Nfdi4bioimage (22)#
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
Bio-Image Data Strudel for Workshop on Research Data Management in TU Dresden Core Facilities#
[‘Cornelia Wetzker’]
Published 2023-11-08
Licensed CC-BY-4.0
This presentation gives a short outline of the complexity of data and metadata in the bioimaging universe. It introduces NFDI4BIOIMAGE as a newly formed consortium as part of the German ‘Nationale Forschungsdateninfrastruktur’ (NFDI) and its goals and tools for data management including its current members on TU Dresden campus.
Tags: Research Data Management, Tu Dresden, Bioimage Data, Nfdi4Bioimage
Content type: Slide
Challenges and opportunities for bio-image analysis core-facilities#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Research Data Management, Bio-Image Analysis, Nfdi4Bioimage
Content type: Slide
I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training#
[‘Christian Schmidt’, ‘Michele Bortolomeazzi’, ‘Tom Boissonnet’, ‘Carsten Fortmann-Grote’, ‘Julia Dohle’, ‘Peter Zentis’, ‘Niraj Kandpal’, ‘Susanne Kunis’, ‘Thomas Zobel’, ‘Stefanie Weidtkamp-Peters’, ‘Elisa Ferrando-May’]
Published 2023-11-13
Licensed CC-BY-4.0
The open-source software OME Remote Objects (OMERO) is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community. The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers’ daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the Research Data Management for Microscopy group (RDM4mic) in Germany, and in the use cases in the I3D:bio project, we created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.
Tags: Omero, Research Data Management, Nfdi4Bioimage, I3Dbio
Content type: Slide, Video
https://zenodo.org/records/8323588
https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU
NFDI4BIOIMAGE#
[‘Carsten Fortmann.Grote’]
Licensed CC-BY-4.0
Presentation was given at the 2nd MPG-NFDI Workshop on April 18th about e NFDI4BIOIMAGE Consortium, FAIRification of Image (meta)data, Zarr, RFC, Training (TA5), contributing.
Tags: Research Data Management, Bioimage Analysis, Fair-Principles, Zarr, Nfdi4Bioimage
Content type: Slides
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 - National Research Data Infrastructure for Microscopy and BioImage Analysis - Online Kick-Off 2023#
[‘Stefanie Weidtkamp-Peters’]
Licensed CC-BY-4.0
NFDI4BIOIMAGE core mission, bioimage data challenge, task areas, FAIR bioimage workflows.
Tags: Research Data Management, Fair-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and BioImage Analysis [conference talk: The Pelagic Imaging Consortium meets Helmholtz Imaging, 5.10.2023, Hamburg]#
[‘Riccardo Massei’]
Licensed CC-BY-4.0
NFDI4BIOIMAGE is a consortium within the framework of the National Research Data Infrastructure (NFDI) in Germany. In this talk, the consortium and the contribution to the work programme by the Helmholtz Centre for Environmental Research (UFZ) in Leipzig are outlined.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
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
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne-Hackathon-2023, GitHub repository)#
[‘Mohamed Abdrabbou’, ‘Mehrnaz Babaki’, ‘Tom Boissonnet’, ‘Michele Bortolomeazzi’, ‘Eik Dahms’, ‘Vanessa Fuchs’, ‘A. F. 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’, ‘Peter Zentis’]
Licensed CC-BY-4.0
This repository documents the first NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon), where topics like ‘Interoperability’, ‘REMBI / Mapping’, and ‘Neuroglancer (OMERO / zarr)’ were explored through collaborative discussions and workflow sessions, culminating in reports that bridge NFDI4Bioimage to DataPLANT. Funded by various DFG initiatives, this event emphasized documentation and use cases, contributing preparatory work for future interoperability projects at the 2nd de.NBI BioHackathon in Bielefeld.
Tags: Research Data Management, Fair-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Github Repository
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/
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
Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data#
[‘Susanne Kunis’]
Published 2022-08-24
Licensed CC-BY-4.0
guided walkthrough of poster at https://doi.org/10.5281/zenodo.6821815
which provides an overview of contexts, frameworks, and models from the world of bioimage data as well as metadata and the techniques for structuring this data as Linked Data.
You can also watch the video in the browser on the I3D:bio website.
Tags: Nfdi4Bioimage, Research Data Management
Content type: Video
Thinking data management on different scales#
[‘Susanne Kunis’]
Licensed CC-BY-4.0
Presentation given at PoL BioImage Analysis Symposium Dresden 2023
Tags: Research Data Management, Nfdi4Bioimage
Content type: Slides
Welcome to BioImage Town#
[‘Josh Moore’]
Licensed CC-BY-4.0
Welcome at NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023
Tags: Omero, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
Who you gonna call? - Data Stewards to the rescue#
[‘Vanessa Fuchs’, ‘Aphaia Fiona’, ‘Jens Wendt’, ‘Maximilian Müller’, ‘Mohsen Ahmadi’, ‘Riccardo Massei’, ‘Cornelia Wetzker’]
Licensed CC-BY-4.0
The Data Steward Team of the NFDI4BIOIMAGE consortium presents themselves and the services (including the Helpdesk) that we offer.
Tags: Research Data Management, Bioimage Analysis, Data Stewardship, Nfdi4Bioimage
Content type: Poster
[ELMI 2024] AI’s Dirty Little Secret: Without FAIR Data, It’s Just Fancy Math#
[‘Josh Moore’, ‘Susanne Kunis’]
Licensed CC-BY-4.0
Poster presented at the European Light Microscopy Initiative meeting in Liverpool (https://www.elmi2024.org/)
Tags: Research Data Management, Fair-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Poster
[SWAT4HCLS 2023] NFDI4BIOIMAGE: Perspective for a national bioimage standard#
[‘Josh Moore’, ‘Susanne Kunis’]
Licensed CC-BY-4.0
Poster presented at Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Feb 13–16, 2023, Basel, Switzerland. NFDI4BIOIMAGE is a newly established German consortium dedicated to the FAIR representation of biological imaging data. A key deliverable is the definition of a semantically-compatible FAIR image object integrating RDF metadata with web-compatible storage of large n-dimensional binary data in OME-Zarr. We invite feedback from and collaboration with other endeavors during the soon-to-begin 5 year funding period.
Tags: Research Data Management, Fair-Principles, Nfdi4Bioimage
Content type: Poster
[Short Talk] NFDI4BIOIMAGE - A consortium in the National Research Data Infrastructure#
[‘Christian Schmidt’]
Licensed CC-BY-4.0
Short Talk about the NFDI4BIOIMAGE consortium presented at the RDM in (Bio-)Medicine Information Event on April 10th, 2024, organized C³RDM & ZB MED.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
https://zenodo.org/doi/10.5281/zenodo.10939519