Publication (60)#
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
BIOMERO - A scalable and extensible image analysis framework#
Torec T. Luik, Rodrigo Rosas-Bertolini, Eric A.J. Reits, Ron A. Hoebe, Przemek M. Krawczyk
Published None
Licensed CC-BY-4.0
The authors introduce BIOMERO (bioimage analysis in OMERO), a bridge connecting OMERO, a renowned bioimaging data management platform, FAIR workflows, and high-performance computing (HPC) environments.
Tags: OMERO, Workflow, Bioimage Analysis, Image Data Management
Content type: Publication
Best practice data life cycle approaches for the life sciences#
Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, et al.
Published 2018-06-04
Licensed UNKNOWN
The authors provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis.
Tags: Bioinformatics, Reproducibility, Research Data Management, Sharing, Open Science
Content type: Publication
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
Bioimage Archive#
Content type: Collection, Data, Publication
https://www.ebi.ac.uk/bioimage-archive/
https://www.sciencedirect.com/science/article/abs/pii/S0022283622000791
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: Metadata
Content type: Publication, Poster
Erstellung und Realisierung einer institutionellen Forschungsdaten-Policy#
Uli Hahn, Kerstin Helbig, Gerald Jagusch, Jessica Rex
Published 2018-10-22
Licensed CC-BY-4.0
Die vorliegende Empfehlung sowie die zugehörigen Erfahrungsberichte geben einen Überblick über die verschiedenen Möglichkeiten der Gestaltung einer Forschungsdatenmanagement Policy sowie Wege zu deren Erstellung.
Tags: Research Data Management
Content type: Publication
FAIR High Content Screening in Bioimaging#
Rohola Hosseini, Matthijs Vlasveld, Joost Willemse, Bob van de Water, Sylvia E. Le Dévédec, Katherine J. Wolstencroft
Published 2023-07-17
Licensed CC-BY-4.0
The authors show the utility of Minimum Information for High Content Screening Microscopy Experiments (MIHCSME) for High Content Screening (HCS) data using multiple examples from the Leiden FAIR Cell Observatory, a Euro-Bioimaging flagship node for high content screening and the pilot node for implementing FAIR bioimaging data throughout the Netherlands Bioimaging network.
Tags: FAIR-Principles, Metadata, Research Data Management, Image Data Management, Bioimage Data
Content type: Publication
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
Insights and Impact From Five Cycles of Essential Open Source Software for Science#
Kate Hertweck, Carly Strasser, Dario Taraborelli
Licensed CC-BY-4.0
Open source software (OSS) is essential for advancing scientific discovery, particularly in biomedical research, yet funding to support these vital tools has been limited. The Chan Zuckerberg Initiative’s Essential Open Source Software for Science (EOSS) program has significantly contributed to this field by providing $51.8 million in funding over five years to support the maintenance, growth, and community engagement of critical OSS tools. The program has impacted scientific OSS projects by improving their technical outputs, community building, and sustainability practices, and fostering collaborations within the OSS community. Additionally, EOSS funding has enhanced diversity, equity, and inclusion within the OSS community, although changes in principal investigator demographics were not observed. The funded projects have had a substantial impact on biomedical research by improving the usability and accessibility of scientific software, which has led to increased adoption and advancements in various biomedical fields.
Tags: Open Source Software, Funding, Sustainability
Content type: 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
Leitlinie? Grundsätze? Policy? Richtlinie? – Forschungsdaten-Policies an deutschen Universitäten#
Bea Hiemenz, Monika Kuberek
Published 2018-07-13
Licensed CC-BY-4.0
As a methodological approach, research data policies of German universities are collected and evaluated, and compared to international recommendations on research data policies.
Tags: Research Data Management, FAIR-Principles
Content type: Publication
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, Metadata
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: Metadata
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: Metadata
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: Metadata
Content type: Publication
Microscopy-BIDS - An Extension to the Brain Imaging Data Structure for Microscopy Data#
Marie-Hélène Bourget, Lee Kamentsky, Satrajit S. Ghosh, Giacomo Mazzamuto, Alberto Lazari, et al.
Published 2022-04-19
Licensed CC-BY-4.0
The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way.
Tags: Research Data Management, Image Data Management, Bioimage Data
Content type: Publication
https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.871228/full
Modeling community standards for metadata as templates makes data FAIR#
Mark A Musen, Martin J O’Connor, Erik Schultes, Marcos Martínez-Romero, Josef Hardi, John Graybeal
Published 2022-11-12
Licensed CC-BY-4.0
The authors have developed a model for scientific metadata, and they have made that model usable by both CEDAR and FAIRware. The approach shows that a formal metadata model can standardize reporting guidelines and that it can enable separate software systems to assist (1) in the authoring of standards-adherent metadata and (2) in the evaluation of existing metadata.
Tags: Data Stewardship, FAIR-Principles, Metadata
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
Multimodal large language models for bioimage analysis#
Shanghang Zhang, Gaole Dai, Tiejun Huang, Jianxu Chen
Licensed [‘CC-BY-NC-SA’]
Multimodal large language models have been recognized as a historical milestone in the field of artificial intelligence and have demonstrated revolutionary potentials not only in commercial applications, but also for many scientific fields. Here we give a brief overview of multimodal large language models through the lens of bioimage analysis and discuss how we could build these models as a community to facilitate biology research
Tags: Bioimage Analysis, Large Language Models, FAIR-Principles, Workflow
Content type: Publication
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, Wah Chiu, Lucy Collinson, Michele C. Darrow, Jan Ellenberg, David Grunwald, et al.
Published 2021-05-21
Licensed UNKNOWN
Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. The authors propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy.
Tags: Metadata, Bioimage Data, Image Data Management, Research Data Management
Content type: Publication
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015/
Research Data Reusability - Conceptual Foundations, Barriers and Enabling Technologies#
Costantino Thanos
Published 2017-01-09
Licensed CC-BY-4.0
This article discusses various aspects of data reusability in the context of scientific research, including technological, legal, and policy frameworks.
Tags: Research Data Management, Open Science, Data Protection
Content type: Publication
Research data management for bioimaging - the 2021 NFDI4BIOIMAGE community survey#
Christian Schmidt, Janina Hanne, Josh Moore, Christian Meesters, Elisa Ferrando-May, et al.
Published 2022-09-20
Licensed CC-BY-4.0
As an initiative within Germany’s National Research Data Infrastructure, the authors conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs.
Tags: Research Data Management, Image Data Management, Bioimage 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
Ten simple rules for making training materials FAIR#
Leyla Garcia, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis Psomopoulos, et al.
Published 2020-05-21
Licensed CC-BY-4.0
The authors offer trainers some simple rules, to help make their training materials FAIR, enabling others to find, (re)use, and adapt them.
Tags: Metadata, Bioinformatics, FAIR-Principles, Training
Content type: Publication
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854
The BioImage Archive – Building a Home for Life-Sciences Microscopy Data#
Matthew Hartley, Gerard J. Kleywegt, Ardan Patwardhan, Ugis Sarkans, Jason R. Swedlow, Alvis Brazma
Published 2022-06-22
Licensed UNKNOWN
The BioImage Archive is a new archival data resource at the European Bioinformatics Institute (EMBL-EBI).
Tags: Image Data Management, Research Data Management, Bioimage Data
Content type: Publication
https://www.sciencedirect.com/science/article/pii/S0022283622000791?via%3Dihub
The FAIR Guiding Principles for scientific data management and stewardship#
Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, et. al
Published 2016-03-15
Licensed CC-BY-4.0
This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
Tags: FAIR-Principles, Research Data Management
Content type: Publication
The FAIR guiding principles for data stewardship - fair enough?#
Martin Boeckhout, Gerhard A. Zielhuis, Annelien L. Bredenoord
Published 2018-05-17
Licensed CC-BY-4.0
The FAIR guiding principles for research data stewardship (findability, accessibility, interoperability, and reusability) look set to become a cornerstone of research in the life sciences. A critical appraisal of these principles in light of ongoing discussions and developments about data sharing is in order.
Tags: FAIR-Principles, Data Stewardship, Sharing
Content type: Publication
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/
The Open Microscopy Environment (OME) Data Model and XML file - open tools for informatics and quantitative analysis in biological imaging#
Ilya G. Goldberg, Chris Allan, Jean-Marie Burel, Doug Creager, Andrea Falconi, et. al
Published 2005-05-03
Licensed CC-BY-4.0
The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results.
Tags: Microscopy Image Analysis, Bioimage Analysis
Content type: Publication
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47
Towards community-driven metadata standards for light microscopy - tiered specifications extending the OME model#
Mathias Hammer, Maximiliaan Huisman, Alessandro Rigano, Ulrike Boehm, James J. Chambers, et al.
Published 2022-07-10
Licensed UNKNOWN
Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata specifications that extend the OME data model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.
Tags: Reproducibility, Microscopy Image Analysis, Metadata, Image Data Management, Bioimage Data
Content type: Publication
Using Glittr.org to find, compare and re-use online training materials#
Geert van Geest, Yann Haefliger, Monique Zahn-Zabal, Patricia M. Palagi
Licensed CC-BY-4.0
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.
Tags: Training, Bioimage Analysis, Research Data Management
Content type: Publication, Preprint
https://www.biorxiv.org/content/10.1101/2024.08.20.608021v1