From b359819ce5fd5afcbe398f444079c0b08b4a8910 Mon Sep 17 00:00:00 2001 From: Yixin Huang Date: Mon, 14 Oct 2024 11:04:47 +0200 Subject: [PATCH] Add new entry --- resources/nfdi4bioimage.yml | 369 +++++++++++++++++++----------------- 1 file changed, 197 insertions(+), 172 deletions(-) diff --git a/resources/nfdi4bioimage.yml b/resources/nfdi4bioimage.yml index 3459ee0..90e7d14 100644 --- a/resources/nfdi4bioimage.yml +++ b/resources/nfdi4bioimage.yml @@ -646,8 +646,7 @@ resources: - Kevin W. Eliceiri - Beth A. Cimini license: BSD-3-CLAUSE - name: "A biologist\u2019s guide to planning and performing quantitative bioimaging\ - \ experiments" + name: A biologist’s guide to planning and performing quantitative bioimaging experiments type: - Collection - Publication @@ -820,7 +819,7 @@ resources: - Documentation url: https://kevinyamauchi.github.io/open-image-data/how_tos/conda_forge_packaging.html - authors: - - "Caterina Fuster-Barcel\xF3" + - Caterina Fuster-Barceló license: UNKNOWN name: AI4Life teams up with Galaxy Training Network (GTN) to enhance training resources tags: @@ -1094,10 +1093,10 @@ resources: url: https://cshlpress.com/default.tpl?cart=1700309488232283050&fromlink=T&linkaction=full&linksortby=oop_title&--eqSKUdatarq=1282 - authors: - Marion Louveaux - - "St\xE9phane Verger" + - Stéphane Verger - Arianne Bercowsky Rama - Ignacio Arganda-Carreras - - "Estibaliz G\xF3mez-de-Mariscal" + - Estibaliz Gómez-de-Mariscal - Kota Miura - et al. license: UNKNOWN @@ -1119,7 +1118,7 @@ resources: - Pejamn Rasti - David Rousseau - Ignacio Arganda-Carreras - - "Si\xE2n Culley" + - Siân Culley - et al. license: UNKNOWN name: NEUBIAS Bioimage Analyst School 2019 @@ -1233,7 +1232,7 @@ resources: - Notebook url: https://github.com/karinsasaki/metabolic-networks-modelling - authors: - - "Carolina W\xE4hlby" + - Carolina Wählby - Maxime Bombrun - Christian Tischer license: UNKNOWN @@ -1382,10 +1381,10 @@ resources: - Daniel Krentzel - Elias Nehme - Martina Lerche - - "Sara Hern\xE1ndez-p\xE9rez" + - Sara Hernández-pérez - Pieta Mattila - Eleni Karinou - - "S\xE9amus Holden" + - Séamus Holden - Ahmet Can Solak - Alexander Krull - Tim-Oliver Buchholz @@ -1408,7 +1407,7 @@ resources: - https://www.nature.com/articles/s41467-021-22518-0 - https://doi.org/10.1038/s41467-021-22518-0 - authors: - - "Iv\xE1n Hidalgo" + - Iván Hidalgo - et al. license: CC-BY-4.0 name: DL4MicEverywhere @@ -1468,8 +1467,8 @@ resources: - authors: - Martin Weigert license: UNKNOWN - name: "CARE/Stardist tutorials for EMBO Practical Course \u2014 Computational optical\ - \ biology 2022" + name: CARE/Stardist tutorials for EMBO Practical Course — Computational optical + biology 2022 tags: - Python - Artificial Intelligence @@ -1480,7 +1479,7 @@ resources: - authors: - Martin Weigert - Olivier Burri - - "Si\xE2n Culley" + - Siân Culley - Uwe Schmidt license: UNKNOWN name: 'Neubias Academy 2020: Introduction to Nuclei Segmentation with StarDist' @@ -1571,7 +1570,7 @@ resources: - https://doi.org/10.6019/TOL.BioImageAnalysis22-w.2022.00001.1 - https://drive.google.com/file/d/1MhuqfKhZcYu3bchWMqogIybKjamU5Msg/view - authors: - - "Estibaliz G\xF3mez-de-Mariscal\\" + - Estibaliz Gómez-de-Mariscal\ license: UNKNOWN name: Building a Bioimage Analysis Workflow using Deep Learning tags: @@ -1581,7 +1580,7 @@ resources: - Slide url: https://github.com/esgomezm/NEUBIAS_chapter_DL_2020 - authors: - - "Estibaliz G\xF3mez-de-Mariscal" + - Estibaliz Gómez-de-Mariscal license: UNKNOWN name: ZIDAS 2020 Introduction to Deep Learning tags: @@ -1591,7 +1590,7 @@ resources: - Slide url: https://github.com/esgomezm/zidas2020_intro_DL - authors: - - "Estibaliz G\xF3mez-de-Mariscal" + - Estibaliz Gómez-de-Mariscal license: UNKNOWN name: Machine Learning - Deep Learning. Applications to Bioimage Analysis tags: @@ -1747,7 +1746,7 @@ resources: - https://doi.org/10.7490/f1000research.1119154.1 - authors: - Beatriz Serrano-Solano - - "Bj\xF6rn Gr\xFCning" + - Björn Grüning license: UNKNOWN name: Image analysis in Galaxy tags: @@ -1756,7 +1755,7 @@ resources: - Slide url: https://docs.google.com/presentation/d/1WG_4307XmKsGfWT3taxMvX2rZiG1k0SM1E7SAENJQkI/edit#slide=id.p - authors: - - "Se\u0301bastien Tosi" + - Sébastien Tosi - Volker Baecker - Benjamin Pavie license: BSD-2-CLAUSE @@ -1808,7 +1807,7 @@ resources: - Anna Poetsch - Biotec Dresden - Marcelo Leomil Zoccoler - - "Johannes Richard M\xFCller" + - Johannes Richard Müller - Robert Haase license: CC-BY-4.0 name: Bio-image analysis, biostatistics, programming and machine learning for computational @@ -1981,8 +1980,8 @@ resources: - https://doi.org/10.5281/zenodo.10654775 - authors: - Josh Moore - description: "Keynote at the NFDI4BIOIMAGE All-Hands Meeting in D\xFCsseldorf, Germany,\ - \ October 16, 2023." + description: Keynote at the NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, + October 16, 2023. license: CC-BY-4.0 name: '[N4BI AHM] Welcome to BioImage Town' num_downloads: 96 @@ -2164,7 +2163,7 @@ resources: - https://zenodo.org/records/11066250 - https://doi.org/10.5281/zenodo.11066250 - authors: - - "Estibaliz G\xF3mez de Mariscal" + - Estibaliz Gómez de Mariscal description: Introduction to FAIR deep learning. Furthermore, tools to deploy trained DL models (deepImageJ), easily train and evaluate them (ZeroCostDL4Mic and DeepBacs) ensure reproducibility (DL4MicEverywhere), and share this technology in an open-source @@ -2374,7 +2373,7 @@ resources: - Poster url: https://doi.org/10.5281/zenodo.8434325 - authors: - - "Torsten St\xF6ter" + - Torsten Stöter - Tobias Gottschall - Andrea Schrader - Peter Zentis @@ -2383,7 +2382,7 @@ resources: - Werner Zuschratter - Astrid Schauss - Timo Dickscheid - - "Timo M\xFChlhaus" + - Timo Mühlhaus - Dirk von Suchodoletz description: Interdisciplinary collaboration and integrating large, diverse datasets are crucial for answering complex research questions, requiring multimodal data @@ -2403,13 +2402,13 @@ resources: url: https://zenodo.org/doi/10.5281/zenodo.8349562 - authors: - Josh Moore - description: "For decades, the sharing of large N-dimensional datasets has posed\ - \ issues across multiple domains. Interactively accessing terabyte-scale data\ - \ has previously required significant server resources to properly prepare cropped\ - \ or down-sampled representations on the fly. Now, a cloud-native chunked format\ - \ easing this burden has been adopted in the bioimaging domain for standardization.\ - \ The format \u2014 Zarr \u2014 is potentially of interest for other consortia\ - \ and sections of NFDI." + description: For decades, the sharing of large N-dimensional datasets has posed + issues across multiple domains. Interactively accessing terabyte-scale data has + previously required significant server resources to properly prepare cropped or + down-sampled representations on the fly. Now, a cloud-native chunked format easing + this burden has been adopted in the bioimaging domain for standardization. The + format — Zarr — is potentially of interest for other consortia and sections of + NFDI. license: CC-BY-4.0 name: '[CORDI 2023] Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays' @@ -2443,11 +2442,11 @@ resources: - Chiara Stringari - Marcelo Zoccoler - Cornelia Wetzker - description: "The presentations introduce open-source software to read in, visualize\ - \ and analyse fluorescence lifetime imaging microscopy (FLIM) raw data developed\ - \ for life scientists. The slides were presented at German Bioimaging (GerBI)\ - \ FLIM Workshop held February 26 to 29 2024 at the Biomedical Center of LMU M\xFC\ - nchen by Anca Margineanu, Chiara Stringari and Conni Wetzker. " + description: 'The presentations introduce open-source software to read in, visualize + and analyse fluorescence lifetime imaging microscopy (FLIM) raw data developed + for life scientists. The slides were presented at German Bioimaging (GerBI) FLIM + Workshop held February 26 to 29 2024 at the Biomedical Center of LMU München by + Anca Margineanu, Chiara Stringari and Conni Wetzker. ' license: CC-BY-4.0 name: A Glimpse of the Open-Source FLIM Analysis Software Tools FLIMfit, FLUTE and napari-flim-phasor-plotter @@ -2565,7 +2564,7 @@ resources: - authors: - Elfi Hesse - Jan-Christoph Deinert - - "Christian L\xF6schen" + - Christian Löschen description: Die Online-Veranstaltung fand am 21.01.2021 im Rahmen der SaxFDM-Veranstaltungsreihe "Digital Kitchen - Küchengespräche mit SaxFDM" statt. SaxFDM-Sprecherin Elfi Hesse (HTW Dresden) erläuterte zunächst Grundsätzliches zum @@ -2584,7 +2583,7 @@ resources: - https://zenodo.org/records/4461261 - https://doi.org/10.5281/zenodo.4461261 - authors: - - "Stephan W\xFCnsche" + - Stephan Wünsche description: 'Wem gehören Forschungsdaten? Diese Frage stellt sich bei Daten, an deren Entstehung mehrere Personen beteiligt waren, und besonders bei Textdaten, Bildern und Videos. Hier lernen Sie, für Ihr eigenes Forschungsvorhaben zu @@ -2596,7 +2595,7 @@ resources:  ' license: CC-BY-4.0 - name: "Alles meins \u2013 oder!? Urheberrechte kl\xE4ren f\xFCr Forschungsdaten" + name: Alles meins – oder!? Urheberrechte klären für Forschungsdaten num_downloads: 35 publication_date: '2024-06-04' tags: @@ -2616,8 +2615,8 @@ resources: teilen und aufbewahren zu können? Mit Hilfe dieses Foliensatzes erhalten Sie Einblicke in datenschutzrechtliche Aspekte beim Umgang mit Ihren Forschungsdaten. ' license: CC-BY-4.0 - name: "So geschlossen wie n\xF6tig, so offen wie m\xF6glich - Datenschutz beim Umgang\ - \ mit Forschungsdaten" + name: So geschlossen wie nötig, so offen wie möglich - Datenschutz beim Umgang mit + Forschungsdaten num_downloads: 30 publication_date: '2024-05-30' tags: @@ -2630,7 +2629,7 @@ resources: - https://zenodo.org/records/11396199 - https://doi.org/10.5281/zenodo.11396199 - authors: - - "Stephan W\xFCnsche" + - Stephan Wünsche - Pia Voigt description: 'Diese Präsentation wurde im Zuge der digitalen Veranstaltungsreihe "Einblicke ins Forschungsdatenmanagement" erstellt. Diese findet seit @@ -2644,8 +2643,8 @@ resources: Erläuterungen zum Datenschutz, Urheberrecht und den Grundsätzen der guten wissenschaftlichen Praxis mit Fokus auf deren Bedeutung im Forschungsdatenmanagement.' license: CC-BY-4.0 - name: "Einblicke ins Forschungsdatenmanagement - Darf ich das ver\xF6ffentlichen?\ - \ Rechtsfragen im Umgang mit Forschungsdaten" + name: Einblicke ins Forschungsdatenmanagement - Darf ich das veröffentlichen? Rechtsfragen + im Umgang mit Forschungsdaten num_downloads: 243 publication_date: '2021-05-11' tags: @@ -2680,7 +2679,7 @@ resources: steckt, welche Elemente ein Datenmanagementplan enthalten sollte und wie sie einen solchen mithilfe interaktiver Tools selbst erstellen können.' license: CC-BY-4.0 - name: "Datenmanagementpl\xE4ne erstellen - Teil 1" + name: Datenmanagementpläne erstellen - Teil 1 num_downloads: 340 publication_date: '2021-03-23' tags: @@ -2722,7 +2721,7 @@ resources: Version 3 ist die überarbeitete und aktualisierte Version der ersten beiden und enthält u.a. Hinweise zur Lizenzierung und zu Nutzungsrechten an Forschungsdaten.' license: CC-BY-4.0 - name: "Datenmanagementpl\xE4ne erstellen - Teil 2" + name: Datenmanagementpläne erstellen - Teil 2 num_downloads: 271 publication_date: '2021-03-30' tags: @@ -2734,8 +2733,8 @@ resources: - https://doi.org/10.5281/zenodo.4748534 - authors: - Barbara Weiner - - "Stephan W\xFCnsche" - - "Stefan K\xFChne" + - Stephan Wünsche + - Stefan Kühne - Pia Voigt - Sebastian Frericks - Clemens Hoffmann @@ -2876,8 +2875,8 @@ resources: description: Blog post about why we should license our work and what is important when choosing a license. license: CC-BY-4.0 - name: "If you license it, it\u2019ll be harder to steal it. Why we should license\ - \ our work" + name: If you license it, it’ll be harder to steal it. Why we should license our + work tags: - Licensing - Research Data Management @@ -2911,7 +2910,7 @@ resources: - Thomas Zobel - Sarah Weischner - Jens Wendt - description: "A use case example from the M\xFCnster Imaging Network" + description: A use case example from the Münster Imaging Network license: ALL RIGHTS RESERVED name: OMERO for microscopy research data management tags: @@ -2999,7 +2998,7 @@ resources: - Elnaz Fazeli - David Legland - Michael Doube - - "Si\xE2n Culley" + - Siân Culley - Ilya Belevich - Eija Jokitalo - Martin Schorb @@ -3034,7 +3033,7 @@ resources: - Benedict Diederich - Barbora Marsikova - Emmanuel G. Reynaud - - "S\xE9amus Holden" + - Séamus Holden - Wiebke Jahr - Robert Haase - Kirti Prakash @@ -3081,9 +3080,9 @@ resources: url: https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full - authors: - Gabriel G. Martins - - "Fabrice P. Cordeli\xE8res" + - Fabrice P. Cordelières - Julien Colombelli - - "Rocco D\u2019Antuono" + - Rocco D’Antuono - Ofra Golani - Romain Guiet - Robert Haase @@ -3106,8 +3105,8 @@ resources: - Ugis Sarkans - et al. license: ALL RIGHTS RESERVED - name: "REMBI: Recommended Metadata for Biological Images\u2014enabling reuse of\ - \ microscopy data in biology" + name: 'REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy + data in biology' tags: - Research Data Management - Meta Data @@ -3116,7 +3115,7 @@ resources: url: https://www.nature.com/articles/s41592-021-01166-8 - authors: - Susanne Kunis - - "Sebastian H\xE4nsch" + - Sebastian Hänsch - Christian Schmidt - Frances Wong - Caterina Strambio-De-Castillia @@ -3145,7 +3144,7 @@ resources: - authors: - Josh Moore - Chris Allan - - "S\xE9bastien Besson" + - Sébastien Besson - Jean-Marie Burel - Erin Diel - David Gault @@ -3185,7 +3184,7 @@ resources: - Tim Treis - Marcella Toth - Rahul Shrestha - - "Harald V\xF6hringer" + - Harald Vöhringer - Wolfgang Huber - Moritz Gerstung - Josh Moore @@ -3229,7 +3228,7 @@ resources: - Varun Kapoor - Ayse Aslihan Koksoy - Judith Lacoste - - "Sylvia Le D\xE9v\xE9dec" + - Sylvia Le Dévédec - Sylvie Le Guyader - Penghuan Liu - Gabriel G Martins @@ -3243,7 +3242,7 @@ resources: - Laure Plantard - Rizwan Ali - Britta Schroth-Diez - - "Lucas Sch\xFCtz" + - Lucas Schütz - Ryan T Scott - Arne Seitz - Olaf Selchow @@ -3278,17 +3277,17 @@ resources: - Publication url: https://doi.org/10.1093/bioinformatics/btab106 - authors: - - "Mat\xFA\u0161 Kala\u0161" + - Matúš Kalaš - Laure Plantard - Joakim Lindblad - Martin Jones - - "Nata\u0161a Sladoje" + - Nataša Sladoje - Moritz A Kirschmann - Anatole Chessel - Leandro Scholz - - "Fabianne R\xF6ssler" - - "Laura Nicol\xE1s S\xE1enz" - - "Estibaliz G\xF3mez de Mariscal" + - Fabianne Rössler + - Laura Nicolás Sáenz + - Estibaliz Gómez de Mariscal - John Bogovic - Alexandre Dufour - Xavier Heiligenstein @@ -3297,11 +3296,11 @@ resources: - Matthia Karreman - Raf Van de Plas - Robert Haase - - "David H\xF6rl" + - David Hörl - Lassi Paavolainen - - "Ivana Vrhovac Maduni\u0107" + - Ivana Vrhovac Madunić - Dean Karaica - - "Arrate Mu\xF1oz-Barrutia" + - Arrate Muñoz-Barrutia - Paula Sampaio - Daniel Sage - Sebastian Munck @@ -3310,7 +3309,7 @@ resources: - Florian Levet - Jon Ison - Alban Gaignard - - "Herv\xE9 M\xE9nager" + - Hervé Ménager - Chong Zhang - Kota Miura - Julien Colombelli @@ -3359,12 +3358,12 @@ resources: - Vanessa A. F. Fuchs - Moritz Hoevels - Niraj Kandpal - - "Christoph M\xF6hl" + - Christoph Möhl - Joshua A. Moore - Astrid Schauss - Andrea Schrader - - "Torsten St\xF6ter" - - "Julia Th\xF6nni\xDFen" + - Torsten Stöter + - Julia Thönnißen - Monica Valencia-S. - H. Lukas Weil - Jens Wendt and Peter Zentis @@ -3389,8 +3388,8 @@ resources: - https://doi.org/10.5281/zenodo.10609770 - authors: - Josh Moore - description: "Welcome at NFDI4BIOIMAGE All-Hands Meeting in D\xFCsseldorf, Germany,\ - \ October 16, 2023" + description: Welcome at NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, + October 16, 2023 license: CC-BY-4.0 name: Welcome to BioImage Town tags: @@ -3424,12 +3423,12 @@ resources: - Vanessa Fuchs - A. F. Moritz Hoevels - Niraj Kandpal - - "Christoph M\xF6hl" + - Christoph Möhl - Joshua A. Moore - Astrid Schauss - Andrea Schrader - - "Torsten St\xF6ter" - - "Julia Th\xF6nni\xDFen" + - Torsten Stöter + - Julia Thönnißen - Monica Valencia-S. - H. Lukas Weil - Jens Wendt @@ -3518,7 +3517,7 @@ resources: - Vanessa Fuchs - Aphaia Fiona - Jens Wendt - - "Maximilian M\xFCller" + - Maximilian Müller - Mohsen Ahmadi - Riccardo Massei - Cornelia Wetzker @@ -3536,9 +3535,9 @@ resources: url: https://zenodo.org/doi/10.5281/zenodo.10730423 - authors: - Christian Schmidt - description: "Short Talk about the NFDI4BIOIMAGE consortium presented at the RDM\ - \ in (Bio-)Medicine Information Event on April 10th, 2024, organized C\xB3RDM\ - \ & ZB MED." + description: Short Talk about the NFDI4BIOIMAGE consortium presented at the RDM + in (Bio-)Medicine Information Event on April 10th, 2024, organized C³RDM & ZB + MED. license: CC-BY-4.0 name: '[Short Talk] NFDI4BIOIMAGE - A consortium in the National Research Data Infrastructure' tags: @@ -3677,7 +3676,7 @@ resources: - Paula Montero Llopis - Michelle S. Itano - Lisa A. Cameron - - "Guillermo Marqu\xE9s" + - Guillermo Marqués - Caterina Strambio-De-Castillia - Mark A. Sanders - Claire M. Brown @@ -3777,7 +3776,7 @@ resources: - Antje Keppler - Beatriz Serrano-Solano - Arina Rybina - - "Bu\u011Fra \xD6zdemir" + - Buğra Özdemir - Johanna Bischof - Ayoub El Ghadraoui - John E. Eriksson @@ -3862,7 +3861,7 @@ resources: url: https://doi.org/10.1016/j.vibspec.2024.103685 - authors: - Ruman Gerst - - "Zolt\xE1n Cseresny\xE9s" + - Zoltán Cseresnyés - Marc Thilo Figge description: JIPipe is an open-source visual programming language for easy-access pipeline development @@ -3877,8 +3876,8 @@ resources: - https://www.nature.com/articles/s41592-022-01744-4 - https://jipipe.hki-jena.de/ - authors: - - "Birgit M\xF6ller" - - "Markus Gla\xDF" + - Birgit Möller + - Markus Glaß - Danny Misiak - Stefan Posch description: The Microscope Image Analysis Toolbox is a toolbox with a collection @@ -4169,24 +4168,30 @@ resources: url: - https://zenodo.org/records/13506641 - https://doi.org/10.5281/zenodo.13506641 - -- authors: +- authors: - Matúš Kalaš et al. - description: EDAM-bioimaging is an extension of the EDAM ontology, dedicated to bioimage analysis, bioimage informatics, and bioimaging. + description: EDAM-bioimaging is an extension of the EDAM ontology, dedicated to + bioimage analysis, bioimage informatics, and bioimaging. license: CC-BY-4.0 - name: EDAM-bioimaging - The ontology of bioimage informatics operations, topics, data, and formats + name: EDAM-bioimaging - The ontology of bioimage informatics operations, topics, + data, and formats tags: - Ontology - Bioimage Analysis type: - Poster - url: https://hal.science/hal-02267597/document + url: https://hal.science/hal-02267597/document - authors: - Geert van Geest - Yann Haefliger - Monique Zahn-Zabal - Patricia M. Palagi - description: Glittr.org is a platform that aggregates and indexes training materials on computational life sciences from public git repositories, making it easier for users to find, compare, and analyze these resources based on various metrics. By providing insights into the availability of materials, collaboration patterns, and licensing practices, Glittr.org supports adherence to the FAIR principles, benefiting the broader life sciences community. + description: Glittr.org is a platform that aggregates and indexes training materials + on computational life sciences from public git repositories, making it easier + for users to find, compare, and analyze these resources based on various metrics. + By providing insights into the availability of materials, collaboration patterns, + and licensing practices, Glittr.org supports adherence to the FAIR principles, + benefiting the broader life sciences community. license: CC-BY-4.0 name: Using Glittr.org to find, compare and re-use online training materials tags: @@ -4199,7 +4204,9 @@ resources: url: https://www.biorxiv.org/content/10.1101/2024.08.20.608021v1 - authors: - Johannes Soltwedel - description: This repository contains a collection of tools for working with OMERO. Such tools can be working with the OMERO command line interface to transfer datasets between repositories, etc. + description: This repository contains a collection of tools for working with OMERO. + Such tools can be working with the OMERO command line interface to transfer datasets + between repositories, etc. license: CC-BY-4.0 name: Omero-tools tags: @@ -4207,16 +4214,17 @@ resources: - Bioimage Analysis type: - Github Repository - url: https://biapol.github.io/omero-tools/ + url: https://biapol.github.io/omero-tools/ - authors: - Manan Lalit - Joran Deschamps - Florian Jug - Ajinkya Kulkarni - description: Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images + description: Code Implementation for EmbedSeg, an Instance Segmentation Method for + Microscopy Images license: CC-BY-NC-4.0 name: EmbedSeg Repository - tags: + tags: - Bioimage Analysis - Instance Segmentation type: @@ -4224,7 +4232,8 @@ resources: url: https://github.com/juglab/EmbedSeg - authors: - Pauli Virtanen et al. - description: This is a conversion and second life of SciPy Cookbook as a bunch of Ipython notebooks. + description: This is a conversion and second life of SciPy Cookbook as a bunch of + Ipython notebooks. license: bsd 3-clause name: Scipy Cookbook tags: @@ -4242,10 +4251,11 @@ resources: - SimpleITK type: - Github Repository - url: https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks + url: https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks - authors: - Juan Nunez-Iglesias et al. - description: skimage-tutorials - a collection of tutorials for the scikit-image package. + description: skimage-tutorials - a collection of tutorials for the scikit-image + package. license: CC0 1.0 Universal name: skimage-tutorials tags: @@ -4277,7 +4287,13 @@ resources: url: https://github.com/yandexdataschool/nlp_course - authors: - Beth Cimini et al. - description: This book is a companion to the Nature Methods publication Community-developed checklists for publishing images and image analyses. In this paper, members of QUAREP-LiMi have proposed 3 sets of standards for publishing image figures and image analysis - minimal requirements, recommended additions, and ideal comprehensive goals. By following this guidance, we hope to remove some of the stress non-experts may face in determining what they need to do, and we also believe that researchers will find their science more interpretable and more reproducible. + description: This book is a companion to the Nature Methods publication Community-developed + checklists for publishing images and image analyses. In this paper, members of + QUAREP-LiMi have proposed 3 sets of standards for publishing image figures and + image analysis - minimal requirements, recommended additions, and ideal comprehensive + goals. By following this guidance, we hope to remove some of the stress non-experts + may face in determining what they need to do, and we also believe that researchers + will find their science more interpretable and more reproducible. license: BSD License name: Community-developed checklists for publishing images and image analyses tags: @@ -4285,10 +4301,11 @@ resources: - Research Data Management type: - Jupyter Book - url: https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html + url: https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html - authors: - EMBL-EBI - description: Online tutorial and webinar library, designed and delivered by EMBL-EBI experts + description: Online tutorial and webinar library, designed and delivered by EMBL-EBI + experts license: CC0 (mostly, but can differ depending on resource) name: EMBL-EBI material collection tags: @@ -4297,111 +4314,113 @@ resources: type: - Collection url: https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query= - - authors: Fuchs, Vanessa Aphaia Fiona, Schmidt, Christian, Boissonnet, Tom description: 'Description - + Microscopy experiments generate information-rich, multi-dimensional data, allowing us to investigate biological processes at high spatial and temporal resolution. - Image processing and analysis is a standard procedure to retrieve quantitative information - from biological imaging. Due to the complex nature of bioimaging files that often - come in proprietary formats, it can be challenging to organize, structure, and annotate - bioimaging data throughout a project. Data often needs to be moved between collaboration - partners, transformed into open formats, processed with a variety of software tools, - and exported to smaller-sized images for presentation. The path from image acquisition - to final publication figures with quantitative results must be documented and reproducible. - + Image processing and analysis is a standard procedure to retrieve quantitative + information from biological imaging. Due to the complex nature of bioimaging files + that often come in proprietary formats, it can be challenging to organize, structure, + and annotate bioimaging data throughout a project. Data often needs to be moved + between collaboration partners, transformed into open formats, processed with + a variety of software tools, and exported to smaller-sized images for presentation. + The path from image acquisition to final publication figures with quantitative + results must be documented and reproducible. + In this workshop, participants learn how to use structured metadata annotations in the image data management platform OMERO (OME Remote Objects) to optimize their data handling. This strategy helps both with organizing data for easier processing and analysis and for the preparation of data publication in journal manuscripts and in public repositories such as the BioImage Archive. Participants learn the - principles of leveraging object-oriented data organization in OMERO to enhance findability - and usability of their data, also in collaborative settings. The integration of - OMERO with image analysis tools, in particular ImageJ/Fiji, will be trained. Moreover, - users learn about community-accepted metadata checklists (REMBI) to enrich the value - of their data toward reproducibility and reusability. In this workshop, we will - provide hands-on training and recommendations on: - - + principles of leveraging object-oriented data organization in OMERO to enhance + findability and usability of their data, also in collaborative settings. The integration + of OMERO with image analysis tools, in particular ImageJ/Fiji, will be trained. + Moreover, users learn about community-accepted metadata checklists (REMBI) to + enrich the value of their data toward reproducibility and reusability. In this + workshop, we will provide hands-on training and recommendations on: + + Structured metadata annotation features in OMERO and how to use them - - Types of metadata in bioimaging: Technical metadata, sample metadata, analysis metadata - + + Types of metadata in bioimaging: Technical metadata, sample metadata, analysis + metadata + The use of ontologies and terminologies for metadata annotation - + REMBI, the recommended metadata for biological images - + Metadata-assisted image analysis streamlining - + Tools for metadata annotation in OMERO - - + + The target group for this workshop - - This workshop is directed at researchers at all career levels who have started using - OMERO for their microscopy research data management. We encourage the workshop participants - to bring example data from their research to discuss suitable metadata annotation - for their everyday practice. - + + This workshop is directed at researchers at all career levels who have started + using OMERO for their microscopy research data management. We encourage the workshop + participants to bring example data from their research to discuss suitable metadata + annotation for their everyday practice. + Who are the trainers (see trainer description below for more details) - - + + Dr. Vanessa Fuchs (NFDI4BIOIMAGE Data Steward, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) - + Dr. Tom Boissonnet (OMERO admin and image metadata specialist, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) - + Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg) - - + + Material Description - + Published here are the presentation slides that were used for input from the trainers - during the different sessions of the programme. Additionally, a Fiji Macro is published - that depends on the OMERO Extensions Plugin by Pouchin et al, 2022, F100Research, - https://doi.org/10.12688/f1000research.110385.2  - + during the different sessions of the programme. Additionally, a Fiji Macro is + published that depends on the OMERO Extensions Plugin by Pouchin et al, 2022, + F100Research, https://doi.org/10.12688/f1000research.110385.2  + Programme Overview - + Day 1 - April 29th, 2024 09.00 a.m. to 10.00 a.m.: Session 1 - Welcome and Introduction - + 10.00 a.m. to 10.30 a.m.:  Session 2 - Introduction to the FAIR principles & data annotation - + 10:30 a.m. to 10:45 a.m.: Coffee break - + 10.45 a.m. to 12.00 a.m.: Session 3 - Data structure (datasets in OMERO) and organization with Tags  - + 12.00 a.m. to 1.00 p.m.:  Lunch Break - - 1.00 p.m. to 2.00 p.m.:  Session 4 - REMBI, Key-Value pair annotations in bioimaging - + + 1.00 p.m. to 2.00 p.m.:  Session 4 - REMBI, Key-Value pair annotations in + bioimaging + 2:00 p.m. to 2.30 p.m.:  Session 5 - Ontologies for Key-Value Pairs in OMERO - + 2:30 p.m. to 2:45 p.m. Coffee break - + 2.45 p.m. to 3.45 p.m.:  Wrap-up, discussion, outlook on day 2 - + Day 2 - April 30th, 2024 - + 09.00 a.m. to 09.30 a.m.:  Arrival and Start into day 2 - + 09.30 a.m. to 11.30 a.m.:  Session 6 - Hands-on : REMBI-based Key-Value Pair annotation in OMERO - + 11.30 a.m. to 12.30 a.m.:  Lunch Break - + 12.30 a.m. to 1.15 p.m.: Session 7 - OMERO and OMERO.plugins - + 1.15 p.m. to 2.00 p.m.: Session 8 - Loading OMERO-hosted data into Fiji - + 2.00 p.m. to 2.15 p.m.: Coffee break  - + 2.15 p.m. to 3.00 p.m.: Discussion, Outlook' license: cc-by-4.0 name: '[Workshop] FAIR data handling for microscopy: Structured metadata annotation @@ -4411,11 +4430,9 @@ resources: url: - https://zenodo.org/records/11109616 - https://doi.org/10.5281/zenodo.11109616 - - - authors: Massei, Riccardo description: 'YMIA python event 2024 - + Presentation :  "Getting started with Python: intro and set-up a conda environment with Dr. Riccardo Massei"' license: cc-by-4.0 @@ -4425,12 +4442,11 @@ resources: url: - https://zenodo.org/records/13908480 - https://doi.org/10.5281/zenodo.13908480 - - authors: Haase, Robert description: In this presentation I introduce bia-bob, an AI-based code generator that integrates into Jupyter Lab and allows for easy generation of Bio-Image Analysis - Python code. It highlights how to get started with using large language models and - prompt engineering to get high-quality bio-image analysis code. + Python code. It highlights how to get started with using large language models + and prompt engineering to get high-quality bio-image analysis code. license: cc-by-4.0 name: Bio-image Analysis Code Generation using bia-bob num_downloads: 101 @@ -4438,4 +4454,13 @@ resources: url: - https://zenodo.org/records/13908108 - https://doi.org/10.5281/zenodo.13908108 - \ No newline at end of file +- authors: This is a test again + license: + - ALL RIGHTS RESERVED + name: This is a test again + description: '123' + tags: + - Artificial Intelligence + type: + - Bioimage Analysis + url: https://cloud.scadsai.uni-leipzig.de/index.php/apps/calendar/timeGridWeek/now