Nfdi4bioimage (46)#
A Cloud-Optimized Storage for Interactive Access of Large Arrays#
Josh Moore, Susanne Kunis
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication, Conference Abstract
A 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
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
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
Content type: Slides
Challenges and opportunities for bio-image analysis core-facilities#
Robert Haase
Licensed CC-BY-4.0
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
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
Engineering a Software Environment for Research Data Management of Microscopy Image Data in a Core Facility#
Kunis
Published 2022-05-30
This thesis deals with concepts and solutions in the field of data management in everyday scientific life for image data from microscopy. The focus of the formulated requirements has so far been on published data, which represent only a small subset of the data generated in the scientific process. More and more, everyday research data are moving into the focus of the principles for the management of research data that were formulated early on (FAIR-principles). The adequate management of this mostly multimodal data is a real challenge in terms of its heterogeneity and scope. There is a lack of standardised and established workflows and also the software solutions available so far do not adequately reflect the special requirements of this area. However, the success of any data management process depends heavily on the degree of integration into the daily work routine. Data management must, as far as possible, fit seamlessly into this process. Microscopy data in the scientific process is embedded in pre-processing, which consists of preparatory laboratory work and the analytical evaluation of the microscopy data. In terms of volume, the image data often form the largest part of data generated within this entire research process. In this paper, we focus on concepts and techniques related to the handling and description of this image data and address the necessary basics. The aim is to improve the embedding of the existing data management solution for image data (OMERO) into the everyday scientific work. For this purpose, two independent software extensions for OMERO were implemented within the framework of this thesis: OpenLink and MDEmic. OpenLink simplifies the access to the data stored in the integrated repository in order to feed them into established workflows for further evaluations and enables not only the internal but also the external exchange of data without weakening the advantages of the data repository. The focus of the second implemented software solution, MDEmic, is on the capturing of relevant metadata for microscopy. Through the extended metadata collection, a corresponding linking of the multimodal data by means of a unique description and the corresponding semantic background is aimed at. The configurability of MDEmic is designed to address the currently very dynamic development of underlying concepts and formats. The main goal of MDEmic is to minimise the workload and to automate processes. This provides the scientist with a tool to handle this complex and extensive task of metadata acquisition for microscopic data in a simple way. With the help of the software, semantic and syntactic standardisation can take place without the scientist having to deal with the technical concepts. The generated metadata descriptions are automatically integrated into the image repository and, at the same time, can be transferred by the scientists into formats that are needed when publishing the data.
Tags: Nfdi4Bioimage, Research Data Managementv
I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training#
Christian Schmidt, Michele Bortolomeazzi, Tom Boissonnet, Carsten Fortmann-Grote, Julia Dohle, Peter Zentis, Niraj Kandpal, Susanne Kunis, Thomas Zobel, Stefanie Weidtkamp-Peters, Elisa Ferrando-May
Published 2023-11-13
Licensed CC-BY-4.0
The open-source software OME Remote Objects (OMERO) is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community. The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers’ daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the Research Data Management for Microscopy group (RDM4mic) in Germany, and in the use cases in the I3D:bio project, we created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.
Tags: OMERO, Research Data Management, Nfdi4Bioimage, I3Dbio
Content type: Slides, Video
https://zenodo.org/records/8323588
https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU
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
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
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
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
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
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
Content type: Slides
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and BioImage Analysis [conference talk: The Pelagic Imaging Consortium meets Helmholtz Imaging, 5.10.2023, Hamburg]#
Riccardo Massei
Licensed CC-BY-4.0
NFDI4BIOIMAGE is a consortium within the framework of the National Research Data Infrastructure (NFDI) in Germany. In this talk, the consortium and the contribution to the work programme by the Helmholtz Centre for Environmental Research (UFZ) in Leipzig are outlined.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
NFDI4BIOIMAGE - a consortium of the National Research Data Infrastructure#
Nfdi4Bioimage
Licensed UNKNOWN
Tags: Bioimage Analysis, Research Data Management, Nfdi4Bioimage
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
NFDI4BIOIMAGE: Perspective for a national bioimaging standard#
Josh Moore, Susanne Kunis
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage
Content type: Publication
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon)#
Mohamed M. Abdrabbou, Mehrnaz Babaki, Tom Boissonnet, Michele Bortolomeazzi, Eik Dahms, Vanessa A. F. Fuchs, Moritz Hoevels, Niraj Kandpal, Christoph Möhl, Joshua A. Moore, Astrid Schauss, Andrea Schrader, Torsten Stöter, Julia Thönnißen, Monica Valencia-S., H. Lukas Weil, Jens Wendt and Peter Zentis
Licensed CC-BY-4.0
Tags: Arc, Dataplant, Hackathon, Nfdi4Bioimage, OMERO, Python, Research Data Management
Content type: Event, Publication, Documentation
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne-Hackathon-2023, GitHub repository)#
Mohamed Abdrabbou, Mehrnaz Babaki, Tom Boissonnet, Michele Bortolomeazzi, Eik Dahms, Vanessa Fuchs, A. F. Moritz Hoevels, Niraj Kandpal, Christoph Möhl, Joshua A. Moore, Astrid Schauss, Andrea Schrader, Torsten Stöter, Julia Thönnißen, Monica Valencia-S., H. Lukas Weil, Jens Wendt, Peter Zentis
Licensed CC-BY-4.0
This repository documents the first NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon), where topics like ‘Interoperability’, ‘REMBI / Mapping’, and ‘Neuroglancer (OMERO / zarr)’ were explored through collaborative discussions and workflow sessions, culminating in reports that bridge NFDI4Bioimage to DataPLANT. Funded by various DFG initiatives, this event emphasized documentation and use cases, contributing preparatory work for future interoperability projects at the 2nd de.NBI BioHackathon in Bielefeld.
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Github Repository
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
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies#
Josh Moore, Chris Allan, Sébastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, Will Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication
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
OMERO for microscopy research data management#
Thomas Zobel, Sarah Weischner, Jens Wendt
Licensed ALL RIGHTS RESERVED
A use case example from the Münster Imaging Network
Tags: Nfdi4Bioimage, OMERO, Research Data Management
Content type: Publication
https://analyticalscience.wiley.com/do/10.1002/was.0004000267/
Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy#
Riccardo Massei, Björn Grüning
Published 2024-12-02
Licensed CC-BY-4.0
Tags: OMERO, Galaxy, Metadata, Nfdi4Bioimage
Content type: Tutorial, Framework, Workflow
Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey#
Christian Schmidt, Janina Hanne, Josh Moore, Christian Meesters, Elisa Ferrando-May, Stefanie Weidtkamp-Peters, members of the NFDI4BIOIMAGE initiative
Licensed CC-BY-4.0
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication
Setting up a data management infrastructure for bioimaging#
Susanne Kunis, Karen Bernhardt, Michael Hensel
Licensed UNKNOWN
Tags: Nfdi4Bioimage, Research Data Management
Content type: Publication
Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data#
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
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
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
Thinking data management on different scales#
Susanne Kunis
Licensed CC-BY-4.0
Presentation given at PoL BioImage Analysis Symposium Dresden 2023
Tags: Research Data Management, Nfdi4Bioimage
Content type: Slides
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
Welcome to BioImage Town#
Josh Moore
Licensed CC-BY-4.0
Welcome at NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023
Tags: OMERO, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
Who you gonna call? - Data Stewards to the rescue#
Vanessa 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
Content type: Poster
[CIDAS] Scalable strategies for a next-generation of FAIR bioimaging#
Josh Moore
Published 2025-01-23
Licensed CC-BY-4.0
Talk given at Georg-August-Universität Göttingen Campus Institute Data Science23rd January 2025 https://www.uni-goettingen.de/en/653203.html
Tags: Nfdi4Bioimage
[CMCB] Scalable strategies for a next-generation of FAIR bioimaging#
Josh Moore
Published 2025-01-16
Licensed CC-BY-4.0
CMCB LIFE SCIENCES SEMINARSTechnische Universität Dresden16th January 2025 https://tu-dresden.de/cmcb/crtd/news-termine/termine/cmcb-life-sciences-seminar-josh-moore-german-bioimaging-e-v-society-for-microscopy-and-image-analysis-constance
Tags: Nfdi4Bioimage
[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
[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
[ELMI 2024] AI’s Dirty Little Secret: Without FAIR Data, It’s Just Fancy Math#
Josh Moore, Susanne Kunis
Licensed CC-BY-4.0
Poster presented at the European Light Microscopy Initiative meeting in Liverpool (https://www.elmi2024.org/)
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Poster
[SWAT4HCLS 2023] NFDI4BIOIMAGE: Perspective for a national bioimage standard#
Josh Moore, Susanne Kunis
Licensed CC-BY-4.0
Poster presented at Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Feb 13–16, 2023, Basel, Switzerland. NFDI4BIOIMAGE is a newly established German consortium dedicated to the FAIR representation of biological imaging data. A key deliverable is the definition of a semantically-compatible FAIR image object integrating RDF metadata with web-compatible storage of large n-dimensional binary data in OME-Zarr. We invite feedback from and collaboration with other endeavors during the soon-to-begin 5 year funding period.
Tags: Research Data Management, FAIR-Principles, Nfdi4Bioimage
Content type: Poster
[Short Talk] NFDI4BIOIMAGE - A consortium in the National Research Data Infrastructure#
Christian Schmidt
Licensed CC-BY-4.0
Short Talk about the NFDI4BIOIMAGE consortium presented at the RDM in (Bio-)Medicine Information Event on April 10th, 2024, organized C³RDM & ZB MED.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
[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
[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
[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
dmtxSampleCreator#
SaibotMagd
Published 2023-06-06T11:52:14+00:00
Licensed APACHE-2.0
firefox extension: reads datamatrix code from camera and create a sample in an inventory to link it into an ELN.
Tags: Nfdi4Bioimage
Content type: Github Repository
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
Content type: Github Repository