From 7d3448cc4550ef4b08177c3b60be6a0498a0d1b4 Mon Sep 17 00:00:00 2001 From: haesleinhuepf Date: Fri, 13 Oct 2023 16:12:51 +0000 Subject: [PATCH] deploy: 0541595cc2b7300a17ec5b40122cbfd749a8bf35 --- _sources/blog/readme.md | 3 +++ _sources/collection/readme.md | 3 +++ _sources/document/readme.md | 1 + _sources/documentation/readme.md | 4 +++ _sources/publication/readme.md | 29 +++++++++++++++++++++ _sources/readme.md | 2 +- _sources/slide/readme.md | 1 + blog/readme.html | 3 +++ collection/readme.html | 3 +++ document/readme.html | 1 + documentation/readme.html | 4 +++ publication/readme.html | 43 ++++++++++++++++++++++++++------ readme.html | 2 +- searchindex.js | 2 +- slide/readme.html | 1 + 15 files changed, 92 insertions(+), 10 deletions(-) diff --git a/_sources/blog/readme.md b/_sources/blog/readme.md index be0ade4..c9bdcac 100644 --- a/_sources/blog/readme.md +++ b/_sources/blog/readme.md @@ -40,6 +40,7 @@ By Elisabeth Kugler [https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/](https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/) ## Running Deep-Learning Scripts in the BiA-PoL Omero Server +By Marcelo Zoccoler @@ -52,6 +53,7 @@ By Elisabeth Kugler [https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html](https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html) ## Getting started with Mambaforge and Python +By Mara Lampert @@ -66,6 +68,7 @@ Tags: python [https://datamanagement.hms.harvard.edu/news/promoting-data-management-nikon-imaging-center-and-cell-biology-microscopy-facility](https://datamanagement.hms.harvard.edu/news/promoting-data-management-nikon-imaging-center-and-cell-biology-microscopy-facility) ## Data handling in large-scale electron microscopy +By Job Fermie diff --git a/_sources/collection/readme.md b/_sources/collection/readme.md index 31158d9..e643618 100644 --- a/_sources/collection/readme.md +++ b/_sources/collection/readme.md @@ -207,12 +207,14 @@ Tags: python,napari [https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop](https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop) ## Research Data Management Seminar - Slides +By Della Chiesa, Stefano [https://zenodo.org/record/6602101](https://zenodo.org/record/6602101) ## A biologist’s guide to planning and performing quantitative bioimaging experiments +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,Beth A. Cimini @@ -221,6 +223,7 @@ Tags: python,napari [https://www.bioimagingguide.org/](https://www.bioimagingguide.org/) ## Annotated high-throughput microscopy image sets for validation +By Vebjorn Ljosa, Katherine L Sokolnicki, Anne E Carpenter diff --git a/_sources/document/readme.md b/_sources/document/readme.md index 9a39bf2..89c80c0 100644 --- a/_sources/document/readme.md +++ b/_sources/document/readme.md @@ -1,5 +1,6 @@ # document ## BiaPy: Bioimage analysis pipelines in Python +By Daniel Franco-Barranco et al diff --git a/_sources/documentation/readme.md b/_sources/documentation/readme.md index 4488144..2bfcae0 100644 --- a/_sources/documentation/readme.md +++ b/_sources/documentation/readme.md @@ -1,5 +1,6 @@ # documentation ## JIPipe: visual batch processing for ImageJ +By Ruman Gerst, Zoltán Cseresnyés & Marc Thilo Figge @@ -12,6 +13,7 @@ Tags: NFDI4BioImage,workflow engine,imagej [https://jipipe.hki-jena.de/](https://jipipe.hki-jena.de/) ## MiToBo - A Toolbox for Image Processing and Analysis +By Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch @@ -24,6 +26,7 @@ Tags: workflow engine,imagej [https://mitobo.informatik.uni-halle.de/](https://mitobo.informatik.uni-halle.de/) ## BiaPy: Bioimage analysis pipelines in Python +By Daniel Franco-Barranco et al @@ -66,6 +69,7 @@ Tags: workflow engine,python [https://academic.oup.com/bioinformatics/article/28/19/2520/290322](https://academic.oup.com/bioinformatics/article/28/19/2520/290322) ## ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ +By Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson diff --git a/_sources/publication/readme.md b/_sources/publication/readme.md index c3e98d8..320c23a 100644 --- a/_sources/publication/readme.md +++ b/_sources/publication/readme.md @@ -1,29 +1,34 @@ # publication ## MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text +By Joel Ryan, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, Claire M. Brown [https://www.nature.com/articles/s41592-021-01290-5](https://www.nature.com/articles/s41592-021-01290-5) ## Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications +By Alessandro Rigano et al. [https://doi.org/10.1038/s41592-021-01315-z](https://doi.org/10.1038/s41592-021-01315-z) ## Metadata matters: access to image data in the real world +By Melissa Linkert et al. Published 2010 [https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real](https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real) ## A call for public archives for biological image data +By Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook, Ugis Sarkans, Ardan Patwardhan, Alvis Brazma, Ewan Birney [https://www.nature.com/articles/s41592-018-0195-8](https://www.nature.com/articles/s41592-018-0195-8) ## 2020 BioImage Analysis Survey: Community experiences and needs for the future +By Nasim Jamali, Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini Published 2021 @@ -32,6 +37,7 @@ Published 2021 [https://github.com/ciminilab/2021_Jamali_BiologicalImaging](https://github.com/ciminilab/2021_Jamali_BiologicalImaging) ## Bridging Imaging Users to Imaging Analysis - A community survey +By Suganya Sivagurunathan, Stefania Marcotti, Carl J Nelson, Martin L Jones, David J Barry, Thomas J A Slater, Kevin W Eliceiri, Beth A Cimini Published 2023 @@ -40,6 +46,7 @@ Published 2023 [https://github.com/COBA-NIH/2023_ImageAnalysisSurvey](https://github.com/COBA-NIH/2023_ImageAnalysisSurvey) ## Understanding metric-related pitfalls in image analysis validation +By Annika Reinke et al Published 2023 @@ -48,18 +55,21 @@ This article gives a detailed overview about pitfalls when using metric for imag [https://arxiv.org/abs/2302.01790v3](https://arxiv.org/abs/2302.01790v3) ## Building a FAIR image data ecosystem for microscopy communities +By Isabel Kemmer, Antje Keppler, Beatriz Serrano-Solano, Arina Rybina, Buğra Özdemir, Johanna Bischof, Ayoub El Ghadraoui, John E. Eriksson, Aastha Mathur [https://link.springer.com/article/10.1007/s00418-023-02203-7](https://link.springer.com/article/10.1007/s00418-023-02203-7) ## A study on long-term reproducibility of image analysis results on ImageJ and Fiji +By Robert Haase, Deborah Schmidt, Wayne Rasband, Curtis Rueden, Florian Jug, Pavel Tomancak, Eugene W. Myers [https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525](https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525) ## JIPipe: visual batch processing for ImageJ +By Ruman Gerst, Zoltán Cseresnyés & Marc Thilo Figge @@ -72,6 +82,7 @@ Tags: NFDI4BioImage,workflow engine,imagej [https://jipipe.hki-jena.de/](https://jipipe.hki-jena.de/) ## MiToBo - A Toolbox for Image Processing and Analysis +By Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch @@ -84,6 +95,7 @@ Tags: workflow engine,imagej [https://mitobo.informatik.uni-halle.de/](https://mitobo.informatik.uni-halle.de/) ## ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ +By Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson @@ -143,6 +155,7 @@ Tags: NFDI4BioImage [https://doi.org/10.52825/cordi.v1i.285](https://doi.org/10.52825/cordi.v1i.285) ## The Fiji Updater +By Robert Haase @@ -153,6 +166,7 @@ Tags: NFDI4BioImage [https://analyticalscience.wiley.com/do/10.1002/was.0004000112/](https://analyticalscience.wiley.com/do/10.1002/was.0004000112/) ## CLIJ: GPU-accelerated image processing for everyone +By Robert Haase, Loic Royer, et al Published 2020 @@ -163,6 +177,7 @@ Tags: NFDI4BioImage [https://doi.org/10.1038/s41592-019-0650-1](https://doi.org/10.1038/s41592-019-0650-1) ## A Hitchhiker's guide through the bio-image analysis software universe +By Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer @@ -173,6 +188,7 @@ Tags: NFDI4BioImage [https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451](https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451) ## Challenges and opportunities for bioimage analysis core-facilities +By Johannes Richard Soltwedel, Robert Haase @@ -183,6 +199,7 @@ Tags: NFDI4BioImage [https://onlinelibrary.wiley.com/doi/full/10.1111/jmi.13192](https://onlinelibrary.wiley.com/doi/full/10.1111/jmi.13192) ## Open microscopy in the life sciences: quo vadis? +By Johannes Hohlbein, Benedict Diederich, Barbora Marsikova, Emmanuel G. Reynaud, Séamus Holden, Wiebke Jahr, Robert Haase, Kirti Prakash Published 2022 @@ -193,6 +210,7 @@ Tags: NFDI4BioImage [https://doi.org/10.1038/s41592-022-01602-3](https://doi.org/10.1038/s41592-022-01602-3) ## Developing open-source software for bioimage analysis: opportunities and challenges +By Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase @@ -203,6 +221,7 @@ Tags: NFDI4BioImage [https://f1000research.com/articles/10-302](https://f1000research.com/articles/10-302) ## Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration +By Anjalie Schlaeppi, Wilson Adams, Robert Haase, Jan Huisken, Ryan B. MacDonald, Kevin W. Eliceiri, Elisabeth C. Kugler @@ -211,6 +230,7 @@ Tags: NFDI4BioImage [https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full](https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full) ## Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists +By Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura Published 2021 @@ -219,6 +239,7 @@ Tags: NFDI4BioImage [https://f1000research.com/articles/10-334/v1](https://f1000research.com/articles/10-334/v1) ## REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology +By Ugis Sarkans et al @@ -227,6 +248,7 @@ Tags: NFDI4BioImage [https://www.nature.com/articles/s41592-021-01166-8](https://www.nature.com/articles/s41592-021-01166-8) ## MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community +By Susanne Kunis, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, Stefanie Weidtkamp-Peters @@ -235,6 +257,7 @@ Tags: NFDI4BioImage [https://www.nature.com/articles/s41592-021-01288-z](https://www.nature.com/articles/s41592-021-01288-z) ## QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy +By Glyn Nelson, Ulrike Boehme, et al @@ -252,6 +275,7 @@ Tags: NFDI4BioImage [https://www.nature.com/articles/s41592-021-01326-w](https://www.nature.com/articles/s41592-021-01326-w) ## NFDI4BIOIMAGE: Perspective for a national bioimaging standard +By Josh Moore, Susanne Kunis @@ -260,6 +284,7 @@ Tags: NFDI4BioImage [https://ceur-ws.org/Vol-3415/paper-27.pdf](https://ceur-ws.org/Vol-3415/paper-27.pdf) ## SpatialData: an open and universal data framework for spatial omics +By Luca Marconato, Giovanni Palla, Kevin A Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Marcella Toth, Rahul Shrestha, Harald Vöhringer, Wolfgang Huber, Moritz Gerstung, Josh Moore, Fabian J Theis, Oliver Stegle @@ -268,6 +293,7 @@ Tags: NFDI4BioImage [https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract) ## Community-developed checklists for publishing images and image analyses +By Christopher Schmied, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, Helena Klara Jambor @@ -276,6 +302,7 @@ Tags: NFDI4BioImage [https://www.nature.com/articles/s41592-023-01987-9](https://www.nature.com/articles/s41592-023-01987-9) ## BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data +By Christian Tischer, Ashis Ravindran, Sabine Reither, Nicolas Chiaruttini, Rainer Pepperkok, Nils Norlin @@ -284,6 +311,7 @@ Tags: NFDI4BioImage [https://doi.org/10.1093/bioinformatics/btab106](https://doi.org/10.1093/bioinformatics/btab106) ## EDAM-bioimaging: The ontology of bioimage informatics operations, topics, data, and formats (update 2020) +By Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A Kirschmann, Anatole Chessel, Leandro Scholz, Fabianne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux @@ -292,6 +320,7 @@ Tags: NFDI4BioImage [https://f1000research.com/posters/9-162](https://f1000research.com/posters/9-162) ## A biologist’s guide to planning and performing quantitative bioimaging experiments +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,Beth A. Cimini diff --git a/_sources/readme.md b/_sources/readme.md index 81d6cbb..7a3ada5 100644 --- a/_sources/readme.md +++ b/_sources/readme.md @@ -1,6 +1,6 @@ # NFDI4BioImage Training Materials -This Jupyter Book contains 108 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2023-10-10. +This Jupyter Book contains 108 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2023-10-13. This is a **preliminary** / **experimental** search index allowing us to explore how such a database could look like. We follow the principle [_release early, release often_](https://en.wikipedia.org/wiki/Release_early,_release_often) and aim at having a functional prototype of the search index at any time. We will use this resource to * explore what kind of meta-data we need to collect for training materials diff --git a/_sources/slide/readme.md b/_sources/slide/readme.md index 460ecf7..b51171a 100644 --- a/_sources/slide/readme.md +++ b/_sources/slide/readme.md @@ -68,6 +68,7 @@ Tags: imagej [https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d](https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d) ## Research Data Management Seminar - Slides +By Della Chiesa, Stefano diff --git a/blog/readme.html b/blog/readme.html index dd3095b..cf88811 100644 --- a/blog/readme.html +++ b/blog/readme.html @@ -754,6 +754,7 @@

Sharing Your Poster on Figshare: A Community Guide to How-To and Why

Running Deep-Learning Scripts in the BiA-PoL Omero Server#

+

By Marcelo Zoccoler

https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html

@@ -762,6 +763,7 @@

Browsing the Open Microscopy Image Data Resource with Python

Getting started with Mambaforge and Python#

+

By Mara Lampert

Tags: python

https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html

@@ -771,6 +773,7 @@

Promoting Data Management at the Nikon Imaging Center and Cell Biology Micro

Data handling in large-scale electron microscopy#

+

By Job Fermie

https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy

diff --git a/collection/readme.html b/collection/readme.html index 750679b..ed5a525 100644 --- a/collection/readme.html +++ b/collection/readme.html @@ -982,15 +982,18 @@

ZEN & Python workshop

Research Data Management Seminar - Slides#

+

By Della Chiesa, Stefano

https://zenodo.org/record/6602101

A biologist’s guide to planning and performing quantitative bioimaging experiments#

+

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,Beth A. Cimini

https://doi.org/10.1371/journal.pbio.3002167

https://www.bioimagingguide.org/

Annotated high-throughput microscopy image sets for validation#

+

By Vebjorn Ljosa, Katherine L Sokolnicki, Anne E Carpenter

Broad Bioimage Benchmark Collection (BBBC)

https://www.nature.com/articles/nmeth.2083

https://bbbc.broadinstitute.org/

diff --git a/document/readme.html b/document/readme.html index 5c8080d..a950a97 100644 --- a/document/readme.html +++ b/document/readme.html @@ -708,6 +708,7 @@

Contents

document#

BiaPy: Bioimage analysis pipelines in Python#

+

By Daniel Franco-Barranco et al

BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.

Tags: python

https://biapy.readthedocs.io/

diff --git a/documentation/readme.html b/documentation/readme.html index 584d439..c76cd5c 100644 --- a/documentation/readme.html +++ b/documentation/readme.html @@ -708,6 +708,7 @@

Contents

documentation#

JIPipe: visual batch processing for ImageJ#

+

By Ruman Gerst, Zoltán Cseresnyés & Marc Thilo Figge

JIPipe is an open-source visual programming language for easy-access pipeline development

Tags: NFDI4BioImage,workflow engine,imagej

https://www.nature.com/articles/s41592-022-01744-4

@@ -715,6 +716,7 @@

JIPipe: visual batch processing for ImageJ

MiToBo - A Toolbox for Image Processing and Analysis#

+

By Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch

The Microscope Image Analysis Toolbox is a toolbox with a collection of algorithms for processing and analyzing digital images.

Tags: workflow engine,imagej

https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103

@@ -722,6 +724,7 @@

MiToBo - A Toolbox for Image Processing and Analysis

BiaPy: Bioimage analysis pipelines in Python#

+

By Daniel Franco-Barranco et al

BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.

Tags: python

https://biapy.readthedocs.io/

@@ -747,6 +750,7 @@

Snakemake Documentation

ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ#

+

By Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson

ModularImageAnalysis is a Fiji plugin providing a modular framework for assembling image and object analysis workflows

Tags: workflow engine,imagej

https://doi.org/10.1111/jmi.13227

diff --git a/publication/readme.html b/publication/readme.html index b2008ba..ea43023 100644 --- a/publication/readme.html +++ b/publication/readme.html @@ -833,49 +833,59 @@

Contents

publication#

MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text#

+

By Joel Ryan, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, Claire M. Brown

https://www.nature.com/articles/s41592-021-01290-5

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications#

+

By Alessandro Rigano et al.

https://doi.org/10.1038/s41592-021-01315-z

Metadata matters: access to image data in the real world#

-

Published 2010

+

By Melissa Linkert et al. +Published 2010

https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real

A call for public archives for biological image data#

+

By Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook, Ugis Sarkans, Ardan Patwardhan, Alvis Brazma, Ewan Birney

https://www.nature.com/articles/s41592-018-0195-8

2020 BioImage Analysis Survey: Community experiences and needs for the future#

-

Published 2021

+

By Nasim Jamali, Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini +Published 2021

https://doi.org/10.1017/s2633903x21000039

ciminilab/2021_Jamali_BiologicalImaging

Bridging Imaging Users to Imaging Analysis - A community survey#

-

Published 2023

+

By Suganya Sivagurunathan, Stefania Marcotti, Carl J Nelson, Martin L Jones, David J Barry, Thomas J A Slater, Kevin W Eliceiri, Beth A Cimini +Published 2023

https://www.biorxiv.org/content/10.1101/2023.06.05.543701v1

COBA-NIH/2023_ImageAnalysisSurvey

Building a FAIR image data ecosystem for microscopy communities#

+

By Isabel Kemmer, Antje Keppler, Beatriz Serrano-Solano, Arina Rybina, Buğra Özdemir, Johanna Bischof, Ayoub El Ghadraoui, John E. Eriksson, Aastha Mathur

https://link.springer.com/article/10.1007/s00418-023-02203-7

A study on long-term reproducibility of image analysis results on ImageJ and Fiji#

+

By Robert Haase, Deborah Schmidt, Wayne Rasband, Curtis Rueden, Florian Jug, Pavel Tomancak, Eugene W. Myers

https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525

JIPipe: visual batch processing for ImageJ#

+

By Ruman Gerst, Zoltán Cseresnyés & Marc Thilo Figge

JIPipe is an open-source visual programming language for easy-access pipeline development

Tags: NFDI4BioImage,workflow engine,imagej

https://www.nature.com/articles/s41592-022-01744-4

@@ -883,6 +893,7 @@

JIPipe: visual batch processing for ImageJ

MiToBo - A Toolbox for Image Processing and Analysis#

+

By Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch

The Microscope Image Analysis Toolbox is a toolbox with a collection of algorithms for processing and analyzing digital images.

Tags: workflow engine,imagej

https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103

@@ -890,6 +901,7 @@

MiToBo - A Toolbox for Image Processing and Analysis

ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ#

+

By Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson

ModularImageAnalysis is a Fiji plugin providing a modular framework for assembling image and object analysis workflows

Tags: workflow engine,imagej

https://doi.org/10.1111/jmi.13227

@@ -928,65 +940,76 @@

A Cloud-Optimized Storage for Interactive Access of Large Arrays

The Fiji Updater#

+

By Robert Haase

Article about the Fiji Updater explaining how it works in the background.

Tags: NFDI4BioImage

https://analyticalscience.wiley.com/do/10.1002/was.0004000112/

CLIJ: GPU-accelerated image processing for everyone#

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Published 2020

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By Robert Haase, Loic Royer, et al +Published 2020

CLIJ is a collection of image processing functions that use graphics processing units for accelerated processing.

Tags: NFDI4BioImage

https://doi.org/10.1038/s41592-019-0650-1

A Hitchhiker’s guide through the bio-image analysis software universe#

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By Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer

This article gives an overview about commonly used bioimage analysis software and which aspects to consider when choosing a software for a specific project.

Tags: NFDI4BioImage

https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451

Challenges and opportunities for bioimage analysis core-facilities#

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By Johannes Richard Soltwedel, Robert Haase

This article outlines common reasons for founding bioimage analysis core-facilities, services they can provide to fulfill certain need and conflicts of interest that arise from these services.

Tags: NFDI4BioImage

https://onlinelibrary.wiley.com/doi/full/10.1111/jmi.13192

Open microscopy in the life sciences: quo vadis?#

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Published 2022

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By Johannes Hohlbein, Benedict Diederich, Barbora Marsikova, Emmanuel G. Reynaud, Séamus Holden, Wiebke Jahr, Robert Haase, Kirti Prakash +Published 2022

This comment article outlines the current state of the art in open hardware publishing in the context of microscopy.

Tags: NFDI4BioImage

https://doi.org/10.1038/s41592-022-01602-3

Developing open-source software for bioimage analysis: opportunities and challenges#

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By Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase

This article outlines common challenges and practices when developing open-source software for bio-image analysis.

Tags: NFDI4BioImage

https://f1000research.com/articles/10-302

Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration#

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By Anjalie Schlaeppi, Wilson Adams, Robert Haase, Jan Huisken, Ryan B. MacDonald, Kevin W. Eliceiri, Elisabeth C. Kugler

Tags: NFDI4BioImage

https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full

Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists#

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Published 2021

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By Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura +Published 2021

Tags: NFDI4BioImage

https://f1000research.com/articles/10-334/v1

MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community#

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By Susanne Kunis, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, Stefanie Weidtkamp-Peters

Tags: NFDI4BioImage

https://www.nature.com/articles/s41592-021-01288-z

QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy#

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By Glyn Nelson, Ulrike Boehme, et al

Tags: NFDI4BioImage

https://onlinelibrary.wiley.com/doi/10.1111/jmi.13041

@@ -998,31 +1021,37 @@

OME-NGFF: a next-generation file format for expanding bioimaging data-access

NFDI4BIOIMAGE: Perspective for a national bioimaging standard#

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By Josh Moore, Susanne Kunis

Tags: NFDI4BioImage

https://ceur-ws.org/Vol-3415/paper-27.pdf

SpatialData: an open and universal data framework for spatial omics#

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By Luca Marconato, Giovanni Palla, Kevin A Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Marcella Toth, Rahul Shrestha, Harald Vöhringer, Wolfgang Huber, Moritz Gerstung, Josh Moore, Fabian J Theis, Oliver Stegle

Tags: NFDI4BioImage

https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract

Community-developed checklists for publishing images and image analyses#

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By Christopher Schmied, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, Helena Klara Jambor

Tags: NFDI4BioImage

https://www.nature.com/articles/s41592-023-01987-9

BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data#

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By Christian Tischer, Ashis Ravindran, Sabine Reither, Nicolas Chiaruttini, Rainer Pepperkok, Nils Norlin

Tags: NFDI4BioImage

https://doi.org/10.1093/bioinformatics/btab106

EDAM-bioimaging: The ontology of bioimage informatics operations, topics, data, and formats (update 2020)#

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By Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A Kirschmann, Anatole Chessel, Leandro Scholz, Fabianne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux

Tags: NFDI4BioImage

https://f1000research.com/posters/9-162

A biologist’s guide to planning and performing quantitative bioimaging experiments#

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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,Beth A. Cimini

https://doi.org/10.1371/journal.pbio.3002167

https://www.bioimagingguide.org/

diff --git a/readme.html b/readme.html index 7df47f1..ed4b5de 100644 --- a/readme.html +++ b/readme.html @@ -675,7 +675,7 @@

Contents

NFDI4BioImage Training Materials#

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This Jupyter Book contains 108 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2023-10-10.

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This Jupyter Book contains 108 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2023-10-13.

This is a preliminary / experimental search index allowing us to explore how such a database could look like. We follow the principle release early, release often and aim at having a functional prototype of the search index at any time. We will use this resource to

  • explore what kind of meta-data we need to collect for training materials

    • diff --git a/searchindex.js b/searchindex.js index 201ca5a..faea04d 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["blog/readme", "book/readme", "collection/readme", "contributing/format", "contributing/readme", "document/readme", "documentation/readme", "event/readme", "imprint", "notebook/readme", "publication/readme", "readme", "slide/readme", "video/readme"], "filenames": ["blog/readme.md", "book/readme.md", "collection/readme.md", "contributing/format.md", "contributing/readme.md", "document/readme.md", "documentation/readme.md", "event/readme.md", "imprint.md", "notebook/readme.md", "publication/readme.md", "readme.md", "slide/readme.md", "video/readme.md"], "titles": ["blog", "book", "collection", "YML format", "How to contribute", "document", "documentation", "event", "Imprint", "notebook", "publication", "NFDI4BioImage Training Materials", "slide", "video"], "terms": {"By": [0, 1, 2, 5, 9, 10, 12, 13], "robert": [0, 2, 8, 9, 12], "haas": [0, 2, 8, 9, 12], "post": [0, 3, 4], "about": [0, 2, 7, 9, 10, 13], "what": [0, 11], "import": [0, 5], "when": [0, 10], "choos": [0, 10], "tag": [0, 2, 3, 5, 6, 9, 10, 12, 13], "nfdi4bioimag": [0, 3, 6, 12, 13], "http": [0, 1, 2, 3, 5, 6, 7, 9, 10, 12, 13], "focalplan": 0, "biologist": 0, "com": [0, 2, 5, 6, 10, 12, 13], "2023": [0, 10, 11], "05": [0, 10], "06": [0, 10], "itll": 0, "us": [0, 2, 3, 4, 5, 6, 9, 10, 13], "org": [0, 1, 5, 6, 7, 10, 12, 13], "02": 0, "15": 0, "introduct": [0, 12], "version": 0, "control": [0, 2, 9], "reproduc": [0, 5, 6], "2021": 0, "09": 0, "04": 0, "elisabeth": 0, "kugler": 0, "07": 0, "26": 0, "biapol": [0, 7, 9], "github": [0, 2, 3, 4, 5, 6, 7, 9, 10, 11], "io": [0, 2, 5, 6, 7, 9, 10], "marcelo_zoccol": 0, "omero_script": 0, "readm": 0, "html": [0, 2, 5, 7, 9], "robert_haas": 0, "browsing_idr": 0, "mara_lampert": 0, "getting_started_with_mambaforge_and_python": 0, "datamanag": 0, "hm": 0, "harvard": 0, "edu": 0, "new": [0, 4], "delmic": 0, "01": [0, 7], "03": 0, "2022": [0, 10], "12": [0, 12], "08": 0, "scientif": [0, 2, 5, 6], "environ": 0, "conda": 0, "mamba": 0, "friend": 0, "13": 0, "anisotropi": 0, "biernacka": [1, 2, 5], "katarzyna": [1, 2, 5], "bierwirth": [1, 2], "maik": [1, 2], "buchholz": [1, 2], "petra": [1, 2], "dolzycka": [1, 2], "dominika": [1, 2], "helbig": [1, 2, 5], "kerstin": [1, 2, 5], "neumann": [1, 2], "janna": [1, 2], "odebrecht": [1, 2], "carolin": [1, 2], "wilj": [1, 2], "cord": [1, 2], "wuttk": [1, 2], "ulrik": [1, 2], "collect": [1, 3, 4, 6, 11, 13], "materi": [1, 3, 4, 9], "from": [1, 2], "fdmentor": [1, 2], "commun": 1, "zenodo": [1, 2, 5, 12, 13], "record": [1, 2, 5, 12, 13], "4071471": [1, 2], "elixir": [2, 7], "europ": [2, 7], "globalbioimag": [2, 7, 13], "intern": [2, 7], "www": [2, 5, 6, 7, 10, 13], "openmicroscopi": [2, 6, 7], "nf": 2, "effort": 2, "curat": 2, "pipelin": [2, 10], "built": 2, "co": 2, "re": 2, "german": [2, 11], "biii": 2, "eu": 2, "et": [2, 9], "al": [2, 8, 9], "haesleinhuepf": [2, 9], "bioimageanalysisnotebook": [2, 9], "intro": [2, 7, 9], "pete": [2, 9], "bankhead": [2, 9], "imagej": [2, 9], "bioimagebook": [2, 9], "readthedoc": [2, 5, 6], "en": [2, 5, 6], "latest": [2, 5], "bioinformat": [2, 5, 6, 10], "provid": [2, 6, 10, 11], "facil": 2, "compani": 2, "gmb": 2, "de": [2, 3, 6, 8, 10, 12], "inform": 2, "portal": 2, "wiki": 2, "all_training_resourc": 2, "i3dbio": 2, "mat": 2, "bioimagelist": 2, "licens": [2, 3, 5, 9, 13], "bsd": [2, 9, 12], "3": [2, 9, 10, 12, 13], "claus": [2, 9, 12], "exercis": [2, 9], "transloc": [2, 9], "pixel": [2, 9], "classif": [2, 9], "qualiti": [2, 9], "gpl": [2, 9], "2": [2, 9], "0": [2, 5, 8, 9, 11, 13], "thi": [2, 3, 4, 9, 10], "repositori": [2, 3, 4, 9, 11], "contain": [2, 4, 5, 6, 9, 11], "univers": [2, 9], "oxford": [2, 9], "dtc": [2, 9], "dwaith": [2, 9], "onbi_image_analysi": [2, 9], "public_domain": 2, "syn": 2, "mrc": 2, "lmb": 2, "cam": 2, "ac": 2, "uk": 2, "acardona": 2, "git": [2, 12], "mpi": [2, 12], "cbg": [2, 12], "rhaas": [2, 12], "lecture_applied_bioimage_analysi": [2, 12], "mit": [2, 8, 9], "seri": [2, 9], "expos": [2, 9], "how": [2, 9, 10, 13], "do": [2, 4, 9, 10], "mostli": [2, 4, 9], "basic": [2, 9], "some": [2, 4, 9], "advanc": [2, 9], "It": [2, 4, 9], "standard": [2, 9], "packag": [2, 9], "numpi": [2, 9], "maplotlib": [2, 9], "part": [2, 9], "heavili": [2, 9], "scikit": [2, 9], "guiwitz": [2, 9], "python_image_process": [2, 9], "agpl": [2, 9], "r": [2, 9, 10, 11], "tpecot": [2, 9], "deeplearningbasedsegmentationforbiologist": [2, 9], "cc": [2, 5, 8, 11, 13], "BY": [2, 5, 8, 11, 13], "nc": [2, 13], "sa": 2, "4": [2, 5, 6, 8, 10, 11], "fabriziomusacchio": 2, "teaching_bioimage_analysi": 2, "syllabu": 2, "zeissmicroscopi": [2, 9], "zen_python_oad_workshop": [2, 9], "6602101": [2, 12], "doi": [2, 3, 6, 10], "10": [2, 6, 8, 10, 11, 12], "1371": [2, 10], "journal": [2, 10], "pbio": [2, 10], "3002167": [2, 10], "bioimagingguid": [2, 10], "broad": 2, "benchmark": 2, "bbbc": 2, "natur": [2, 6, 10], "articl": [2, 5, 6, 10], "nmeth": 2, "2083": 2, "broadinstitut": 2, "webinar": [2, 13], "where": [2, 13], "commonli": [2, 10, 13], "author": [2, 3, 4, 13], "sourc": [2, 5, 6, 13], "softwar": [2, 4, 5, 6, 13], "explain": [2, 10, 13], "sreeni": [2, 13], "bhattiprolu": [2, 13], "video": [2, 3, 4], "gener": [2, 13], "machin": [2, 13], "watch": [2, 13], "v": [2, 13], "e": [2, 4, 8, 11, 13], "2dbkuwkk4": [2, 13], "pl5esqnfm5lc7samsteu082ivw4bdmvd0u": [2, 13], "next": [2, 4, 13], "file": [2, 3, 4, 13], "format": [2, 4, 13], "ngff": [2, 13], "idr": [2, 13], "platform": [2, 5, 6, 13], "plugin": [2, 6, 13], "openmicroscopyenviron": [2, 13], "c": [2, 13], "eurobioimagingcommun": [2, 13], "nd": [2, 13], "deed": [2, 13], "biologi": [2, 13], "In": [3, 4], "we": [3, 4, 11], "store": 3, "train": [3, 4], "simpl": 3, "These": 3, "ar": [3, 4, 11], "structur": 3, "like": [3, 4, 11], "resourc": [3, 4, 12, 13], "name": [3, 8], "websit": 3, "type": [3, 4], "url": 3, "entri": [3, 4], "can": [3, 4, 10, 11], "have": [3, 4, 11], "multipl": 3, "properti": 3, "mandatori": 3, "A": [3, 13], "descript": 3, "titl": 3, "must": 3, "avail": 3, "internet": [3, 8], "content": [3, 4, 5, 6, 10, 11], "blog": [3, 4], "etc": 3, "option": 3, "recommend": 3, "publication_d": 3, "list": [3, 4, 7, 11, 13], "meta": [3, 11], "data": [3, 4, 6, 11], "extens": [3, 4], "just": 3, "let": [3, 4], "know": [3, 4], "issu": [3, 11], "which": [3, 4, 10, 11], "kind": [3, 11], "you": [3, 4, 11], "would": [3, 4], "add": [3, 4], "here": [3, 4], "pull": 4, "request": 4, "find": [4, 11], "guid": [4, 5, 9], "bottom": 4, "page": [4, 11], "The": [4, 5, 6], "document": 4, "consid": [4, 10, 11], "ad": [4, 11], "your": [4, 11], "favorit": [4, 11], "case": [4, 10], "all": [4, 11], "individu": 4, "work": [4, 10], "them": 4, "automat": [4, 11], "howev": 4, "specif": 4, "think": 4, "particlar": 4, "valuabl": 4, "feel": 4, "free": 4, "now": 4, "merg": 4, "link": [4, 10, 11], "educ": 4, "onlin": [4, 11, 12, 13], 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    Working with objects in 2D and 3D

    Research Data Management Seminar - Slides#

    +

    By Della Chiesa, Stefano

    https://zenodo.org/record/6602101