Publication (41)#
2020 BioImage Analysis Survey: Community experiences and needs for the future#
[‘Nasim Jamali’, ‘Ellen T. A. Dobson’, ‘Kevin W. Eliceiri’, ‘Anne E. Carpenter’, ‘Beth A. Cimini’]
Published 2021
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis
Content type: Publication
A Cloud-Optimized Storage for Interactive Access of Large Arrays#
[‘Josh Moore’, ‘Susanne Kunis’]
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication, Conference Abstract
A Hitchhiker’s guide through the bio-image analysis software universe#
[‘Robert Haase’, ‘Elnaz Fazeli’, ‘David Legland’, ‘Michael Doube’, ‘Siân Culley’, ‘Ilya Belevich’, ‘Eija Jokitalo’, ‘Martin Schorb’, ‘Anna Klemm’, ‘Christian Tischer’]
Licensed CC-BY-4.0
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: Bioimage Analysis
Content type: Publication
https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451
A biologist’s guide to planning and performing quantitative bioimaging experiments#
[‘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’]
Licensed BSD-3-CLAUSE
Content type: Collection, Publication
A call for public archives for biological image data#
[‘Jan Ellenberg’, ‘Jason R. Swedlow’, ‘Mary Barlow’, ‘Charles E. Cook’, ‘Ugis Sarkans’, ‘Ardan Patwardhan’, ‘Alvis Brazma’, ‘Ewan Birney’]
Tags: Research Data Management
Content type: Publication
A practical guide to bioimaging research data management in core facilities#
[‘Christian Schmidt’, ‘Tom Boissonnet’, ‘Julia Dohle’, ‘Karen Bernhardt’, ‘Elisa Ferrando-May’, ‘Tobias Wernet’, ‘Roland Nitschke’, ‘Susanne Kunis’, ‘Stefanie Weidtkamp-Peters’]
Tags: Research Data Management
Content type: Publication
A study on long-term reproducibility of image analysis results on ImageJ and Fiji#
[‘Robert Haase’, ‘Deborah Schmidt’, ‘Wayne Rasband’, ‘Curtis Rueden’, ‘Florian Jug’, ‘Pavel Tomancak’, ‘Eugene W. Myers’]
Tags: Imagej
Content type: Publication, Poster
https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525
BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data#
[‘Christian Tischer’, ‘Ashis Ravindran’, ‘Sabine Reither’, ‘Nicolas Chiaruttini’, ‘Rainer Pepperkok’, ‘Nils Norlin’]
Licensed CC-BY-4.0
Tags: Research Data Management, Bioimage Analysis
Content type: Publication
BioEngine#
[‘Jeremy Metz’, ‘Beatriz Serrano-Solano’, ‘Wei Ouyang’]
Licensed UNKNOWN
BioEnging is a cloud infrastructure to run BioImage model zoo based workflows in the cloud.
Tags: Artificial Intelligence, Workflow Engine
Content type: Publication
Bridging Imaging Users to Imaging Analysis - A community survey#
[‘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
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis
Content type: Publication, Preprint
Building a FAIR image data ecosystem for microscopy communities#
[‘Isabel Kemmer’, ‘Antje Keppler’, ‘Beatriz Serrano-Solano’, ‘Arina Rybina’, ‘Buğra Özdemir’, ‘Johanna Bischof’, ‘Ayoub El Ghadraoui’, ‘John E. Eriksson’, ‘Aastha Mathur’]
Tags: Research Data Management
Content type: Publication
https://link.springer.com/article/10.1007/s00418-023-02203-7
CLIJ: GPU-accelerated image processing for everyone#
[‘Robert Haase’, ‘Loic Royer’, ‘et al.’]
Published 2020
Licensed ALL RIGHTS RESERVED
CLIJ is a collection of image processing functions that use graphics processing units for accelerated processing.
Tags: Imagej, Bioimage Analysis
Content type: Publication
Challenges and opportunities for bioimage analysis core-facilities#
[‘Johannes Richard Soltwedel’, ‘Robert Haase’]
Licensed CC-BY-4.0
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: Bioimage Analysis, Research Data Management
Content type: Publication
Community-developed checklists for publishing images and image analyses#
[‘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’]
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Publication
Developing open-source software for bioimage analysis: opportunities and challenges#
[‘Florian Levet’, ‘Anne E. Carpenter’, ‘Kevin W. Eliceiri’, ‘Anna Kreshuk’, ‘Peter Bankhead’, ‘Robert Haase’]
Licensed CC-BY-4.0
This article outlines common challenges and practices when developing open-source software for bio-image analysis.
Tags: Neubias
Content type: Publication
EDAM-bioimaging: The ontology of bioimage informatics operations, topics, data, and formats (update 2020)#
[‘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’]
Licensed CC-BY-4.0
Tags: Meta Data
Content type: Publication, Poster
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists#
[‘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
Licensed CC-BY-4.0
Tags: Bioimage Analysis, Neubias
Content type: Publication
Image Data Resources#
Content type: Collection, Data, Publication
JIPipe: visual batch processing for ImageJ#
[‘Ruman Gerst’, ‘Zoltán Cseresnyés’, ‘Marc Thilo Figge’]
JIPipe is an open-source visual programming language for easy-access pipeline development
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community#
[‘Susanne Kunis’, ‘Sebastian Hänsch’, ‘Christian Schmidt’, ‘Frances Wong’, ‘Caterina Strambio-De-Castillia’, ‘Stefanie Weidtkamp-Peters’]
Licensed ALL RIGHTS RESERVED
Tags: Research Data Management, Meta Data
Content type: Publication
Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration#
[‘Anjalie Schlaeppi’, ‘Wilson Adams’, ‘Robert Haase’, ‘Jan Huisken’, ‘Ryan B. MacDonald’, ‘Kevin W. Eliceiri’, ‘Elisabeth C. Kugler’]
Licensed CC-BY-4.0
Tags: Bioimage Analysis
Content type: Publication
https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full
Metadata matters: access to image data in the real world#
[‘Melissa Linkert’, ‘et al.’]
Published 2010
Tags: Meta Data
Content type: Publication
https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real
MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text#
[‘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’]
Tags: Meta Data
Content type: Publication
MiToBo - A Toolbox for Image Processing and Analysis#
[‘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
Content type: Publication, Documentation
https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications#
[‘Alessandro Rigano’, ‘et al.’]
Tags: Meta Data
Content type: Publication
ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ#
[‘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
Content type: Publication, Documentation
NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data#
[‘Christian Schmidt’, ‘Elisa Ferrando-May’]
Licensed CC-BY-SA-4.0
Tags: Nfdi4Bioimage, Research Data Management
Content type: Poster, Publication
NFDI4BIOIMAGE: Perspective for a national bioimaging standard#
[‘Josh Moore’, ‘Susanne Kunis’]
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage
Content type: Publication
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon)#
[‘Mohamed M. Abdrabbou’, ‘Mehrnaz Babaki’, ‘Tom Boissonnet’, ‘Michele Bortolomeazzi’, ‘Eik Dahms’, ‘Vanessa A. F. Fuchs’, ‘Moritz Hoevels’, ‘Niraj Kandpal’, ‘Christoph Möhl’, ‘Joshua A. Moore’, ‘Astrid Schauss’, ‘Andrea Schrader’, ‘Torsten Stöter’, ‘Julia Thönnißen’, ‘Monica Valencia-S.’, ‘H. Lukas Weil’, ‘Jens Wendt and Peter Zentis’]
Licensed CC-BY-4.0
Tags: Arc, Dataplant, Hackathon, Nfdi4Bioimage, Omero, Python, Research Data Management
Content type: Event, Publication, Documentation
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies#
[‘Josh Moore’, ‘Chris Allan’, ‘Sébastien Besson’, ‘Jean-Marie Burel’, ‘Erin Diel’, ‘David Gault’, ‘Kevin Kozlowski’, ‘Dominik Lindner’, ‘Melissa Linkert’, ‘Trevor Manz’, ‘Will Moore’, ‘Constantin Pape’, ‘Christian Tischer’, ‘Jason R. Swedlow’]
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication
OMERO for microscopy research data management#
[‘Thomas Zobel’, ‘Sarah Weischner’, ‘Jens Wendt’]
Licensed ALL RIGHTS RESERVED
A use case example from the Münster Imaging Network
Tags: Nfdi4Bioimage, Omero, Research Data Management
Content type: Publication
https://analyticalscience.wiley.com/do/10.1002/was.0004000267/
Open microscopy in the life sciences: quo vadis?#
[‘Johannes Hohlbein’, ‘Benedict Diederich’, ‘Barbora Marsikova’, ‘Emmanuel G. Reynaud’, ‘Séamus Holden’, ‘Wiebke Jahr’, ‘Robert Haase’, ‘Kirti Prakash’]
Published 2022
Licensed ALL RIGHTS RESERVED
This comment article outlines the current state of the art in open hardware publishing in the context of microscopy.
Content type: Publication
Photonic data analysis in 2050#
[‘Oleg Ryabchykov’, ‘Shuxia Guo’, ‘Thomas Bocklitz’]
Licensed CC-BY-4.0
Photonic data analysis, combining imaging, spectroscopy, machine learning, and computer science, requires flexible methods and interdisciplinary collaborations to advance. Essential developments include standardizing data infrastructure for comparability, optimizing data-driven models for complex investigations, and creating techniques to handle limited or unbalanced data and device variations.
Tags: Fair-Principles, Machine Learning, Research Data Management
Content type: Publication
Plants & Python - A series of lessons in coding, plant biology, computation, and bioinformatics#
[‘Dan Chitwood’, ‘Sourabh Palande’]
Tags: Notebook
Content type: Publication
https://academic.oup.com/plcell/article/34/7/e1/6628764
https://plantsandpython.github.io/PlantsAndPython/00_Opening_page.html
QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy#
[‘Glyn Nelson’, ‘Ulrike Boehme’, ‘et al.’]
Licensed CC-BY-4.0
Tags: Quareo-Limi
Content type: Publication
REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology#
[‘Ugis Sarkans’, ‘et al.’]
Licensed ALL RIGHTS RESERVED
Tags: Research Data Management, Meta Data
Content type: Publication
Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey#
[‘Christian Schmidt’, ‘Janina Hanne’, ‘Josh Moore’, ‘Christian Meesters’, ‘Elisa Ferrando-May’, ‘Stefanie Weidtkamp-Peters’, ‘members of the NFDI4BIOIMAGE initiative’]
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication
Setting up a data management infrastructure for bioimaging#
[‘Susanne Kunis’, ‘Karen Bernhardt’, ‘Michael Hensel’]
Licensed UNKNOWN
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication
SpatialData: an open and universal data framework for spatial omics#
[‘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’]
Licensed CC-BY-4.0
Tags: Python
Content type: Publication, Preprint
https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract
The Fiji Updater#
[‘Robert Haase’]
Licensed ALL RIGHTS RESERVED
Article about the Fiji Updater explaining how it works in the background.
Tags: Imagej
Content type: Publication
https://analyticalscience.wiley.com/do/10.1002/was.0004000112/