diff --git a/README.md b/README.md index 4b78e2c..1591c42 100644 --- a/README.md +++ b/README.md @@ -14,57 +14,69 @@ Beth's bio page with contact email ### CellProfiler -downloads +[downloads](https://cellprofiler.org/releases) -manual +[manual](https://broad.io/CellProfilerManual) -tutorials +[plugins documentation]() -GitHub +[tutorials](https://tutorials.cellprofiler.org/) + +[GitHub]() [help forum]() -papers - [2021 (CellProfiler 4)]() [2018 (CellProfiler 3)]() +[pipeline suggester](https://www.boaq.org) + +papers - [CellProfiler-plugins [2023]](https://doi.org/10.1111/jmi.13223) [CellProfiler 4 [2021](https://doi.org/10.1186/s12859-021-04344-9) [CellProfiler 3 [2018]](https://doi.org/10.1371/journal.pbio.2005970) ### CellProfiler Analyst -downloads +[downloads]() -manual +[manual]() -GitHub +[GitHub]() [help forum]() -papers - 2021 (CellProfiler Analyst 3) +papers - [2021 (CellProfiler Analyst 3)](https://doi.org/10.1093/bioinformatics/btab634) ### Piximi -downloads +[Piximi.app](https://piximi.app/) + +[manual](https://documentation.piximi.app/) + +[GitHub](https://github.com/piximi/piximi) + +[help forum]() -manual +[preprint](https://doi.org/10.1101/2024.06.03.597232v1) -GitHub +### Distributed-Something -help forum +[GitHub](https://distributedscience.github.io/Distributed-Something/introduction.html) -preprint +[paper](https://doi.org/10.1038/s41592-023-01918-8) ### Bilayers -demo app +[demo app]() -GitHub +[GitHub]() ## Educational materials -### Papers we wrote +### Educational papers we wrote -Twenty Questions +[The Twenty Questions of Bioimage Object Analysis[2023]](https://doi.org/10.1038/s41592-023-01919-7) -Beginner's Guide +[A biologist’s guide to planning and performing quantitative bioimaging experiments[2023]](https://doi.org/10.1371/journal.pbio.3002167) -Common solutions +[Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions[2024]](https://doi.org/10.1111/jmi.13288) + +[A postdoctoral training program in bioimage analysis[2024]](https://doi.org/10.1091/mbc.E24-05-0214) ### Stuff we make @@ -72,24 +84,58 @@ Lab website Lab paper pages -[Beth's CV's preprints section](https://docs.google.com/document/d/1zZfoo2b-IbEDbpJ5pH6V0KlfdiY7A-clsAdRr-ouYX8/preview#heading=h.ea9i2felg8yq) +[Current lab preprints (from Beth's CV)](https://docs.google.com/document/d/1zZfoo2b-IbEDbpJ5pH6V0KlfdiY7A-clsAdRr-ouYX8/preview#heading=h.ea9i2felg8yq) + +[Imaging Platform Blog](https://blog.cellprofiler.org) -YouTube tutorials +YouTube tutorials]() [Office hours link](broad.io/imagingofficehours) -Forum.image.sc +The Scientific Community Image Forum - Forum.image.sc]() [paper](https://doi.org/10.1371/journal.pbio.3000340) + +[COBA website]() -COBA website +Bioimaging Guide - [English](https://www.bioimagingguide.org/welcome.html) [Spanish](https://es.bioimagingguide.org/) [Portuguese](https://pt.bioimagingguide.org/) [Czech](https://cs.bioimagingguide.org/) -Bioimaging Guide - English Spanish Portuguese Czech +The Image Based Profiling Handbook]() -The Cell Painting Gallery - [Website] [Paper] +The Cell Painting Gallery (image repository) - [Website]() [Paper](https://doi.org/10.1038/s41592-024-02399-z) ### Stuff we contributed to (but others led) -Online guide for checklists for imaging and image analysis +[Online guide for checklists for imaging and image analysis]() [Paper - Community-developed checklists for publishing images and image analysis [2023]](https://doi.org/10.1038/s41592-023-01987-9) + +Metrics Reloaded online metric chooser]() [Paper 1](https://doi.org/10.1038/s41592-023-02151-z) [Paper 2](https://doi.org/10.1038/s41592-023-02150-0) + +Microtutor imaging education platform]() + +## Papers you might find useful + +### Protocols + +[ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis[2020]](https://doi.org/10.1002/cpz1.89) + +[Interpreting image-based profiles using Morpheus and single-cell visualization[2023]](https://doi.org/10.1002/cpz1.713) + +[Optimizing the Cell Painting assay for image-based profiling[2023]](https://doi.org/10.1038/s41596-023-00840-9) + +### Reviews + +[Open-source deep-learning software for bioimage segmentation[2021]](https://doi.org/10.1091/mbc.E20-10-0660) + +[Defining the boundaries: challenges and advances in identifying cells in microscopy images[2024]](https://doi.org/10.1016/j.copbio.2023.103055) + +### Community Surveys + +[2020 BioImage Analysis Survey: Community experiences and needs for the future[2021]](https://doi.org/10.1017/S2633903X21000039) + +[Bridging Imaging Users to Imaging Analysis - A community survey[2023]](https://doi.org/10.1111/jmi.13229) + +### Opinions/Perspectives + +[Moving beyond the desktop: Prospects for Practical Bioimage Analysis via the Web[2023]](https://doi.org/10.3389/fbinf.2023.1233748) -Metrics Reloaded metric chooser +[A Call for FAIR and Open-Access Training Materials to advance Bioimage Analysis[2024]](https://doi.org/10.31219/osf.io/2zgmc) -Microtutor imaging education +[The Crucial Role of BioImage Analysts in Scientific Research and Publication](https://doi.org/10.5281/zenodo.11457452)