Fair-principles (16)#
Combining the BIDS and ARC Directory Structures for Multimodal Research Data Organization#
[‘Torsten Stöter’, ‘Tobias Gottschall’, ‘Andrea Schrader’, ‘Peter Zentis’, ‘Monica Valencia-Schneider’, ‘Niraj Kandpal’, ‘Werner Zuschratter’, ‘Astrid Schauss’, ‘Timo Dickscheid’, ‘Timo Mühlhaus’, ‘Dirk von Suchodoletz’]
Licensed CC-BY-4.0
Interdisciplinary collaboration and integrating large, diverse datasets are crucial for answering complex research questions, requiring multimodal data analysis and adherence to FAIR principles. To address challenges in capturing the full research cycle and contextualizing data, DataPLANT developed the Annotated Research Context (ARC), while the neuroimaging community extended the Brain Imaging Data Structure (BIDS) for microscopic image data, both providing standardized, file system-based storage structures for organizing and sharing data with metadata.
Tags: Research Data Management, Fair-Principles
Content type: Poster
Cultivating Open Training#
[‘Robert Haase’]
Published 2024-03-14
Licensed CC-BY-4.0
In this SaxFDM Digital Kitchen, I introduced current challenges and potential solutions for openly sharing training materials, softly focusing on bio-image analysis. In this field a lot of training materials circulate in private channels, but openly shared, reusable materials, according to the FAIR-principles, are still rare. Using the CC-BY license and uploading materials to publicly acessible repositories are proposed to fill this gap.
Tags: Open Science, Research Data Management, Fair-Principles, Bio-Image Analysis, Licensing
Content type: Slides
Cultivating Open Training to advance Bio-image Analysis#
[‘Robert Haase’]
Published 2024-04-25
Licensed CC-BY-4.0
These slides introduce current challenges and potential solutions for openly sharing training materials, focusing on bio-image analysis. In this field a lot of training materials circulate in private channels, but openly shared, reusable materials, according to the FAIR-principles, are still rare. Using the CC-BY license and publicly acessible repositories are proposed to fill this gap.
Tags: Research Data Management, Licensing, Fair-Principles
Content type: Slides
Euro-BioImaging’s Guide to FAIR BioImage Data - Practical Tasks#
[‘Isabel Kemmer’, ‘Euro-BioImaging ERIC’]
Published 2024-06-04
Licensed CC-BY-4.0
Hands-on exercises on FAIR Bioimage Data from the interactive online workshop “Euro-BioImaging’s Guide to FAIR BioImage Data 2024” (https://www.eurobioimaging.eu/news/a-guide-to-fair-bioimage-data-2024/). Types of tasks included: FAIR characteristics of a real world dataset Data Management Plan (DMP) Journal Policies on FAIR data sharing Ontology search Metadata according to REMBI scheme (Image from: Sarkans, U., Chiu, W., Collinson, L. et al. REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology. Nat Methods 18, 1418–1422 (2021). https://doi.org/10.1038/s41592-021-01166-8) Matching datasets to bioimage repositories Browsing bioimage repositories
Tags: Bioimage Analysis, Fair-Principles, Research Data Management
Content type: Slides, Tutorial
Euro-BioImaging’s Template for Research Data Management Plans#
[‘Isabel Kemmer’, ‘Euro-BioImaging ERIC’]
Published 2024-06-04
Licensed CC-BY-4.0
Euro-BioImaging has developed a Data Management Plan (DMP) template with questions tailored to bioimaging research projects. Outlining data management practices in this way ensures traceability of project data, allowing for a continuous and unambiguous flow of information throughout the research project. This template can be used to satisfy the requirement to submit a DMP to certain funders. Regardless of the funder, Euro-BioImaging users are encouraged to provide a DMP and can use this template accordingly. This DMP template is available as a fillable PDF with further instructions and sample responses available by hovering over the fillable fields.
Tags: Bioimage Analysis, Fair-Principles, Research Data Management
Content type: Collection, Tutorial
FAIRy deep-learning for bioImage analysis#
[‘Estibaliz Gómez de Mariscal’]
Licensed CC-BY-4.0
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 and reproducible manner (BioImage Model Zoo) are introduced.
Tags: Deep Learning, Fair-Principles, Microscopy Image Analysis
Content type: Slides
Kollaboratives Arbeiten und Versionskontrolle mit Git#
[‘Robert Haase’]
Published 2024-04-15
Licensed CC-BY-4.0
Gemeinsames Arbeiten im Internet stellt uns vor neue Herausforderungen: Wer hat eine Datei wann hochgeladen? Wer hat zum Inhalt beigetragen? Wie kann man Inhalte zusammenfuehren, wenn mehrere Mitarbeiter gleichzeitig Aenderungen gemacht haben? Das Versionskontrollwerkzeug git stellt eine umfassende Loesung fuer solche Fragen bereit. Die Onlineplatform github.com stellt nicht nur Softwareentwicklern weltweit eine git-getriebene Platform zur Verfuegung und erlaubt ihnen effektiv zusammen zu arbeiten. In diesem Workshop lernen wir:
Infuerung in FAIR-Prinzipien im Softwarecontext Arbeiten mit git: Pull-requests Aufloesen von Merge-Konflikten Automatisiertes Archivieren von Inhalten nach Zenodo.org Eigene Webseiten auf github.io publizieren
Tags: Research Data Management, Fair-Principles, Git, Zenodo
Content type: Slides
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 - 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 - 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
Open Science, Sharing & Licensing#
[‘Robert Haase’]
Published 2024-04-18
Licensed CC-BY-4.0
Wir tauchen ein in die Welt der Open Science und definieren Begriffe wie Open Source, Open Access und die FAIR-Prinzipien (Findable, Accessible, Interoperable and Reuasable). Wir diskutieren, wie diese Methoden der [wissenschaftlichen] Kommunikation und des Datenmanagements die Welt verändern und wie wir sie praktisch in unsere Arbeit integrieren können. Dabei spielen Aspekte wie Copyright und Lizenzierung eine wichtige Rolle.
Tags: Research Data Management, Open Access, Fair-Principles, Licensing
Content type: Slides
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
RDF as a bridge to domain-platforms like OMERO, or There and back again.#
[‘Josh Moore’, ‘Andra Waagmeester’, ‘Kristina Hettne’, ‘Katherine Wolstencroft’, ‘Susanne Kunis’]
Licensed CC-BY-4.0
In 2005, the first version of OMERO stored RDF natively. However, just a year after the 1.0 release of RDF, performance considerations led to the development of a more traditional SQL approach for OMERO. A binary protocol makes it possible to query and retrieve metadata but the resulting information cannot immediately be combined with other sources. This is the adventure of rediscovering the benefit of RDF triples as a – if not the – common exchange mechanism.
Tags: Research Data Management, Fair-Principles, Bioimage Analysis
Content type: Slides
So geschlossen wie nötig, so offen wie möglich - Datenschutz beim Umgang mit Forschungsdaten#
[‘Pia Voigt’]
Published 2024-05-30
Licensed CC-BY-4.0
Der Umgang mit personenbezogenen Daten stellt Forschende oft vor rechtliche Herausforderungen: Unter welchen Bedingungen dürfen personenbezogene Daten verarbeitet werden? Welche Voraussetzungen müssen erfüllt sein und welche Strategien können angewendet werden, um Daten sicher speichern, verarbeiten, teilen und aufbewahren zu können? Mit Hilfe dieses Foliensatzes erhalten Sie Einblicke in datenschutzrechtliche Aspekte beim Umgang mit Ihren Forschungsdaten.
Tags: Research Data Management, Data Protection, Fair-Principles
Content type: Slides
[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
https://zenodo.org/doi/10.5281/zenodo.7928332