Research data management (148)#
“ZENODO und Co.” Was bringt und wer braucht ein Repositorium?#
Elfi Hesse, Jan-Christoph Deinert, Christian Löschen
Published 2021-01-25
Licensed CC-BY-4.0
Die Online-Veranstaltung fand am 21.01.2021 im Rahmen der SaxFDM-Veranstaltungsreihe “Digital Kitchen - Küchengespräche mit SaxFDM” statt. SaxFDM-Sprecherin Elfi Hesse (HTW Dresden) erläuterte zunächst Grundsätzliches zum Thema Repositorien. Anschließend teilten Nutzer (Jan Deinert – HZDR) und Anbieter (Christian Löschen – TU Dresden/ZIH) lokaler Repositorien ihre Erfahrungen mit uns.
Tags: Research Data Management, Include In Dalia
Content type: Slides
6 Steps Towards Reproducible Research#
Heidi Seibold
Licensed CC-BY-4.0
A short book with 6 steps that get you closer to making your work reproducible.
Tags: Reproducibility, Research Data Management, Include In Dalia
Content type: Book
A Cloud-Optimized Storage for Interactive Access of Large Arrays#
Josh Moore, Susanne Kunis
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Content type: Publication, Conference Abstract
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, Exclude From Dalia
Content type: Publication
A checklist for designing and improving the visualization of scientific data#
Helena Klara Jambor
Published 2025-06-13
Licensed COPYRIGHT
Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data visualization research in a checklist that can help researchers to improve their data visualization, by focusing on clarity, accessibility and design best practices.
Tags: Copyright, Research Data Management, Exclude From Dalia
Content type: Publication
A journey to FAIR microscopy data#
Stefanie Weidtkamp-Peters, Janina Hanne, Christian Schmidt
Published 2023-05-03
Licensed CC-BY-4.0
Oral presentation, 32nd MoMAN “From Molecules to Man” Seminar, Ulm, online. Monday February 6th, 2023
Abstract:
Research data management is essential in nowadays research, and one of the big opportunities to accelerate collaborative and innovative scientific projects. To achieve this goal, all our data needs to be FAIR (findable, accessible, interoperable, reproducible). For data acquired on microscopes, however, a common ground for FAIR data sharing is still to be established. Plenty of work on file formats, data bases, and training needs to be performed to highlight the value of data sharing and exploit its potential for bioimaging data.
In this presentation, Stefanie Weidtkamp-Peters will introduce the challenges for bioimaging data management, and the necessary steps to achieve data FAIRification. German BioImaging - GMB e.V., together with other institutions, contributes to this endeavor. Janina Hanne will present how the network of imaging core facilities, research groups and industry partners is key to the German bioimaging community’s aligned collaboration toward FAIR bioimaging data. These activities have paved the way for two data management initiatives in Germany: I3D:bio (Information Infrastructure for BioImage Data) and NFDI4BIOIMAGE, a consortium of the National Research Data Infrastructure. Christian Schmidt will introduce the goals and measures of these initiatives to the benefit of imaging scientist’s work and everyday practice.
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
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, Include In Dalia
Content type: Publication
Abstract - NFDI Basic Service for Data Management Plans#
Licensed CC-BY-4.0
The NFDI Basic Service DMP4NFDI supports consortia in developing and providing data management plans (DMP) services for their community.
Tags: Research Data Management, Exclude From Dalia
Content type: Document
Alles meins – oder!? Urheberrechte klären für Forschungsdaten#
Stephan Wünsche
Published 2024-06-04
Licensed CC-BY-4.0
Wem gehören Forschungsdaten? Diese Frage stellt sich bei Daten, an deren Entstehung mehrere Personen beteiligt waren, und besonders bei Textdaten, Bildern und Videos. Hier lernen Sie, für Ihr eigenes Forschungsvorhaben zu erkennen, wessen Urheber- und Leistungsschutzrechte zu berücksichtigen sind. Sie erfahren, wie Sie mit Hilfe von Vereinbarungen frühzeitig Rechtssicherheit herstellen, etwa um Daten weitergeben oder publizieren zu können.
Tags: Research Data Management, Licensing, Include In Dalia
Content type: Slides
Angebote der NFDI für die Forschung im Bereich Zoologie#
Birgitta König-Ries, Robert Haase, Daniel Nüst, Konrad Förstner, Judith Sophie Engel
Published 2024-12-04
Licensed CC-BY-4.0
In diesem Slidedeck geben wir einen Einblick in Angebote und Dienste der Nationalen Forschungsdaten Infrastruktur (NFDI), die Relevant für die Zoologie und angrenzende Disziplinen relevant sein könnten.
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Annotated Research Context (ARC#
Kevin Frey, Kevin Schneider, Lukas Weil, Dominik Brilhaus, Timo Mühlhaus, Manuel Feser, Hannah-Doerpholz
Licensed UNKNOWN
The ARC is a framework for organizing and documenting research data, as well as a container that continuously supports collaboration, data exchange, and adherence to FAIR principles among various researchers. The ARC can be checked for completeness and quality at any time and converted into a citable data publication without interrupting the research or documentation process. It is built on widely accepted research data standards such as RO-Crate, ISA, and abstract CWL.
Tags: Research Data Management, Fair, Exclude From Dalia
Content type: Framework
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, Include In Dalia
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, Exclude From Dalia
Content type: Publication
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, Nfdi4Bioimage, Include In Dalia
Content type: Slides
Bio-image Data Science#
Robert Haase
Licensed CC-BY-4.0
This repository contains training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python.
Tags: Research Data Management, Artificial Intelligence, Bioimage Analysis, Python, Include In Dalia
Content type: Notebook
Bring your own data workshops#
Tags: Bioimage Analysis, Research Data Management, Exclude From Dalia
Content type: Workshop
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, Exclude From Dalia
Content type: Publication
https://link.springer.com/article/10.1007/s00418-023-02203-7
Challenges and opportunities for bio-image analysis core-facilities#
Robert Haase
Licensed CC-BY-4.0
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage, Include In Dalia
Content type: Slides
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, Include In Dalia
Content type: Publication
Collaborative Working and Version Control with git[hub]#
Robert Haase
Published 2024-01-10
Licensed CC-BY-4.0
This slide deck introduces the version control tool git, related terminology and the Github Desktop app for managing files in Git[hub] repositories. We furthermore dive into:* Working with repositories* Collaborative with others* Github-Zenodo integration* Github pages* Artificial Intelligence answering Github Issues
Tags: Nfdi4Bioimage, Globias, Research Data Management, Research Software Management, Include In Dalia
Collaborative bio-image analysis script editing with git#
Robert Haase
Licensed CC-BY-4.0
Introduction to version control using git for collaborative, reproducible script editing.
Tags: Sharing, Research Data Management, Include In Dalia
Content type: Blog Post
Collaborative working and Version Control with Git[Hub]#
Robert Haase
Published 2025-05-10
Licensed CC-BY-4.0
Working together on the internet presents us with new challenges: Who uploaded a file and when? Who contributed to the project when and why? How can content be merged when multiple team members make changes at the same time? The version control tool Git offers a comprehensive solution to these questions. The online platform GitHub.com provides a Git-driven platform that enables effective collaboration. Attendees of this hands-on tutorial will learn:
Introduction to version control with Git[Hub]
Working with Git: Pull requests
Resolving merge conflicts
Artificial intelligence that can respond to GitHub issues
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Combining the BIDS and ARC Directory Structures for Multimodal Research Data Organization#
Torsten Stöter, Tobias Gottschall, Andrea Schrager, Peter Zentis, Monica Valencia-Schneider, Niraj Kandpal, Werner Zuschratter, Astrid Schauss, Timo Dickscheid, Timo Mühlhaus, Dirk von Suchodoletz
Published 2023-09-12
Licensed CC-BY-4.0
Interdisciplinary collaboration and integration of large and diverse datasets are becoming increasingly important. Answering complex research questions requires combining and analysing multimodal datasets. Research data management follows the FAIR principles making data findable, accessible, interoperable, and reusable. However, there are challenges in capturing the entire research cycle and contextualizing data according, not only for the DataPLANT and NFDI4BIOIMAGE communities. To address these challenges, DataPLANT developed a data structure called Annotated Research Context (ARC). The Brain Imaging Data Structure (BIDS) originated from the neuroimaging community extended for microscopic image data. Both concepts provide standardised and file system based data storage structures for organising and sharing research data accompanied with metadata. We exemplarily compare the ARC and BIDS designs and propose structural and metadata mapping.
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
Content type: Poster
Community-developed checklists for publishing images and image analyses#
Beth Cimini et al.
Licensed BSD-3-CLAUSE
This book is a companion to the Nature Methods publication Community-developed checklists for publishing images and image analyses. In this paper, members of QUAREP-LiMi have proposed 3 sets of standards for publishing image figures and image analysis - minimal requirements, recommended additions, and ideal comprehensive goals. By following this guidance, we hope to remove some of the stress non-experts may face in determining what they need to do, and we also believe that researchers will find their science more interpretable and more reproducible.
Tags: Bioimage Analysis, Research Data Management, Include In Dalia
Content type: Notebook, Collection
https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html
Conda, Container and Bots - How to Build and Maintain Tool Dependencies in Workflows and Training Materials#
Paul Zierep, Sanjay Kumar Srikakulam, Sebastian Schaaf, Bjoern Gruening
Published 2023-09-07
Licensed CC-BY-4.0
The lifecycle of scientific tools comprises the creation of code releases, packages and containers which can be deployed into cloud platforms, such as the Galaxy Project, where they are run and integrated into workflows. The tools and workflows are further used to create training material that benefits a broad community. The need to organize and streamline this tool development lifecycle has led to a sophisticated development and deployment architecture.
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
Content type: Publication
Crashkurs Forschungsdatenmanagement#
Barbara Weiner, Stephan Wünsche, Stefan Kühne, Pia Voigt, Sebastian Frericks, Clemens Hoffmann, Romy Elze, Ronny Gey
Published 2020-04-30
Licensed CC-BY-4.0
Diese Präsentation bietet einen Einstieg in alle relevanten Bereiche des Forschungsdatenmanagements an der Universität Leipzig. Behandelt werden Grundlagen des Forschungsdatenmanagements, technische, ethische und rechtliche Aspekte sowie die Archivierung und Publikation von Forschungsdaten. Die Präsentation enthält zahlreiche weiterführende Links (rot) und Literaturhinweise.
Ergänzend hierzu wird eine Präsentation mit Übungsaufgaben angeboten, die helfen soll, das Gelernte zu festigen und in der eigenen Forschungspraxis umzusetzen. Den Aufgaben folgen jeweils eine Antwortfolie sowie deren Auflösung.
Tags: Research Data Management, Include In Dalia
Content type: Slides
Creating a Research Data Management Plan using chatGPT#
Robert Haase
Published 2023-11-06
Licensed CC-BY-4.0
In this blog post the author demonstrates how chatGPT can be used to combine a fictive project description with a DMP specification to produce a project-specific DMP.
Tags: Research Data Management, Artificial Intelligence, Include In Dalia
Content type: Blog Post
https://focalplane.biologists.com/2023/11/06/creating-a-research-data-management-plan-using-chatgpt/
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, Bioimage Analysis, Licensing, Include In Dalia
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, Include In Dalia
Content type: Slides
Data Stewardship Wizard#
Licensed UNKOWN
Leading open-source platform for collaborative and living data management plans.
Tags: Data Stewardship, Open Source, Research Data Management, FAIR-Principles, Exclude From Dalia
Content type: Website, Online Tutorial
Data handling in large-scale electron microscopy#
Job Fermie
Tags: Research Data Management, Include In Dalia
Content type: Blog Post
https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy
Data life cycle#
ELIXIR (2021) Research Data Management Kit
Licensed CC-BY-4.0
In this section, information is organised according to the stages of the research data life cycle.
Tags: Data Life Cycle, Research Data Management, Exclude From Dalia
Content type: Collection, Website, Online Tutorial
Data management at France BioImaging#
Published 2024-29-05
Licensed UNKNOWN
Tags: Research Data Management, Bioimage Analysis, Open Science, Include In Dalia
Content type: Slides, Presentation
DataPLANT knowledge base#
Published 2022-12-14
Licensed CC-BY-4.0
Explore fundamental topics on research data management (RDM), how DataPLANT implements these aspects to support plant researchers with RDM tools and services, read guides and manuals or search for some teaching materials.
Tags: Research Data Management, Dataplant, Include In Dalia
Content type: Collection
https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html
Datenmanagement#
Robert Haase
Published 2024-04-14
Licensed CC-BY-4.0
In dieser Data Management Session wird der Lebenszyklus von Daten näher beleuchtet. Wie entstehen Daten, was passiert mit ihnen, wenn sie verarbeitet werden? Wem gehören die Daten und wer ist dafür verantwortlich, sie zu veröffentlichen, zu archivieren und gegebenenfalls wiederzuverwenden? Wir werden einen Datenmanagementplan in Gruppenarbeit entwerfen, ggf. mit Hilfe von ChatGPT.
Tags: Research Data Management, Include In Dalia
Content type: Slides
Datenmanagement im Fokus: Organisation, Speicherstrategien und Datenschutz#
Pia Voigt, Carolin Hundt
Published 2024-04-19
Licensed CC-BY-4.0
Workshop zum Thema „Datenmanagement im Fokus: Organisation, Speicherstrategien und Datenschutz“ auf der Data Week Leipzig Der Umgang mit Daten ist im Alltag nicht immer leicht: Wie und wo speichert man Daten idealerweise? Welche Strategien helfen, den Überblick zu behalten und wie geht man mit personenbezogenen Daten um? Diese Fragen möchten wir gemeinsam mit Ihnen anhand individueller Datenprobleme besprechen und Ihnen Lösungen aufzeigen, wie Sie ihr Datenmanagement effizient gestalten können.
Tags: Research Data Management, Include In Dalia
Content type: Slides
Datenmanagementpläne erstellen - Teil 1#
Pia Voigt, Barbara Weiner
Published 2021-03-23
Licensed CC-BY-4.0
Was ist ein Datenmanagementplan? Welche Vorgaben sollte ich beachten? Wie erstelle ich einen solchen für mein Forschungsprojekt und welche nützlichen Tools kann ich hierfür verwenden?
Die Anforderungen der Forschungsförderer zum Datenmanagement steigen stetig. Damit verbunden ist häufig auch das Erstellen eines Datenmanagementplans. Dabei erwarten DFG, BMBF oder die EU jeweils unterschiedliche Angaben zur Erhebung, Speicherung und Veröffentlichung von projektbezogenen Forschungsdaten. Zudem bietet das Erstellen eines Datenmanagementplans viele Vorteile und hilft Ihnen nicht zuletzt, die Anforderungen der guten wissenschaftlichen Praxis strukturiert umzusetzen.
Was im ersten Moment unübersichtlich und überfordernd wirkt, soll in diesem Kurs anhand einer grundlegenden theoretischen Einführung im ersten und praxisorientierter Beispiele im zweiten Teil der Veranstaltung handhabbar gemacht werden. Sie lernen, was hinter den Anforderungen der Forschungsförderer steckt, welche Elemente ein Datenmanagementplan enthalten sollte und wie sie einen solchen mithilfe interaktiver Tools selbst erstellen können.
Tags: Research Data Management, Include In Dalia
Content type: Slides
Datenmanagementpläne erstellen - Teil 2#
Pia Voigt, Barbara Weiner
Published 2021-03-30
Licensed CC-BY-4.0
Was ist ein Datenmanagementplan? Welche Vorgaben sollte ich beachten? Wie erstelle ich einen solchen für mein Forschungsprojekt und welche nützlichen Tools kann ich hierfür verwenden?
Die Anforderungen der Forschungsförderer zum Datenmanagement steigen stetig. Damit verbunden ist häufig auch das Erstellen eines Datenmanagementplans. Dabei erwarten DFG, BMBF oder die EU jeweils unterschiedliche Angaben zur Erhebung, Speicherung und Veröffentlichung von projektbezogenen Forschungsdaten. Zudem bietet das Erstellen eines Datenmanagementplans viele Vorteile und hilft Ihnen nicht zuletzt, die Anforderungen der guten wissenschaftlichen Praxis strukturiert umzusetzen.
Was im ersten Moment unübersichtlich und überfordernd wirkt, soll in diesem Kurs anhand einer grundlegenden theoretischen Einführung im ersten und praxisorientierter Beispiele im zweiten Teil der Veranstaltung handhabbar gemacht werden. Sie lernen, was hinter den Anforderungen der Forschungsförderer steckt, welche Elemente ein Datenmanagementplan enthalten sollte und wie sie einen solchen mithilfe interaktiver Tools selbst erstellen können.
Version 2 enthält aktuelle Links und weiterführende Hinweise zu einzelnen Aspekten eines Datenmanagementplans.
Version 3 ist die überarbeitete und aktualisierte Version der ersten beiden und enthält u.a. Hinweise zur Lizenzierung und zu Nutzungsrechten an Forschungsdaten.
Tags: Research Data Management, Include In Dalia
Content type: Slides
Dokumentation und Anleitung zum elektronischen Laborbuch (eLabFTW)#
Lienhard Wegewitz, F. Strauß
Published 2020-03-23
Licensed AGPL-3.0
Documentation for eLabFTW. With eLabFTW you get a secure, modern and compliant system to track your experiments efficiently but also manage your lab with a powerful and versatile database.
Tags: Research Data Management, Exclude From Dalia
Content type: Documentation, Document, Tutorial
https://www.fdm.tu-clausthal.de/fileadmin/FDM/documents/Manual_eLab_v0.3_20200323.pdf
Efficiently starting institutional research data management#
Katarzyna Biernacka, Katrin Cortez, Kerstin Helbig
Published 2019-10-15
Licensed CC-BY-4.0
Researchers are increasingly often confronted with research data management (RDM) topics during their work. Higher education institutions therefore begin to offer services for RDM at some point to give support and advice. However, many groundbreaking decisions have to be made at the very beginning of RDM services. Priorities must be set and policies formulated. Likewise, the staff must first be qualified in order to provide advice and adequately deal with the manifold problems awaiting. The FDMentor project has therefore bundled the expertise of five German universities with different experiences and levels of RDM knowledge to jointly develop strategies, roadmaps, guidelines, and open access training material. Humboldt-Universität zu Berlin, Freie Universität Berlin, Technische Universität Berlin, University of Potsdam, and European University Viadrina Frankfurt (Oder) have worked together on common solutions that are easy to adapt. With funding of the German Federal Ministry of Education and Research, the collaborative project addressed four problem areas: strategy development, legal issues, policy development, and competence enhancement. The aim of the project outcomes is to provide other higher education institutions with the best possible support for the efficient introduction of research data management. Therefore, all project results are freely accessible under the CC-BY 4.0 international license. The early involvement of the community in the form of workshops and the collection of feedback has proven its worth: the FDMentor strategies, roadmaps, guidelines, and training materials are applied and adapted beyond the partner universities.
Tags: Research Data Management, Include In Dalia
Content type: Document
Einblicke ins Forschungsdatenmanagement - Darf ich das veröffentlichen? Rechtsfragen im Umgang mit Forschungsdaten#
Stephan Wünsche, Pia Voigt
Published 2021-05-11
Licensed CC-BY-4.0
Diese Präsentation wurde im Zuge der digitalen Veranstaltungsreihe “Einblicke ins Forschungsdatenmanagement” erstellt. Diese findet seit dem SS 2020 an der Universität Leipzig für alle Interessierten zu verschiedenen Themen des Forschungsdatenmanagements statt.
Dieser Teil der Reihe dreht sich um Rechtsfragen im Umgang mit Forschungsdaten und deren Bedeutung für die wissenschaftliche Praxis. Sie finden in der vorliegenden Präsentation einen Überblick über relevante Rechtsbereiche sowie Erläuterungen zum Datenschutz, Urheberrecht und den Grundsätzen der guten wissenschaftlichen Praxis mit Fokus auf deren Bedeutung im Forschungsdatenmanagement.
Tags: Research Data Management, Data Protection, Include In Dalia
Content type: Slides
Enabling Global Image Data Sharing in the Life Sciences#
Peter Bajcsy, Sreenivas Bhattiprolu, Katy Boerner, Beth A Cimini, Lucy Collinson, Jan Ellenberg, Reto Fiolka, Maryellen Giger, Wojtek Goscinski, Matthew Hartley, Nathan Hotaling, Rick Horwitz, Florian Jug, Anna Kreshuk, Emma Lundberg, Aastha Mathur, Kedar Narayan, Shuichi Onami, Anne L. Plant, Fred Prior, Jason Swedlow,, Adam Taylor, Antje Keppler
Published 2024-01-23
Licensed CC-BY-NC-SA-4.0 INTERNATIONAL
Coordinated collaboration is essential to realize the added value of and infrastructure requirements for global image data sharing in the life sciences. In this White Paper, we take a first step at presenting some of the most common use cases as well as critical/emerging use cases of (including the use of artificial intelligence for) biological and medical image data, which would benefit tremendously from better frameworks for sharing (including technical, resourcing, legal, and ethical aspects).
Tags: Research Data Management, Exclude From Dalia
Content type: Publication
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, Include In Dalia
Content type: Publication
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, Include In Dalia
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, Exclude From Dalia
Content type: Collection, Tutorial
FAIR BioImage Data#
Licensed CC-BY-4.0
Tags: Research Data Management, Fair, Bioimage Analysis, Exclude From Dalia
Content type: Collection, Video
https://www.youtube.com/watch?v=8zd4KTy-oYI&list=PLW-oxncaXRqU4XqduJzwFHvWLF06PvdVm
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, Exclude From Dalia
Content type: Publication
FAIR Priciples#
Licensed CC-BY-4.0
In 2016, the ‘FAIR Guiding Principles for scientific data management and stewardship’ were published in Scientific Data. The authors intended to provide guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets.
Tags: FAIR-Principles, Data Stewardship, Research Data Management, Include In Dalia
Content type: Collection
File Naming Convention Worksheet#
Kristin Briney
Published 2020-06-02
Licensed CC-BY-4.0
This worksheet walks researchers through the process of creating a file naming convention for a group of files. This process includes: choosing metadata, encoding and ordering the metadata, adding version information, and properly formatting the file names. Two versions of the worksheet are available: a Caltech Library branded version and a generic editable version.
Tags: Research Data Management, Include In Dalia
Content type: Worksheet
Finding and Choosing a Data Repository#
Christian Schmidt
Published 2023-07-01
Licensed UNKNOWN
Funding agencies may demand that original source data of a publication be published, too. So the question is - where should one publish the data? And how does it get there?
Tags: I3Dbio, Research Data Management, Include In Dalia
Content type: Tutorial
https://gerbi-gmb.de/2023/06/01/finding-and-choosing-a-repository/
Fit for OMERO: How imaging facilities and IT departments work together to enable RDM for bioimaging#
Starts Oct 16, 2024, 9:00 AM, Ends Oct 17, 2024, 5:00 PM
Tags: Bioimage Analysis, OMERO, Research Data Management, Exclude From Dalia
Content type: Workshop
Forschungsdaten.info#
Licensed PUBLIC DOMAIN
Research Data Management Information Portal in German
Tags: Research Data Management, Include In Dalia
Content type: Collection
Forschungsdaten.org#
Licensed CC-BY-4.0
Research Data Management Wiki in German
Tags: Research Data Management, Include In Dalia
Content type: Collection
Ghent University Research Data Management (RDM) - policy and support#
University of Ghent
Licensed UNKNOWN
The website provides resources and guidelines for managing research data efficiently and responsibly. Its focus is to ensure that data are properly organized, stored, documented, and shared throughout a research project, and even beyond, in a way that aligns with Open Science principles.
Tags: Research Data Management, Exclude From Dalia
Content type: Website
Guidance for Developing a Research Data Management (RDM) Policy#
Published 2017
Licensed CC-BY-4.0
This document provides the essential elements of a Research Data Management (RDM) Policy and is part of the LEARN Toolkit containing the Model Policy for Research Data Management (RDM) at Research Institutions/Institutes.
Tags: Research Data Management, Include In Dalia
Content type: Book
https://discovery.ucl.ac.uk/id/eprint/1546596/1/26_Learn_Guidance_137-140.pdf
Hackaton Results - Conversion of KNIME image analysis workflows to Galaxy#
Riccardo Massei
Licensed CC-BY-4.0
Results of the project ‘Conversion of KNIME image analysis workflows to Galaxy’ during the Hackathon ‘Image Analysis in Galaxy’ (Freiburg 26 Feb - 01 Mar 2024)
Tags: Research Data Management, Exclude From Dalia
Content type: Slides
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data#
Nikki Bialy, Frank Alber, Brenda Andrews, Michael Angelo, Brian Beliveau, Lacramioara Bintu, Alistair Boettiger, Ulrike Boehm, Claire M. Brown, Mahmoud Bukar Maina, James J. Chambers, Beth A. Cimini, Kevin Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N. Germain, Wojtek Goscinski, David Grunwald, Michael Halter, Dorit Hanein, John W. Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A. Pimentel, Anne L. Plant, Andrea J. Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M. Spraggins, Damir Sudar, Wouter-Michiel Adrien Maria Vierdag, Niels Volkmann, Carolina Wählby, Siyuan (Steven)Wang, Ziv Yaniv, Caterina Strambio-De-Castillia
Published 2024-08-30
Licensed CC-BY-NC-SA-4.0 INTERNATIONAL
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated.
Tags: Research Data Management, Exclude From Dalia
Content type: Publication
How open-source software could finally get the world’s microscopes speaking the same language#
Michael Brooks
Published 2023-10-02
Licensed UNKNOWN
A plethora of standards mean shareable and verifiable microscopy data often get lost in translation. Biologists are working on a solution.
Tags: Research Data Management, Microscopy, Exclude From Dalia
Content type: Blog Post
I3D bio – Information Infrastructure for BioImage Data - Bioimage Metadata#
Christian Schmidt
Licensed UNKNOWN
A Microscopy Research Data Management Resource.
Tags: Metadata, I3Dbio, Research Data Management, Exclude From Dalia
Content type: Collection
https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/
I3D:bio list of online training material#
Licensed UNKNOWN
List of links to training materials by the I3D:bio community.
Tags: Research Data Management, Exclude From Dalia
Content type: Collection
https://gerbi-gmb.de/i3dbio/i3dbio-teaching/train-mat/bioimagelist/
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, Include In Dalia
Content type: Slides, Video
https://zenodo.org/records/8323588
https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU
If you license it, it’ll be harder to steal it. Why we should license our work#
Robert Haase
Licensed CC-BY-4.0
Blog post about why we should license our work and what is important when choosing a license.
Tags: Licensing, Research Data Management, Include In Dalia
Content type: Blog Post
Introduction to OMERO - Frankfurt - online#
Michele Bortolomeazzi, Tom Boissonnet
Published 2025-04-05
Licensed CC-BY-4.0
These slides were presented during an online introductory session to OMERO for the UB Frankfurt. The two-hour session consisted of a first part highlighting the benefits that image data management brings to the lab. The second part showcased image analysis workflows with a Fiji macro and a Python notebook.
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
Introduction to Research Data Management and Open Research#
Shanmugasundaram
Published 2024-05-17
Licensed CC-BY-4.0
Introduction to RDM primarily for researchers. Can be seen as primer to all other materials in this catalogue.
Tags: Research Data Management, Open Science, Include In Dalia
Content type: Slides
Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI)#
Silke Tulok, Anja Nobst, Anett Jannasch, Tom Boissonnet, Gunar Fabig
Published 2024-06-28
Licensed CC-BY-4.0
This Key-Value pair template is used for the data documentation during imaging experiments and the later data annotation in OMERO. It is tailored for the usage and image acquisition at the slide scanning system Zeiss AxioScan 7 in the Core Facility Cellular Imaging (CFCI). It contains important metadata of the imaging experiment, which are not saved in the corresponding imaging files. All users of the Core Facility Cellular Imaging are trained to use that file to document their imaging parameters directly during the data acquisition with the possibility for a later upload to OMERO. Furthermore, there is a corresponding public example image used in the publication “Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users” and is available here: https://omero.med.tu-dresden.de/webclient/?show=image-33248 This template was developed by the CFCI staff during the setup and usage of the AxioScan 7 and is based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015). With this template it is possible to create a csv-file, that can be used to annotate an image or dataset in OMERO using the annotation script (ome/omero-scripts). How to use:
fill the template sheet with your metadata select and copy the data range containing the Keys and Values open a new excel sheet and paste transpose in cell A1 Important: cell A1 contains always the name ‘dataset’ and cell A2 contains the exact name of the image/dataset, which should be annotated in OMERO save the new excel sheet in csv-file (comma separated values) format
An example can be seen in sheet 3 ‘csv_AxioScan’. Important note: The code has to be 8-Bit UCS transformation format (UTF-8) otherwise several characters (for example µ, %,°) might be not able to decode by the annotation script. We encountered this issue with old Microsoft-Office versions (MS Office 2016). Note: By filling the values in the excel sheet, avoid the usage of comma as decimal delimiter. See cross reference: 10.5281/zenodo.12547566 Key-Value pair template for annotation of datasets in OMERO for light- and electron microscopy data within the research group of Prof. Mueller-Reichert 10.5281/zenodo.12546808 Key-Value pair template for annotation of datasets in OMERO (PERIKLES study)
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Key-Value pair template for annotation of datasets in OMERO (PERIKLES study)#
Anett Jannasch, Silke Tulok, Vanessa Aphaia Fiona Fuchs, Tom Boissonnet, Christian Schmidt, Michele Bortolomeazzi, Gunar Fabig, Chukwuebuka Okafornta
Published 2024-06-26
Licensed CC-BY-4.0
This is a Key-Value pair template used for the annotation of datasets in OMERO. It is tailored for a research study (PERIKLES project) on the biocompatibility of newly designed biomaterials out of pericardial tissue for cardiovascular substitutes (https://doi.org/10.1063/5.0182672) conducted in the research department of Cardiac Surgery at the Faculty of Medicine Carl Gustav Carus at the Technische Universität Dresden . A corresponding public example dataset is used in the publication “Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users” and is available here (https://omero.med.tu-dresden.de/webclient/?show=dataset-1557). The template is based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015) and it was developed during the PoL-Bio-Image Analysis Symposium in Dresden Aug 28th- Sept 1th 2023. With this template it is possible to create a csv-file, that can be used to annotate a dataset in OMERO using the annotation script (ome/omero-scripts). How to use: select and copy the data range containing Keys and Values open a new excel sheet and paste transpose in column B1 type in A1 ‘dataset’ insert in A2 the exact name of the dataset, which should be annotated in OMERO save the new excel sheet in csv- (comma seperated values) file format
Example can be seen in sheet 1 ‘csv import’. Important note; the code has to be 8-Bit UCS transformation format (UTF-8) otherwise several characters (for example µ, %,°) might not be able to decode by the annotation script. We encountered this issue with old Microsoft Office versions (e.g. MS Office 2016). Note: By filling the values in the excel sheet, avoid the usage of decimal delimiter. See cross reference: 10.5281/zenodo.12547566 Key-Value pair template for annotation of datasets in OMERO (light- and electron microscopy data within the research group of Prof. Mueller-Reichert) 10.5281/zenodo.12578084 Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI)
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
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, Include In Dalia
Content type: Slides
LEO#
Rodrigo Escobar Diaz Guerrero
Published 2025-01-08T10:20:30+00:00
Licensed MIT
Linking Electronic Lab Notebooks and other sources with OMERO objects
Tags: OMERO, Research Data Management, Electronic Lab Notebooks, Exclude From Dalia
Content type: Github Repository
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, Exclude From Dalia
Content type: Publication
Lund Declaration on Maximising the Benefits of Research Data#
Tags: Research Data Management, Exclude From Dalia
Content type: Document
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, Exclude From Dalia
Content type: Publication
Making your project citable#
A tutorial explaining how to make Github repositories citable by automatically creating DOIs using the Github-Zenodo integration.
Tags: Sharing, Citing, Research Data Management, Include In Dalia
Content type: Tutorial
https://coderefinery.github.io/github-without-command-line/doi/
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, Exclude From Dalia
Content type: Publication
https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.871228/full
NFDI - Daten als gemeinsames Gut für exzellente Forschung, organisiert durch die Wissenschaft in Deutschland.#
Licensed UNKNOWN
Schritt für Schritt verbessern wir die Nutzungsmöglichkeiten von Daten für Wissenschaft und Gesellschaft. Durch unser Zusammenwirken im NFDI-Verein entsteht eine Dachorganisation für das Forschungsdatenmanagement in allen Wissenschaftszweigen.
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Content type: Website
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, Include In Dalia
Content type: Slides
NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data#
Christian Schmidt, Elisa Ferrando-May
Published 2021-04-29
Licensed CCY-BY-SA-4.0
Align existing and establish novel services & solutions for data management tasks throughout the bioimage data lifecycle.
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Content type: Conference Abstract, 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, Include In Dalia
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, Exclude From Dalia
Content type: Slides
NFDI4BIOIMAGE - a consortium of the National Research Data Infrastructure#
Nfdi4Bioimage
Licensed UNKNOWN
Tags: Bioimage Analysis, Research Data Management, Nfdi4Bioimage, Exclude From Dalia
Content type: Collection
NFDI4BIOIMAGE data management illustrations by Henning Falk#
NFDI4BIOIMAGE Consortium
Published 2024-11-29
Licensed CC-BY-4.0
These illustrations were contracted by the Heinrich Heine University Düsseldorf in the frame of the consortium NFDI4BIOIMAGE from Henning Falk for the purpose of education and public outreach. The illustrations are free to use under a CC-BY 4.0 license.AttributionPlease include an attribution similar to: “Data annoation matters”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping.
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
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, Exclude From Dalia
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, Exclude From Dalia
Content type: Github Repository
NFDI4Bioimage Calendar 2024 October; original image#
Christian Jüngst, Peter Zentis
Published 2024-09-25
Licensed CC-BY-4.0
Raw microscopy image from the NFDI4Bioimage calendar October 2024
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Name Styles#
Nick Radcliffe
Published None
Licensed UNKNOWN
This playful exploration delves into the quirky world of naming conventions in computing and data, humorously comparing them to Boston Box matrices and D&D alignments while poking fun at the chaos of categorizing what makes sense in metadata standards.
Tags: Research Data Management, Include In Dalia
Content type: Blog Post
OME Event Database#
Tags: OMERO, Research Data Management, Exclude From Dalia
Content type: Collection, Event
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, Exclude From Dalia
Content type: Publication
OME2024 NGFF Challenge Results#
Josh Moore
Published 2024-11-01
Licensed CC-BY-4.0
Presented at the 2024 FoundingGIDE event in Okazaki, Japan: https://founding-gide.eurobioimaging.eu/event/foundinggide-community-event-2024/ Note: much of the presentation was a demonstration of the OME2024-NGFF-Challenge – https://ome.github.io/ome2024-ngff-challenge/ especially of querying an extraction of the metadata (ome/ome2024-ngff-challenge-metadata)
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
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, Exclude From Dalia
Content type: Publication
https://analyticalscience.wiley.com/do/10.1002/was.0004000267/
Open Image Data Handbook#
Kevin Yamauchi
Licensed CC-BY-4.0
Tags: Neubias, Research Data Management, Napari, Python, Bioimage Analysis, Include In Dalia
Content type: Book, Notebook
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, Include In Dalia
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, Include In Dalia
Content type: Publication
Promoting Data Management at the Nikon Imaging Center and Cell Biology Microscopy Facility#
Jennifer Waters
Tags: Research Data Management, Include In Dalia
Content type: Blog Post
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, Exclude From Dalia
Content type: Slides
RDM Starter Kit#
GO FAIR
Licensed CC-BY-4.0
This page is supposed to serve as a Starter Kit for research data management (RDM). It lists resources designed to help researchers get started to organize their data.
Tags: Research Data Management, Include In Dalia
Content type: Website
RDM4Mic Presentations#
Licensed CC-BY-4.0
Tags: Research Data Management, Exclude From Dalia
Content type: Collection
RDM4mic#
Licensed UNKNOWN
Tags: Research Data Management, OMERO, Exclude From Dalia
Content type: Collection, Video
RDMKit Training Resources#
Licensed CC-BY-4.0
Tags: Research Data Management, Include In Dalia
Content type: Collection
RDMO - Research Data Management Organiser#
Licensed UNKNOWN
Der Research Data Management Organiser (RDMO) unterstützt Forschungsprojekte bei der Planung, Umsetzung und Verwaltung aller Aufgaben des Forschungsdatenmanagements.
Tags: Research Data Management, Open Source Software, Exclude From Dalia
Content type: Website, Online Tutorial
RDM_system_connector#
SaibotMagd
Licensed UNKNOWN
This tool is intended to link different research data management platforms with each other.
Tags: Research Data Management, Exclude From Dalia
Content type: Github Repository
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, Research Data Management, Exclude From Dalia
Content type: Publication
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015/
REMBI Overview#
Licensed CC0-1.0
Recommended Metadata for Biological Images (REMBI) provides guidelines for metadata for biological images to enable the FAIR sharing of scientific data.
Tags: FAIR-Principles, Metadata, Research Data Management, Include In Dalia
Content type: Collection
Research Data Management Seminar - Slides#
Stefano Della Chiesa
Published 2022-05-18
Licensed CC-BY-4.0
This Research Data Management (RDM) Slides introduce to the multidisciplinary knowledge and competencies required to address policy compliance and research data management best practices throughout a project lifecycle, and beyond it.
Module 1 - Introduces the RDM giving its context in the Research Data Governance
Module 2 - Illustrates the most important RDM policies and principles
Module 3 - Provides the most relevant RDM knowledge bricks
Module 4 - Discuss the Data Management Plans (DMPs), examples, templates and guidance
Tags: Research Data Management, Include In Dalia
Content type: Slides
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, Exclude From Dalia
Content type: Publication
Research data - what are the key issues to consider when publishing this kind of material?#
Licensed UNKNOWN
The website offers detailed advice on publishing research data, focusing on key issues like data management, FAIR data principles, legal considerations, and repository selection.
Tags: Research Data Management, FAIR-Principles, Licensing, Exclude From Dalia
Content type: Tutorial
https://www.publisso.de/en/advice/publishing-advice-faqs/research-data
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, Exclude From Dalia
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, Exclude From Dalia
Content type: Publication
Scientific colour maps#
Fabio Crameri
Published 2023-10-05
Licensed ALL RIGHTS RESERVED
Scientific, colour-vision deficiency friendly and perceptually-uniform colour maps that include all readers and significantly reduce visual errors.
Tags: FAIR-Principles, Research Data Management, Exclude From Dalia
Content type: Website
Setting up a data management infrastructure for bioimaging#
Susanne Kunis, Karen Bernhardt, Michael Hensel
Licensed UNKNOWN
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
Content type: Publication
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, Include In Dalia
Content type: Slides
Software Citation with CITATION.cff#
How to make your Github repository citable by adding a citation.cff file.
Tags: Sharing, Citing, Research Data Management, Include In Dalia
Content type: Tutorial
https://the-turing-way.netlify.app/communication/citable/citable-cff.html
Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data#
Sarah Weischer, Jens Wendt, Thomas Zobel
Published 2022-07-12
Licensed CC-BY-4.0
Provides an overview of contexts, frameworks, and models from the world of bioimage data as well as metadata. Visualizes the techniques for structuring this data as Linked Data. (Walkthrough Video: https://doi.org/10.5281/zenodo.7018928 )
Content:
Types of metadata
Data formats
Data Models Microscopy Data
Tools to edit/gather metadata
ISA Framework
FDO Framework
Ontology
RDF
JSON-LD
SPARQL
Knowledge Graph
Linked Data
Smart Data
...
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
Submitting data to the BioImage Archive#
Licensed CC0-1.0
To submit, you’ll need to register an account, organise and upload your data, prepare a file list, and then submit using our web submission form. These steps are explained here.
Tags: Research Data Management, Exclude From Dalia
Content type: Tutorial, Video
Sustainable Data Stewardship#
Stefano Della Chiesa
Published 2024-03-25
Licensed CC-BY-4.0
These slides were presented at the 2. SaxFDM-Beratungsstammtisch and delve into the strategic integration of Research Data Management (RDM) within research organizations. The Leibniz IOER presented an insightful overview of RDM activities and approaches, emphasizing the criticality of embedding RDM strategically within research institutions. The presentation showcases some best practices in RDM implementation through practical examples, offering valuable insights for optimizing data stewardship processes.
Tags: Research Data Management, Data Stewardship, Include In Dalia
Content type: Slides
Tess Search for Data Life Cycle#
Licensed UNKNOWN
Tags: Data Life Cycle, Research Data Management, Exclude From Dalia
Content type: Collection
https://tess.elixir-europe.org/search?q=data+life+cycle#materials
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: Research Data Management, Exclude From Dalia
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, Exclude From Dalia
Content type: Publication
The Information Infrastructure for BioImage Data (I3D:bio) project to advance FAIR microscopy data management for the community#
Christian Schmidt, Michele Bortolomeazzi, Tom Boissonnet, Julia Dohle, Tobias Wernet, Janina Hanne, Roland Nitschke, Susanne Kunis, Karen Bernhardt, Stefanie Weidtkamp-Peters, Elisa Ferrando-May
Published 2024-03-04
Licensed CC-BY-4.0
Research data management (RDM) in microscopy and image analysis is a challenging task. Large files in proprietary formats, complex N-dimensional array structures, and various metadata models and formats can make image data handling inconvenient and difficult. For data organization, annotation, and sharing, researchers need solutions that fit everyday practice and comply with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. International community-based efforts have begun creating open data models (OME), an open file format and translation library (OME-TIFF, Bio-Formats), data management software platforms, and microscopy metadata recommendations and annotation tools. Bringing these developments into practice requires support and training. Iterative feedback and tool improvement is needed to foster practical adoption by the scientific community. The Information Infrastructure for BioImage Data (I3D:bio) project works on guidelines, training resources, and practical assistance for FAIR microscopy RDM adoption with a focus on the management platform OMERO and metadata annotations.
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
The role of Helmholtz Centers in NFDI4BIOIMAGE - A national consortium enhancing FAIR data management for microscopy and bioimage analysis#
Riccardo Massei, Christian Schmidt, Michele Bortolomeazzi, Julia Thoennissen, Jan Bumberger, Timo Dickscheid, Jan-Philipp Mallm, Elisa Ferrando-May
Published 2024-06-06
Licensed CC-BY-4.0
Germany’s National Research Data Infrastructure (NFDI) aims to establish a sustained, cross-disciplinary research data management (RDM) infrastructure that enables researchers to handle FAIR (findable, accessible, interoperable, reusable) data. While FAIR principles have been adopted by funders, policymakers, and publishers, their practical implementation remains an ongoing effort. In the field of bio-imaging, harmonization of data formats, metadata ontologies, and open data repositories is necessary to achieve FAIR data. The NFDI4BIOIMAGE was established to address these issues and develop tools and best practices to facilitate FAIR microscopy and image analysis data in alignment with international community activities. The consortium operates through its Data Stewards team to provide expertise and direct support to help overcome RDM challenges. The three Helmholtz Centers in NFDI4BIOIMAGE aim to collaborate closely with other centers and initiatives, such as HMC, Helmholtz AI, and HIP. Here we present NFDI4BIOIMAGE’s work and its significance for research in Helmholtz and beyond
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
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, Include In Dalia
Content type: Slides
Towards FAIR Data Workflows for Multidisciplinary Science: Ongoing Endeavors and Future Perspectives in Plasma Technology#
Robert Wagner, Dagmar Waltemath, Kristina Yordanova, Markus Becker
Licensed CC-BY-NC-ND-4.0
This paper focuses on the ongoing process of establishing a FAIR (Findable, Accessible, Interoperable and Reusable) data workflow for multidisciplinary research and development in applied plasma science. The presented workflow aims to support researchers in handling their project data while also fulfilling the requirements of modern digital research data management.
Tags: Research Data Management, Exclude From Dalia
Content type: Publication
https://www.scitepress.org/Link.aspx?doi=10.5220/0012808000003756
Towards Preservation of Life Science Data with NFDI4BIOIMAGE#
Robert Haase
Published 2024-09-03
Licensed CC-BY-4.0
This talk will present the initiatives of the NFDI4BioImage consortium aimed at the long-term preservation of life science data. We will discuss our efforts to establish metadata standards, which are crucial for ensuring data reusability and integrity. The development of sustainable infrastructure is another key focus, enabling seamless data integration and analysis in the cloud. We will take a look at how we manage training materials and communicate with our community. Through these actions, NFDI4BioImage seeks to enable FAIR bioimage data management for German researchers, across disciplines and embedded in the international framework.
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Train-the-Trainer Concept on Research Data Management#
Katarzyna Biernacka, Maik Bierwirth, Petra Buchholz, Dominika Dolzycka, Kerstin Helbig, Janna Neumann, Carolin Odebrecht, Cord Wiljes, Ulrike Wuttke
Published 2020-11-04
Licensed CC-BY-4.0
Within the project FDMentor, a German Train-the-Trainer Programme on Research Data Management (RDM) was developed and piloted in a series of workshops. The topics cover many aspects of research data management, such as data management plans and the publication of research data, as well as didactic units on learning concepts, workshop design and a range of didactic methods.
After the end of the project, the concept was supplemented and updated by members of the Sub-Working Group Training/Further Education (UAG Schulungen/Fortbildungen) of the DINI/nestor Working Group Research Data (DINI/nestor-AG Forschungsdaten). The newly published English version of the Train-the-Trainer Concept contains the translated concept, the materials and all methods of the Train-the-Trainer Programme. Furthermore, additional English references and materials complement this version.
Tags: Research Data Management, Include In Dalia
Content type: Book
Training concepts in research data management and data science with the focus on health research#
Jens Dierkes, Julia Fürst, Tanja Hörner, Sebastian Klammt, Birte Lindstädt, Iris Pigeot, Katja Restel, Carsten Oliver Schmidt, Dagmar Waltemath, Atinkut Zeleke
Published 2023-08-22
Licensed CC-BY-4.0
This handbook provides an overview of Research Data Management (RDM) and FAIR principles, with a focus on practical implementation and training for master students, doctoral researchers, and professionals in biomedical sciences. The handbook is a living document that will be updated iteratively to address the specific needs and requirements of the target group, with a focus on the NFDI4Health domain.
Tags: FAIR-Principles, Research Data Management, Include In Dalia
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: Bioimage Analysis, Research Data Management, Exclude From Dalia
Content type: Publication, Preprint
Who you gonna call? - Data Stewards to the rescue#
Vanessa Aphaia Fiona Fuchs, 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, Include In Dalia
Content type: Poster
Workflow for user introduction into microscopy, OMERO and data management at Center for Advanced imaging#
Ksenia Krooß, Fuchs, Vanessa Aphaia Fiona, Tom Boissonnet, Stefanie Weidtkamp-Peters
Published 2025-03-07
Licensed CC-BY-4.0
At the Center for Advanced Imaging (CAi) at the Heinrich Heine University Düsseldorf, Germany, we have established a workflow to guide users through all aspects of bioimaging. The process begins with an initial consultation with our imaging specialists regarding microscopy techniques for their specific project. Users then receive training in microscope operation, ensuring they can handle the equipment effectively. If needed, our specialists also provide support in image analysis. Next, we introduce users to OMERO, highlighting its features and the advantages of using a bioimage data management system. They are then trained to structure and annotate their data within OMERO according to the Recommended Metadata for Biological Images (REMBI), taking their specific research topics into account. As users prepare for data publication, we assist with data organization and repository uploads. Our goal is to educate researchers in managing bioimage data throughout its entire lifecycle, with a strong emphasis on the FAIR (findable, accessible, interoperable, reusable) principles.
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
[CORDI 2023] Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays#
Josh Moore
Licensed CC-BY-4.0
For decades, the sharing of large N-dimensional datasets has posed issues across multiple domains. Interactively accessing terabyte-scale data has previously required significant server resources to properly prepare cropped or down-sampled representations on the fly. Now, a cloud-native chunked format easing this burden has been adopted in the bioimaging domain for standardization. The format — Zarr — is potentially of interest for other consortia and sections of NFDI.
Tags: Research Data Management, Bioimage Analysis, Data Science, Exclude From Dalia
Content type: Poster
[Community Meeting 2024] Overview Team Image Data Analysis and Management#
Susanne Kunis, Thomas Zobel
Published 2024-03-08
Licensed CC-BY-4.0
Overview of Activities of the Team Image Data Analysis and Management of German BioImaging e.V.
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
[ELMI 2024] AI’s Dirty Little Secret: Without#
FAIR Data, It’s Just Fancy Math
Josh Moore, Susanne Kunis
Published 2024-05-21
Licensed CC-BY-4.0
Poster presented at the European Light Microscopy Initiative meeting in Liverpool (https://www.elmi2024.org/)
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
[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, Include In Dalia
Content type: Poster
[N4BI AHM] Welcome to BioImage Town#
Josh Moore
Published 2023-10-16
Licensed CC-BY-4.0
Keynote at the NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023.
Tags: Research Data Management, Exclude From Dalia
Content type: Slides
[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, Include In Dalia
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, Include In Dalia
Content type: Slides
[Webinar] A journey to FAIR bioimage data#
Stefanie Weidtkamp-Peters, Tom Boissonnet, Christian Schmidt
Published 2025-07-03
Licensed CC-BY-4.0
Presentation slides from an EMBL-EBI Webinar Talk within the webinar series: “How to organise and share my imaging data? - Multimodal data management for marine biologists, environmental scientists and imaging specialists” Abstract / Description Bioimaging is a pervasive and indispensable methodological approach in the life and biomedical sciences. Due to the development of new technologies and the easier access to compute resources, bioimaging experiments have become a big data discipline, facing the same challenges as other omics technologies within the life sciences. However, to fully exploit the potential of bioimage data, it is necessary to make the data FAIR. In this webinar we will present viable solutions for storing, processing, analysing, and, first and foremost, sharing bioimaging data. We will introduce services provided to the scientific community, that are dealing with various aspects of the bioimage data life cycle such as:
Where to get support for bioimage data management- Local bioimage data management: OMERO and beyond- Annotation of bioimage data: metadata, ontologies, REMBI etc- Linking your image data with experimental protocols and analysis results- Large data living in the cloud: ome.zarr- Publication of bioimage data Who is this course for? This webinar is suitable for marine biologists and environmental scientists collecting samples from the natural environment, generating, visualising, annotating and analysing large, multimodal datasets such as imaging data, and sharing their data by submitting them to public data repositories. The webinar will support you to set up an efficient data flow that is aligned with FAIR principles. This event is part of a webinar series organised by the STANDFLOW project, an initiative supported by EMBL’s Planetary biology Transversal Theme. STANDFLOW is about a collaborative effort towards creating a standardised data management workflow. The project primarily utilises imaging data derived from samples collected through the TREC (Traversing European Coastlines) and the Roscoff Culture Collection. For details on all topics covered in this series and registration information, please visit the following link: How to organise and share my imaging data?: Multimodal data management for marine biologists, and environmental scientists and imaging specialists Outcomes By the end of the webinar you will be able to:
Find resources and support for bioimage data management Get started with bioimage data annotation Identify the dos and don’ts for bioimage data publication
(taken from: https://www.ebi.ac.uk/training/events/journey-fair-bioimage-data/)
Tags: Nfdi4Bioimage, Fair Principles, Research Data Management, Include In Dalia
[Workshop Material] Fit for OMERO - How imaging facilities and IT departments work together to enable RDM for bioimaging, October 16-17, 2024, Heidelberg#
Tom Boissonnet, Bettina Hagen, Susanne Kunis, Christian Schmidt, Stefanie Weidtkamp-Peters
Published 2024-11-18
Licensed CC-BY-4.0
Fit for OMERO: How imaging facilities and IT departments work together to enable RDM for bioimaging Description: Research data management (RDM) in bioimaging is challenging because of large file sizes, heterogeneous file formats and the variability of imaging methods. The image data management system OMERO (OME Remote Objects) allows for centralized and secure storage, organization, annotation, and interrogation of microscopy data by researchers. It is an internationally well-supported open-source software tool that has become one of the best-known image data management tools among bioimaging scientists. Nevertheless, the de novo setup of OMERO at an institute is a multi-stakeholder process that demands time, funds, organization and iterative implementation. In this workshop, participants learn how to begin setting up OMERO-based image data management at their institution. The topics include:
Stakeholder identification at the university / research institute Process management, time line expectations, and resources planning Learning about each other‘s perspectives on chances and challenges for RDM Funding opportunities and strategies for IT and imaging core facilities Hands-on: Setting up an OMERO server in a virtual machine environment
Target audience: This workshop was directed at universities and research institutions who consider or plan to implement OMERO, or are in an early phase of implementation. This workshop was intended for teams from IT departments and imaging facilities to participate together with one person from the IT department, and one person from the imaging core facility at the same institution. The trainers:
Prof. Dr. Stefanie Weidtkamp-Peters (Imaging Core Facility Head, Center for Advanced Imaging, Heinrich Heine University of Düsseldorf) Dr. Susanne Kunis (Software architect, OMERO administrator, metadata specialist, University of Osnabrück) Dr. Tom Boissonnet (OMERO admin and image metadata specialist, Center for Advanced Imaging, Heinrich Heine University of Düsseldorf) Dr. Bettina Hagen (IT Administration and service specialist, Max Planck Institute for the Biology of Ageing, Cologne) Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center (DKFZ), Heidelberg)
Time and place The format was a two-day, in-person workshop (October 16-17, 2024). Location: Heidelberg, Germany Workshop learning goals
Learn the steps to establish a local RDM environment fit for bioimaging data Create a network of IT experts and bioimaging specialists for bioimage RDM across institutions Establish a stakeholder process management for installing OMERO-based RDM Learn from each other, leverage different expertise Learn how to train users, establish sustainability strategies, and foster FAIR RDM for bioimaging at your institution
Tags: Nfdi4Bioimage, Research Data Management, Exclude From Dalia
[Workshop] Bioimage data management and analysis with OMERO#
Riccardo Massei, Michele Bortolomeazzi, Christian Schmidt
Published 2024-05-13
Licensed CC-BY-4.0
Here we share the material used in a workshop held on May 13th, 2024, at the German Cancer Research Center in Heidelberg (on-premise) Description:Microscopy experiments generate information-rich, multi-dimensional data, allowing us to investigate biological processes at high spatial and temporal resolution. Image processing and analysis is a standard procedure to retrieve quantitative information from biological imaging. Due to the complex nature of bioimaging files that often come in proprietary formats, it can be challenging to organize, structure, and annotate bioimaging data throughout a project. Data often needs to be moved between collaboration partners, transformed into open formats, processed with a variety of software tools, and exported to smaller-sized images for presentation. The path from image acquisition to final publication figures with quantitative results must be documented and reproducible. In this workshop, participants learn how to use OMERO to organize their data and enrich the bioimage data with structured metadata annotations.We also focus on image analysis workflows in combination with OMERO based on the Fiji/ImageJ software and using Jupyter Notebooks. In the last part, we explore how OMERO can be used to create publication figures and prepare bioimage data for publication in a suitable repository such as the Bioimage Archive. Module 1 (9 am - 10.15 am): Basics of OMERO, data structuring and annotation Module 2 (10.45 am - 12.45 pm): OMERO and Fiji Module 3 (1.45 pm - 3.45 pm): OMERO and Jupyter Notebooks Module 4 (4.15 pm - 6. pm): Publication-ready figures and data with OMERO The target group for this workshopThis workshop is directed at researchers at all career levels who plan to or have started to use OMERO for their microscopy research data management. We encourage the workshop participants to bring example data from their research to discuss suitable metadata annotation for their everyday practice. Prerequisites:Users should bring their laptops and have access to the internet through one of the following options:- eduroam- institutional WiFi- VPN connection to their institutional networks to access OMERO Who are the trainers? Dr. Riccardo Massei (Helmholtz-Center for Environmental Research, UFZ, Leipzig) - Data Steward for Bioimaging Data in NFDI4BIOIMAGE Dr. Michele Bortolomeazzi (DKFZ, Single cell Open Lab, bioimage data specialist, bioinformatician, staff scientist in the NFDI4BIOIMAGE project) Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg, Project Coordinator of the NFDI4BIOIMAGE project)
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
[Workshop] Managing FAIR microscopy data at scale for universities and research institutions: an introduction for non-imaging stakeholders#
Christian Schmidt, Michele Bortolomeazzi, Ksenia Krooß, Jan-Philipp Mallm, Elisa Ferrando-May, Stefanie Weidtkamp-Peters
Published 2025-03-14
Licensed CC-BY-4.0
These slides were used in a workshop at the 2025 E-Science Tage in Heidelberg. Workshop Abstract: Effective Research Data Management (RDM) requires collaboration between infrastructure providers, support units, and domain-specific experts across scientific disciplines. Microscopy, or bioimaging, is a widely used technology at universities and research institutions, generating large, multi-dimensional datasets. Scientists now routinely produce microscopy data using advanced imaging modalities, often through centrally-provided instruments maintained by core facilities. Bioimaging data management presents unique challenges: files are often large (e.g., 15+ GB for whole slide images), come in various proprietary formats, and are accessed frequently for viewing as well as for complex image processing and analysis workflows. Collaboration between experimenters, clinicians, group leaders, core facility staff, and image analysts adds to the complexity, increasing the risk of data fragmentation and metadata loss. The DFG-funded project I3D:bio and the consortium NFDI4BIOIMAGE, part of Germany’s National Research Data Infrastructure (NFDI), are addressing these challenges by developing solutions and best practices for managing large, complex microscopy datasets. This workshop introduces the challenges of bioimaging RDM to institutional support personnel, including, for example, library staff, IT departments, and data stewards. Participants will explore the bioimaging RDM system OMERO, and apply structured metadata annotation and object-oriented data organization to a simple training dataset. OMERO offers centralized, secure access to data, allowing collaboration and reducing the data fragementation risk. Moreover, participants will experience the benefits of OME-Zarr, a chunked open file format designed for FAIR data sharing and remote access. OME-Zarr enables streaming of large, N-dimensional array-typed data over the Internet without the need to download whole files. An expanding toolbox for leveraging OME-Zarr for bioimaging data renders this file type a promising candidate for a standard file format suitable for use in FAIR Digital Object (FDO) implementations for microscopy data. OME-Zarr has become a pillar for imaging data sharing in two bioimaging-specific data repositories, i.e., the Image Data Resource (IDR) and the BioImage Archive (BIA). The team of Data Stewards from both abovenmentioned projects help researchers and research support staff to manage und publish bioimaging data. By the end of the workshop, participants will have gained hands-on experience with bioimaging data and will be aware of support resources like the NFDI4BIOIMAGE Help Desk for addressing specific local use cases. Our goal is to promote collaboration across disciplines to effectively manage complex bioimaging data in compliance with the FAIR principles.
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
[Workshop] Research Data Management for Microscopy and BioImage Analysis#
Christian Schmidt, Tom Boissonnet, Michele Bortolomeazzi, Ksenia Krooß
Published 2024-09-30
Licensed CC-BY-4.0
Research Data Management for Microscopy and BioImage Analysis
Introduction to BioImaging Research Data Management, NFDI4BIOIMAGE and I3D:bioChristian Schmidt /DKFZ Heidelberg OMERO as a tool for bioimaging data managementTom Boissonnet /Heinrich-Heine Universität Düsseldorf Reproducible image analysis workflows with OMERO software APIsMichele Bortolomeazzi /DKFZ Heidelberg Publishing datasets in public archives for bioimage dataKsenia Krooß /Heinrich-Heine Universität Düsseldorf
Date & Venue:Thursday, Sept. 26, 5.30 p.m.Haus 22 / Paul Ehrlich Lecture Hall (H22-1)University Hospital Frankfurt
Tags: Nfdi4Bioimage, Research Data Management, Include In Dalia
cba-support-template#
Arif Khan, Christian Tischer, Sebastian Gonzalez, Dominik Kutra, Felix Schneider, et al.
Published 2021-12-01
Licensed MIT
Tags: Workflow, Research Data Management, Exclude From Dalia
Content type: Tutorial
datenbiene#
Torsten Stöter
Published 2025-02-02T18:50:20+00:00
Licensed GNU GENERAL PUBLIC LICENSE V3.0
Tags: Research Data Management, Exclude From Dalia
Content type: Github Repository, Software
ome2024-ngff-challenge#
Will Moore, Josh Moore, sherwoodf, jean-marie burel, Norman Rzepka, dependabot[bot], JensWendt, Joost de Folter, Torsten St\xF6ter, AybukeKY, Eric Perlman, Tom Boissonnet
Published 2024-08-30T12:00:53+00:00
Licensed BSD-3-CLAUSE
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
Tags: Sharing, Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Content type: Github Repository
omero-arc#
Christoph Moehl, Peter Zentis, Niraj Kandpal
Published 2023-12-18T16:11:04+00:00
Licensed GNU GENERAL PUBLIC LICENSE V3.0
Library to export OMERO projects to ARC repositories
Tags: OMERO, Research Data Management, Exclude From Dalia
Content type: Github Repository, Software
re3data.org - registry of Research Data Repositories#
Licensed CC-BY-4.0
Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines. It includes repositories that enable permanent storage of and access to data sets to researchers, funding bodies, publishers, and scholarly institutions.
Tags: Research Data Management, Exclude From Dalia
Content type: Website