red, far-red), for example Green-Fluorescent Protein is shown in green " +"color, be reminded that intensity values on a black background reduces " +"the level of detail." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:56 +msgid "" +"When channels are over-laid in โ€˜compositeโ€™ images, authors should ensure " +"that structures are visible, i.e., that the overlay does not obstruct " +"features and that the colors used are clearly distinguishable." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:53 +msgid "multicolor image composition" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:65 +msgid "" +"For composite images consider if color combinations are accessible to " +"color-blind audiences (e.g. not combine red with green, but rather " +"magenta and green, see reference below for examples) and possibly " +"additionally show individual channels in grayscale for maximizing " +"accessibility and detail. Tools for color blindness simulation of the " +"images exist in image processing software (ImageJ/Fiji) and visibility of" +" colors in final image figures can be tested with applications such as " +"ColorOracle." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:69 +msgid "" +"๐Ÿ“„ [Creating clear and informative image-based figures for scientific " +"publications](https://doi.org/10.1371/journal.pbio.3001161) " +"{cite}`Jambor2021-qe`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Annotate key image features" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:74 +msgid "" +"Each image needs a reference to its physical dimensions. This is " +"typically achieved by including a scale bar with dimensions annotated in " +"the image or the figure legend." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:76 +msgid "" +"In addition, authors should remember to annotate the colors used, any " +"symbols and arrows used to guide readers, and, if used, the origin of any" +" zoom/inset. If specialized images are shown (time-lapse, volumes, " +"reconstructions) authors are encouraged to consider annotating important " +"information in the figures." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:73 +msgid "speech bubbles" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:85 +msgid "" +"Lack of details and missing of key explanations will make it impossible " +"for audiences to interpret image data in figures. To unambiguously " +"reference probes consider using terms from the ISAC Probe Tag Dictionary," +" a standardized nomenclature for probers used in cytometry and " +"microscopy." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:89 +msgid "" +"๐Ÿ“„ [ISAC Probe Tag Dictionary: Standardized Nomenclature for Detection and" +" Visualization Labels Used in Cytometry and Microscopy Imaging " +"](https://doi.org/10.1002/cyto.a.24224) {cite}`Blenman2021-ki`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md +msgid "Explain the image" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:95 +msgid "" +"To rapidly orient audiences, a minimal explanatory text should be " +"presented along with images. This includes the figure legend and the " +"methods section in scientific papers or the title of figures in posters " +"and slides. Consider using a controlled vocabulary to reduce ambiguity " +"and increase machine-readability of the descriptions of specimens, " +"tissues, cell lines, and proteins etc. A useful tool is the [RRID " +"(Reseach Resource Identifying " +"Data)index](https://scicrunch.org/resources) , which provides indices for" +" commonly used biological reagents and resources, e.g., plasmids, cell " +"lines and antibodies ." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:101 +msgid "" +"Missing explanations of image details/methods may result in non-" +"reproducible data and limits the insights from the data." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:104 +msgid "" +"๐Ÿ“„ [Replication Study: Biomechanical remodeling of the microenvironment by" +" stromal caveolin-1 favors tumor invasion and " +"metastasis](https://doi.org/10.7554/eLife.45120) {cite}`Sheen2019-bg`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:105 +msgid "" +"๐Ÿ“„ [Imaging methods are vastly underreported in biomedical " +"research](https://doi.org/10.7554/eLife.55133) {cite}`Marques2020-nx`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:106 +msgid "" +"๐Ÿ“„ [Are figure legends sufficient? Evaluating the contribution of " +"associated text to biomedical figure " +"comprehension.](https://doi.org/10.1186/1747-5333-4-1) {cite}`Yu2009-ip`" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:110 +msgid "Where can I learn more?" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:112 +msgid "" +"Check out _Creating clear and informative image-based figures for " +"scientific publications_{cite}`Jambor2021-qe` and _Community-developed " +"checklists for publishing images and image " +"analysis_{cite}`Schmied2023-ad` for more tips and best practices for " +"making image figures." +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:114 +msgid "" +"A cheat sheet on how to do basic image preparation with open source " +"software:" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:124 +msgid "Instructions for common image processing operations in Fiji" +msgstr "" + +#: ../../04_Data_presentation/Presentation_images.md:124 +msgid "" +"**How to correctly perform various image manipulations in Fiji.** Figure " +"by Christopher Schmied and Helena Jambor. " +"[Source](https://doi.org/10.12688/f1000research.27140.2)" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:1 +msgid "Resources for learning more" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:8 +msgid "**Resource Name**" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:9 +msgid "**Link**" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:10 +msgid "**Brief description**" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:11 +msgid "" +"๐Ÿ“„ Creating clear and informative image-based figures for scientific " +"publications {cite}`Jambor2021-qe`" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:12 +msgid "" +"[link](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001161" +" )" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:13 +msgid "" +"Review article on how to create accessible, fair scientific figures, " +"including guidelines for microscopy images" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:14 +msgid "" +"๐Ÿ“„ Community-developed checklists for publishing images and image analysis" +" {cite}`Schmied2023-ad`" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:15 +msgid "[link](https://arxiv.org/abs/2302.07005)" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:16 +msgid "" +"A paper recommending checklists and best practices for publishing image " +"data" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:17 +msgid "๐Ÿ“– Modern Statistics for Modern Biology {cite}`Holmes2019-no`" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:18 +msgid "[link](https://www.huber.embl.de/msmb/)" +msgstr "" + +#: ../../04_Data_presentation/Resources.md:19 +msgid "Online statistics for biologists textbook with code examples (in R)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:1 +msgid "Statistics" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:5 +msgid "" +"Quantitative data is often summarized and analysed with statistical " +"methods and visualized with plots/graphs/diagrams. Statistical methods " +"reveal quantitative trends, patterns, and outliers in data, while plots " +"and graphs help to convey them to audiences. Carrying out a suitable " +"statistical analysis and choosing a suitable chart type for your data, " +"identifying their potential pitfalls, and faithfully realising the " +"analysis or generating the chart with suitable software are essential to " +"back up experimental conclusions with data and reach communication goals." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:7 +msgid "Dimensionality reduction" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:10 +msgid "" +"Dimensionality reduction (also called dimension reduction) aims at " +"mapping high-dimensional data onto a lower-dimensional space in order to " +"better reveal trends and patterns. Algorithms performing this task " +"attempt to retain as much information as possible when reducing the " +"dimensionality of the data: this is achieved by assigning importance " +"scores to individual features, removing redundancies, and identifying " +"uninformative (for instance constant) features. Dimensionality reduction " +"is an important step in quantitative analysis as it makes data more " +"manageable and easier to visualize. It is also an important preprocessing" +" step in many downstream analysis algorithms, such as machine learning " +"classifiers." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md +msgid "๐Ÿ“ How do I do it?" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:13 +msgid "" +"The most traditional dimensionality reduction technique is principal " +"component analysis (PCA){cite}`Lever2017-pca`. In a nutshell, PCA " +"recovers a linear transformation of the input data into a new coordinate " +"system (the principal components) that concentrates variation into its " +"first axes. This is achieved by relying on classical linear algebra, by " +"computing an eigendecomposition of the covariance matrix of the data. As " +"a result, the first 2 or 3 principal components provide a low-dimensional" +" version of the data distribution that is faithful to the variance that " +"was originally present. More advanced dimensionality reduction methods " +"that are popular in biology include t-distributed stochastic neighbor " +"embedding (t-SNE) and Uniform Manifold Approximation and Projection " +"(UMAP). In contrast to PCA, these methods are non-linear and can " +"therefore exploit more complex relationships between features when " +"building the lower-dimensional representation. This however comes at a " +"cost: both t-SNE and UMAP are stochastic, meaning that the results they " +"produce are highly dependent on the choice of hyperparameters and can " +"differ across different runs." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:18 +msgid "" +"Although reducing dimensionality can be very useful for data exploration " +"and analysis, it may also wipe information or structure that is relevant " +"to the problem being studied. This is famously well illustrated by the " +"[Datasaurus " +"dataset](https://cran.r-project.org/web/packages/datasauRus/vignettes/Datasaurus.html)," +" which demonstrates how very differently-looking sets of measurements can" +" become indistinguishable when described by a small set of summary " +"statistics. The best way to minimize this risk is to start by visually " +"exploring the data whenever possible, and carefully checking any " +"underlying assumptions of the dimensionality reduction method being used " +"to ensure that they hold for the considered data. Dimensionality " +"reduction may also enhance and reveal patterns that are not biologically " +"relevant, due to noise or systematic artifacts in the original data (see " +"Batch effect correction section below). In addition to applying " +"normalization and batch correction to the data prior to reducing " +"dimensionality, some dimensionality reduction methods also offer so-" +"called regularization strategies to mitigate this. In the end, any " +"pattern identified in dimension-reduced data should be considered while " +"keeping in mind the biological context of the data in order to interpret " +"the results appropriately." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:26 +msgid "" +"๐Ÿ“– [Dimension Reduction: A Guided " +"Tour](https://www.researchgate.net/publication/220416606_Dimension_Reduction_A_Guided_Tour)" +" {cite}`Burges2010-fi`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:27 +msgid "" +"๐Ÿ’ป [UMAP introduction and Python implementation](https://umap-" +"learn.readthedocs.io/en/latest/index.html)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:28 +msgid "" +"๐Ÿ’ป [t-SNE Python implementation](https://scikit-" +"learn.org/stable/modules/generated/sklearn.manifold.TSNE.html)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:32 +msgid "Batch correction" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:35 +msgid "" +"Batch effects are systematic variations across samples correlated with " +"experimental conditions (such as different times of the day, different " +"days of the week, or different experimental tools) that are not related " +"to the biological process of interest. Batch effects must be mitigated " +"prior to making comparisons across several datasets as they impact the " +"reproducibility and reliability of computational analysis and can " +"dramatically bias conclusions. Algorithms for batch effect correction " +"address this by identifying and quantifying sources of technical " +"variation, and adjusting the data so that these are minimized while the " +"biological signal is preserved. Most batch effect correction methods were" +" originally developed for microarray data and sequencing data, but can be" +" adapted to feature vectors extracted from images." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:38 +msgid "" +"Two of the most used methods for batch effect correction are ComBat and " +"Surrogate Variable Analysis (SVA), depending on whether the sources of " +"batch effects are known a priori or not. In a nutshell, ComBat involves " +"three steps: 1) dividing the data into known batches, 2) estimating batch" +" effect by fitting a linear model that includes the batch as a covariate " +"and 3) adjusting the data by removing the estimated effect of the batch " +"from each data point. In contrast, SVA aims at identifying \"surrogate " +"variables\" that capture unknown sources of variability in the data. The " +"surrogate variables can be estimated relying on linear algebra methods " +"(such as singular value decomposition) or through a Bayesian factor " +"analysis model. SVA has been demonstrated to reduce unobserved sources of" +" variability and is therefore of particular help when identifying " +"possible causes of batch effects is challenging, but comes at a higher " +"computational cost than ComBat." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:41 +msgid "" +"As important as it is for analysis, batch effect correction can go wrong " +"when too much or too little of it is done. Both over- and under-" +"correction can happen when methods are not used properly or when their " +"underlying assumptions are not met. As a result, either biological " +"signals can be removed (in the case of over-correction) or irrelevant " +"sources of variation can remain (in the case of under-correction) - both " +"potentially leading to inaccurate conclusions. Batch effect correction " +"can be particularly tricky when the biological variation of interest is " +"suspected to confound with the batch. In this case in particular " +"(although always a good approach), the first lines of fight against batch" +" effects should be thought-through experimental design and careful " +"quality control, as well as visual exploration of the " +"data{cite}`Lord2020-sp`. Plotting data batch-by-batch before applying any" +" correction can help confirm (or infirm) that the observed trends are " +"similar across batches." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:49 +msgid "" +"๐Ÿ“„ [Why Batch Effects Matter in Omics Data, and How to Avoid " +"Them](https://doi.org/10.1016/j.tibtech.2017.02.012) {cite}`Goh2017-kd`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:50 +msgid "" +"๐Ÿ’ป [pyComBat (ComBat Python " +"implementation)](https://epigenelabs.github.io/pyComBat/)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:51 +msgid "" +"๐Ÿ“„ [The sva package for removing batch effects and other unwanted " +"variation in high-throughput " +"experiments](https://doi.org/10.1093/bioinformatics/bts034) " +"{cite}`Leek2012-rv`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:55 +msgid "Normality testing" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:58 +msgid "" +"Normality testing is about assessing whether data follow a Gaussian (or " +"nomal) distribution. Because the Gaussian distribution is frequently " +"found in nature and has important mathematical properties, normality is a" +" core assumption in many widely-used statistical tests. When this " +"assumption is violated, their conclusions may not hold or be flawed. " +"Normality testing is therefore an important step of the data analysis " +"pipeline prior to any sort of statistical testing." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:61 +msgid "" +"Normality of a data distribution can be qualitatively assessed through " +"plotting, for instance relying on a histogram. For a more quantitative " +"readout, statistical methods such as the Kolmogorov-Smirnov (KS) and " +"Shapiro-Wilk tests (among many others) report how much the observed data " +"distribution deviates from a Gaussian. These tests usually return and a " +"p-value linked to the hypothesis that the data are sampled from a " +"Gaussian distribution. A high p-value indicates that the data are not " +"inconsistent with a normal distribution, but is not sufficient to prove " +"that they indeed follow a Gaussian. A p-values smaller than a pre-defined" +" significance threshold (usually 0.05) indicates that the data are not " +"sampled from a normal distribution." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:65 +msgid "" +"Although lots of the โ€œstandardโ€ statistical methods have been designed " +"with a normnality assumption, alternative approaches exist for non-" +"normally-ditributed data. Many biological processes result in multimodal " +"โ€œstatesโ€ (for instance differentiation) that are inherently not Gaussian." +" Normality testing should therefore not be mistaken for a quality " +"assessment of the data: it merely informs on the types of tools that are " +"appropriate to use when analyzing them." +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:68 +msgid "" +"๐Ÿ“– [Modern statistics for modern biology](https://www.huber.embl.de/msmb/)" +" {cite}`Holmes2019-no`" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:69 +msgid "" +"๐Ÿ’ป [To get started with statistical analysis: " +"R](https://www.r-project.org/)" +msgstr "" + +#: ../../04_Data_presentation/Statistics.md:70 +msgid "" +"๐Ÿ’ป [To do statistics in Python: " +"scipy.stats](https://docs.scipy.org/doc/scipy/reference/stats.html)" +msgstr "" + +#: ../../04_Data_presentation/_notinyet_Presentation_graphs.md:1 +msgid "Presentation of graphs" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/Glossary.po b/locale/fi/LC_MESSAGES/Glossary.po new file mode 100644 index 000000000..0f083e3ff --- /dev/null +++ b/locale/fi/LC_MESSAGES/Glossary.po @@ -0,0 +1,317 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-19 07:07-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../Glossary.md:1 +msgid "Glossary" +msgstr "" + +#: ../../Glossary.md +msgid "Blocking" +msgstr "" + +#: ../../Glossary.md:5 +msgid "" +"During the immunostaining procedure, it is important to minimize " +"nonspecific binding of the primary or secondary antibodies. In most " +"cases, this is achieved by blocking, which typically involves adding " +"substances such as normal sera, gelatin, or albumin before immunostaining" +" in order to \"occupy\" all the non-specific binding sites in the sample." +msgstr "" + +#: ../../Glossary.md:3 +msgid "Deconvolution" +msgstr "" + +#: ../../Glossary.md:8 +msgid "" +"The process of computationally removing blur from microscopy images by " +"using the known optical properties of the light path to \"reassign\" " +"pixel intensity away from where it hit the camera and back onto the " +"structure that emitted the light." +msgstr "" + +#: ../../Glossary.md:6 +msgid "Ex-Vivo imaging" +msgstr "" + +#: ../../Glossary.md:11 +#, python-format +msgid "" +"Refers to imaging performed on live animal tissue in an external " +"controllable environment (e.g., tissue explant on a petri dish). It " +"enables high-resolution imaging of live tissue that may be otherwise " +"inaccessible within the animal. The tissue is maintained alive on the " +"imaging system through perfusion of oxygenated (95% oxygen and 5% CO2), " +"temperature-controlled media using peristaltic pumps and microfluidics." +msgstr "" + +#: ../../Glossary.md:9 +msgid "Fiji" +msgstr "" + +#: ../../Glossary.md:14 +msgid "" +"[Fiji](https://imagej.net/software/fiji/) Is Just ImageJ. ImageJ2 plus a " +"lot of common plugins." +msgstr "" + +#: ../../Glossary.md:12 +msgid "Fixation" +msgstr "" + +#: ../../Glossary.md:17 +msgid "" +"Fixation of a specimen refers to the stabilization of the " +"cellular/molecular components within the sample while at the same time " +"stopping any biological function in that sample. The fixative used (e.g.," +" paraformaldehyde, glutaraldehyde, methanol), concentration and " +"conditions (e.g., buffer, temperature) determine the extent of " +"preservation of the cellular and/or molecular structures within a sample," +" and needs to be optimized depending on the sample or structure that is " +"being imaged." +msgstr "" + +#: ../../Glossary.md:15 +msgid "Image processing" +msgstr "" + +#: ../../Glossary.md:20 +msgid "" +"Is an operation that can be performed on an image, resulting in another " +"image. Image processing operations can be simple (e.g. resizing or " +"rotating) or more advanced (e.g. enhancing particular features of an " +"image like circles or lines)." +msgstr "" + +#: ../../Glossary.md:18 +msgid "Immersion media" +msgstr "" + +#: ../../Glossary.md:23 +msgid "" +"The immersion media is the medium that fills the gap between your " +"objective lens and the glass coverslip or sample. It impacts the " +"numerical aperture of the objective lens {math}`NA=RI * sin(ฮธ)`, thus " +"impacting lateral and axial resolution. It is critical to match the RI of" +" the immersion media with that of the mounting media to minimize " +"aberrations and improve image quality. Immersion media can be air, water," +" silicone oil, glycerol or oil." +msgstr "" + +#: ../../Glossary.md:21 +msgid "Immunolabeling" +msgstr "" + +#: ../../Glossary.md:26 +msgid "" +"Immunolabeling is one of the most common labeling techniques for fixed " +"samples. You can use fluorescently conjugated primary antibodies to " +"detect the protein of interest or a two-step labeling with a primary " +"antibody and a fluorescently conjugated secondary antibody. Primary-" +"secondary labeling tends to result in signal amplification. The main " +"issue with immunolabeling is the size of the antibodies, which require " +"extensive permeabilization. Another good option is to use nano-bodies, " +"which only have the heavy-chain and are significantly smaller than " +"regular antibodies." +msgstr "" + +#: ../../Glossary.md:24 +msgid "Intravital imaging" +msgstr "" + +#: ../../Glossary.md:29 +msgid "" +"It refers to the imaging of cellular structures or biological processes " +"inside a live animal in real time, without extracting the organs or " +"fixing the sample. In general, it requires specific instrumentation or " +"modalities with improved light penetration, such as multiphoton " +"microscopy and is limited to the ability to access the specific organ, " +"often through optical windows. Intravital imaging is overseen by " +"bioethical committees and needs to be approved by IACUC and/or other " +"institutional committees." +msgstr "" + +#: ../../Glossary.md:27 +msgid "Mounting media" +msgstr "" + +#: ../../Glossary.md:32 +msgid "" +"Is the solution in which your specimen is placed in (mounted). Its " +"purpose is to preserve the sample, including the fluorophores in it, and" +" enhance the imaging quality during acquisition, by buffering the pH, " +"matching the refractive index throughout the sample (ideally matching it " +"to that of glass) and minimizing photobleaching (depending on the " +"medium). Mounting media prevents the sample from drying out allowing " +"long-term storage." +msgstr "" + +#: ../../Glossary.md:30 +msgid "Object detection" +msgstr "" + +#: ../../Glossary.md:35 +msgid "" +"Is the image processing technique to detect objects within an image. It " +"would not give you a mask of the objects but it could give you a bounding" +" box, or and x,y position." +msgstr "" + +#: ../../Glossary.md:33 +msgid "Oxygen scavengers" +msgstr "" + +#: ../../Glossary.md:38 +msgid "" +"Oxygen tends to induce photobleaching of organic dyes and other " +"fluorophores. Addition of oxygen scavengers to the imaging media such as " +"glucose oxidase or pyranose 2-oxidase can significantly reduce " +"photobleaching of the fluorophores present in the sample. It is important" +" to understand that the use of oxygen scavengers may affect live cell " +"imaging, as these scavengers can affect the ATP and oxygen levels within " +"the sample, compromising its health and therefore biological function." +msgstr "" + +#: ../../Glossary.md:36 +msgid "Permeabilization" +msgstr "" + +#: ../../Glossary.md:41 +msgid "" +"In order for the antibodies used during immunostaining or other " +"fluorophores to penetrate and bind to their antigen within a cell or " +"tissue, the membrane integrity (holes) needs to be challenged with a mild" +" detergent. The permeabilization step needs to be carefully optimized " +"depending on the antigen of interest, as it can result in a loss of " +"cytoplasm or a degradation of the signal." +msgstr "" + +#: ../../Glossary.md:39 +msgid "Refractive index" +msgstr "" + +#: ../../Glossary.md:44 +msgid "" +"It's a measure of how light travels through a specific medium. It is an " +"important value when calculating the numerical aperture of an objective, " +"Ideally, a mismatch in refractive index between the sample (mounting " +"medium), the coverslip and immersion media should be minimized in order " +"to enhance the image quality. [See an interactive demo of refactive index" +" at MicroscopyU](https://www.microscopyu.com/microscopy-basics" +"/refractive-index-index-of-refraction)" +msgstr "" + +#: ../../Glossary.md:42 +msgid "ROIs" +msgstr "" + +#: ../../Glossary.md:47 +msgid "" +"Regions Of Interest. Pixels in your image that you care about (e.g., a " +"region in tissue, a cell, a tumor, etc.)" +msgstr "" + +#: ../../Glossary.md:45 +msgid "Segmentation" +msgstr "" + +#: ../../Glossary.md:50 +msgid "" +"Method of dividing an image into multiple parts or regions. There are " +"three different types of segmentation." +msgstr "" + +#: ../../Glossary.md:51 +msgid "" +"Semantic segmentation, where all parts of an image are part of a class, " +"common in cell biology will be detecting cells and background on an " +"image." +msgstr "" + +#: ../../Glossary.md:52 +msgid "" +"Instance segmentation, the segmentation is object based, not just " +"detecting were the cells are but diving each cell as a separate object." +msgstr "" + +#: ../../Glossary.md:53 +msgid "" +"Panoptic Segmentation, it can be defined as a combination of the prior " +"two, because it identifies the object but also classifies them. An " +"example in biology might be detecting all the cells on an image and " +"classifying them as dividing vs not." +msgstr "" + +#: ../../Glossary.md:51 +msgid "Thresholding" +msgstr "" + +#: ../../Glossary.md:56 +msgid "" +"The easiest form of image segmentation, it divides the image into two " +"part the background and the foreground (or signal). It creates a binary " +"image where usually the background pixels would be change to a 0 value " +"and the foreground pixels values would be 1." +msgstr "" + +#: ../../Glossary.md:54 +msgid "Tissue clearing" +msgstr "" + +#: ../../Glossary.md:59 +msgid "" +"Fluorescence imaging of the whole thickness of a piece of tissue is very " +"challenging due to light absorption and scattering induced by the " +"inhomogeneities in refractive indexes within the tissue itself, resulting" +" in poor light penetration. Additionally, light coming from different " +"parts of the sample contribute to fluorescence blur, drastically reducing" +" contrast and resolution in any given plane. As a result, researchers " +"tend to use tissue sectioning techniques to extract information about " +"cellular components and their spatial distribution or relationships from " +"a thin two-dimensional volume. However, most components in any complex " +"biological system such as an organ are not contained within this two-" +"dimensional volume, and therefore, this approach compromises the " +"understanding of the spatial relationships among cellular components. " +"Tissue clearing focused on reducing the inhomogeneities in the tissue by " +"equilibrating the refractive index throughout the sample. This allows " +"light to pass through the tissue and therefore enables high resolution, " +"volumetric imaging of whole organs and tissues using conventional " +"microscopy techniques such as confocal microscopy without the need to " +"physically section the sample." +msgstr "" + +#: ../../Glossary.md:57 +msgid "Tissue sectioning" +msgstr "" + +#: ../../Glossary.md:62 +msgid "" +"Light penetration and fluorescence imaging is negatively impacted by " +"light scattering within a thick specimen. This scattering is due to the " +"different refractive indexes present within a tissue. To facilitate " +"imaging of tissues, researchers often cut thick tissues into slices of " +"different thicknesses. This process is called tissue sectioning. In most " +"cases the samples are fixed and embedded in paraffin or frozen in tissue " +"freezing medium and later cut into thin slices by a machine like a " +"cryostat, microtome, or vibratome and sections collected into a tube or " +"onto a slide." +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/QuantitativeBioimaging.po b/locale/fi/LC_MESSAGES/QuantitativeBioimaging.po new file mode 100644 index 000000000..1277684a8 --- /dev/null +++ b/locale/fi/LC_MESSAGES/QuantitativeBioimaging.po @@ -0,0 +1,99 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-28 07:29-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../QuantitativeBioimaging.md:1 +msgid "Quantitative Bioimaging" +msgstr "" + +#: ../../QuantitativeBioimaging.md:3 +msgid "What do we mean by quantitative bioimaging?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:5 +msgid "" +"While microscopy was by necessity a qualitative science for most of its " +"history, we now live in an era where microscope images can be used to " +"precisely quantify observable phenotypes." +msgstr "" + +#: ../../QuantitativeBioimaging.md:7 +msgid "" +"The ability to draw accurate quantitative answers from these experiments " +"relies on certain best practices being followed. If one can confidently " +"say \"Yes\" to each of the following 4 questions, one is likely to be " +"able to quantify their sample." +msgstr "" + +#: ../../QuantitativeBioimaging.md:9 +msgid "" +"Have I prepared my sample in a way that minimizes technical artifacts and" +" lets me understand exactly which molecule(s) I am observing?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:10 +msgid "" +"Have I conducted my microscopy so that I minimize technical artifacts and" +" am in the quantitative range of the detector attached to my microscope?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:11 +msgid "" +"Have I selected analysis metric(s) that truly answer my biological " +"question and measured them in a way that minimizes technical artifacts?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:12 +msgid "" +"Have I chosen appropriate statistical comparisons and data presentation " +"approaches so that the distribution of my metric(s) can be fairly " +"compared across samples, answering my biolgical question?" +msgstr "" + +#: ../../QuantitativeBioimaging.md:14 +msgid "" +"Answering each of these questions requires thought, expertise, and often " +"a fair amount of trial and error; it can feel overwhelming to grapple " +"with all the technical aspects and caveats present in a bioimaging " +"experiment. These questions **_can_** be answered, however, though often " +"not in a single pass - [continuous optimization through multiple rounds " +"of answering these questions](qb-decision-cycle) is typically needed for " +"best results." +msgstr "" + +#: ../../QuantitativeBioimaging.md:16 +msgid "" +"The resources linked in this guide are designed to help a reader develop " +"skills in each or all of these areas, helping them get the most from " +"their microscopy data." +msgstr "" + +#: ../../QuantitativeBioimaging.md:25 +msgid "cycle" +msgstr "" + +#: ../../QuantitativeBioimaging.md:25 +msgid "" +"**The decision cycle of quantitative bioimaging {cite}`Senft2023-zy`** " +"Reproduced from Senft and Diaz-Rohrer et al, [**_A biologistโ€™s guide to " +"planning and performing quantitative bioimaging " +"experiments_**](https://doi.org/10.1371/journal.pbio.3002167)." +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/README.po b/locale/fi/LC_MESSAGES/README.po new file mode 100644 index 000000000..5dba28fbf --- /dev/null +++ b/locale/fi/LC_MESSAGES/README.po @@ -0,0 +1,37 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-30 07:32-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../README.md:1 +msgid "Microscopy For Beginners Reference Guide" +msgstr "" + +#: ../../README.md:2 +msgid "Website :link: :arrow_right: [CLICK HERE](https://bioimagingguide.org)" +msgstr "" + +#: ../../README.md:4 +msgid "" +"A Beginner's guide to microscopy, from sample prep to acquisition, image " +"analysis, and data interpretation. See the paper " +"[here](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167)" +" (original preprint [here](https://doi.org/10.5281/zenodo.7439283))" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/bibliography.po b/locale/fi/LC_MESSAGES/bibliography.po new file mode 100644 index 000000000..a00d4b078 --- /dev/null +++ b/locale/fi/LC_MESSAGES/bibliography.po @@ -0,0 +1,25 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../bibliography.md:1 +msgid "Bibliography" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/community_resources.po b/locale/fi/LC_MESSAGES/community_resources.po new file mode 100644 index 000000000..5683e006d --- /dev/null +++ b/locale/fi/LC_MESSAGES/community_resources.po @@ -0,0 +1,173 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../community_resources.md:1 +msgid "Community resources" +msgstr "" + +#: ../../community_resources.md:3 +msgid "Below are globally and locally available community resources" +msgstr "" + +#: ../../community_resources.md:5 +msgid "Global and online resources" +msgstr "" + +#: ../../community_resources.md:12 ../../community_resources.md:35 +msgid "**Resource Name**" +msgstr "" + +#: ../../community_resources.md:13 ../../community_resources.md:36 +msgid "**Link**" +msgstr "" + +#: ../../community_resources.md:14 +msgid "**Brief description**" +msgstr "" + +#: ../../community_resources.md:15 +msgid "Global BioImaging" +msgstr "" + +#: ../../community_resources.md:16 +msgid "[link](https://globalbioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:17 +msgid "" +"Training resources, working groups, recommendations for standardization " +"and research reproducibility for global bioimaging efforts" +msgstr "" + +#: ../../community_resources.md:18 +msgid "Microforum" +msgstr "" + +#: ../../community_resources.md:19 +msgid "[link](https://forum.microlist.org/)" +msgstr "" + +#: ../../community_resources.md:20 +msgid "Discussion forum for bioimaging sample preparation and acquisition" +msgstr "" + +#: ../../community_resources.md:21 +msgid "Scientific Community Image Forum (Image . sc)" +msgstr "" + +#: ../../community_resources.md:22 +msgid "[link](https://forum.image.sc/)" +msgstr "" + +#: ../../community_resources.md:23 +msgid "Discussion forum for bioimage analysis software {cite}`Rueden2019-qp`" +msgstr "" + +#: ../../community_resources.md:24 +msgid "HMS Nikon Imaging Center \"Favorite References\"" +msgstr "" + +#: ../../community_resources.md:25 +msgid "[link](https://nic.med.harvard.edu/fav_references/)" +msgstr "" + +#: ../../community_resources.md:26 +msgid "" +"A curated list of references related to many aspects of microscopy and " +"image analysis" +msgstr "" + +#: ../../community_resources.md:29 +msgid "Local resources" +msgstr "" + +#: ../../community_resources.md:37 +msgid "BioImaging North America (BINA)" +msgstr "" + +#: ../../community_resources.md:38 +msgid "[link](https://www.bioimagingnorthamerica.org/)" +msgstr "" + +#: ../../community_resources.md:39 +msgid "Latin America BioImaging" +msgstr "" + +#: ../../community_resources.md:40 +msgid "[link](https://www.latambioimaging.org/ )" +msgstr "" + +#: ../../community_resources.md:41 +msgid "African BioImaging Consortium" +msgstr "" + +#: ../../community_resources.md:42 +msgid "[link](https://www.africanbioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:43 +msgid "South Africa BioImaging" +msgstr "" + +#: ../../community_resources.md:44 +msgid "[link](https://www.sabioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:45 +msgid "Euro-bioimaging" +msgstr "" + +#: ../../community_resources.md:46 +msgid "[link](https://www.eurobioimaging.eu/)" +msgstr "" + +#: ../../community_resources.md:47 +msgid "Advanced BioImaging support (Japan)" +msgstr "" + +#: ../../community_resources.md:48 +msgid "[link](https://www.nibb.ac.jp/abis/)" +msgstr "" + +#: ../../community_resources.md:49 +msgid "Microscopy Australia" +msgstr "" + +#: ../../community_resources.md:50 +msgid "[link](https://micro.org.au/)" +msgstr "" + +#: ../../community_resources.md:51 +msgid "Canada BioImaging" +msgstr "" + +#: ../../community_resources.md:52 +msgid "[link](https://www.canadabioimaging.org/)" +msgstr "" + +#: ../../community_resources.md:53 +msgid "Singapore Microscopy Infrastructure Network" +msgstr "" + +#: ../../community_resources.md:54 +msgid "[link](https://www.singascope.sg/)" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/contributors.po b/locale/fi/LC_MESSAGES/contributors.po new file mode 100644 index 000000000..e22778c86 --- /dev/null +++ b/locale/fi/LC_MESSAGES/contributors.po @@ -0,0 +1,90 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-30 07:32-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../contributors.md:1 +msgid "Contributing to this guide" +msgstr "" + +#: ../../contributors.md:3 +msgid "Contributors" +msgstr "" + +#: ../../contributors.md:5 +msgid "" +"The original material for this book was created as part of the paper " +"\"[**_A biologistโ€™s guide to planning and performing quantitative " +"bioimaging " +"experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " +"{cite}`Senft2023-zy`. by Rebecca A. Senft*, Barbara Diaz-Rohrer*, Pina " +"Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig " +"Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew" +" Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W Eliceiri and Beth" +" A. Cimini." +msgstr "" + +#: ../../contributors.md:7 +msgid "" +"Since this guide has become available, we gratefully acknowledge " +"contributions from the following members of the microscopy and bioimage " +"analysis community!" +msgstr "" + +#: ../../contributors.md:8 +msgid "William Giang" +msgstr "" + +#: ../../contributors.md:9 +msgid "Robert Haase" +msgstr "" + +#: ../../contributors.md:11 +msgid "How can I become a contributor?" +msgstr "" + +#: ../../contributors.md:13 +msgid "" +"Please feel free to open an " +"[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" +" or pull request to contribute! We hope for this to be a living document " +"reflecting the best practices and resources available." +msgstr "" + +#: ../../contributors.md:15 +msgid "" +"We currently also offer a [Google " +"Form](https://docs.google.com/forms/d/e/1FAIpQLScWQbemviI2OkvVkeTKUOozAzKNndcZpXIB_nE0qFMl72lqvQ/viewform)" +" for contributions, though note these may be responded to more slowly " +"than direct contributions to the GitHub repository." +msgstr "" + +#: ../../contributors.md:18 +msgid "Translation" +msgstr "" + +#: ../../contributors.md:20 +msgid "" +"Work is underway to translate this guide into other languages - " +"translation is planned or has begun in French, Spanish, Portuguese, " +"Czech, and Polish. To help translate into one of these languages, or " +"another language not listed here, please contact bcimini AT " +"broadinstitute DOT org." +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/genindex.po b/locale/fi/LC_MESSAGES/genindex.po new file mode 100644 index 000000000..308aa69f5 --- /dev/null +++ b/locale/fi/LC_MESSAGES/genindex.po @@ -0,0 +1,25 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-05-02 14:28-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../genindex.md:1 +msgid "Index" +msgstr "" + diff --git a/locale/fi/LC_MESSAGES/welcome.po b/locale/fi/LC_MESSAGES/welcome.po new file mode 100644 index 000000000..1de0a6a7b --- /dev/null +++ b/locale/fi/LC_MESSAGES/welcome.po @@ -0,0 +1,167 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2023 +# This file is distributed under the same license as the Python package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Python \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-06-28 07:29-0400\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language: fi\n" +"Language-Team: fi \n" +"Plural-Forms: nplurals=2; plural=(n != 1);\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" + +#: ../../welcome.md:1 +msgid "Sample Preparation" +msgstr "" + +#: ../../welcome.md:1 +msgid "Sample Acquisition" +msgstr "" + +#: ../../welcome.md:1 +msgid "Image Analysis and Data Handling" +msgstr "" + +#: ../../welcome.md:1 +msgid "Data Interpretation" +msgstr "" + +#: ../../welcome.md:1 +msgid "Additional Resources" +msgstr "" + +#: ../../welcome.md:1 +msgid "Welcome" +msgstr "" + +#: ../../welcome.md:3 +msgid "Welcome to the world of bioimaging and bioimage analysis! ๐ŸŽ‰" +msgstr "" + +#: ../../welcome.md:11 +msgid "BBBC image montage" +msgstr "" + +#: ../../welcome.md:11 +msgid "" +"**Montage of fluorescence microscopy images from " +"[BBBC](https://bbbc.broadinstitute.org/) {cite}`Ljosa2012-fr` (Broad " +"Institute).** Images shown are from experiments BBBC007, BBBC008, " +"BBBC034, BBBC038, BBBC039, and BBBC020 from left to right, top to bottom." +msgstr "" + +#: ../../welcome.md:13 +msgid "What is this book?" +msgstr "" + +#: ../../welcome.md:15 +msgid "" +"This book is a companion website to our paper \"[**_A biologistโ€™s guide " +"to planning and performing quantitative bioimaging " +"experiments_**](https://doi.org/10.1371/journal.pbio.3002167)\" " +"{cite}`Senft2023-zy`. Our goal is to provide recommendations and a " +"curated set of resources for biologists looking to understand the factors" +" that impact their fluorescence microscopy experiments." +msgstr "" + +#: ../../welcome.md:17 +msgid "" +"This book is a collaborative effort from experts in biology, imaging, " +"image analysis, and data management, interpretation, and presentation. " +"Our tips and recommendations come from real experiences training and " +"working with biologists who are beginners to bioimaging and bioimage " +"analysis. When starting out in a new field, you often don't know what you" +" don't know. Here we provide context, tips for avoiding common beginner " +"errors, and a focused list of high-quality, open source resources (full " +"list available [here](bibliography)). We use icons to indicate the type " +"of resource:" +msgstr "" + +#: ../../welcome.md:39 +msgid "What **isn't** this book?" +msgstr "" + +#: ../../welcome.md:41 +msgid "" +"This book is **not** meant to be an exhaustive list of all resources. " +"Many others have curated excellent such resources(see " +"[here](https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14451) " +"{cite}`Haase2022-ad` and [here](https://www.bioimagingnorthamerica.org" +"/training-education-resources/) and [here](https://biii.eu/) {cite}`Paul-" +"Gilloteaux2021-vw`). Our goal is to create a more streamlined, beginner-" +"accessible guide." +msgstr "" + +#: ../../welcome.md:42 +msgid "" +"This book is **not** a protocol or step by step guide, though certain " +"resources we link to might be. Each subsection from sample prep to data " +"interpretation are massive topics that we can't exhaustively cover in a " +"guide for beginners." +msgstr "" + +#: ../../welcome.md:45 +msgid "How to use this book:" +msgstr "" + +#: ../../welcome.md:46 +msgid "" +"Please select a section using the navigation panel on the left to get " +"started or begin with sample preparation by clicking the \"Next\" button " +"below โ†˜๏ธ." +msgstr "" + +#: ../../welcome.md:48 +msgid "" +"Most sections will guide you through individual subtopics using some or " +"all of the following list of questions:" +msgstr "" + +#: ../../welcome.md:49 +msgid "What is it?" +msgstr "" + +#: ../../welcome.md:50 +msgid "What are my options?" +msgstr "" + +#: ../../welcome.md:51 +msgid "How do I do it?" +msgstr "" + +#: ../../welcome.md:52 +msgid "Where can things go wrong?" +msgstr "" + +#: ../../welcome.md:53 +msgid "Where can I learn more? (links to resources)" +msgstr "" + +#: ../../welcome.md:55 +msgid "" +"Which questions are used and the exact phrasing may vary by section, but " +"we hope this structure helps guide users to a deeper understanding of " +"each subtopic." +msgstr "" + +#: ../../welcome.md:57 +msgid "What if my resource/topic is not included?" +msgstr "" + +#: ../../welcome.md:58 +msgid "" +"Please feel free to open an " +"[issue](https://github.com/broadinstitute/MicroscopyForBeginnersReferenceGuide/issues)" +" or pull request to contribute! We hope for this to be a living document " +"reflecting the best practices and resources available." +msgstr "" +