From 34e1e536fe412d7c6520c5b5ffc18943c8846b36 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 25 Nov 2024 12:12:31 +0000 Subject: [PATCH] Normalize data for PR #511 --- resources/nfdi4bioimage.yml | 2639 ++++++++++++++++++++--------------- 1 file changed, 1480 insertions(+), 1159 deletions(-) diff --git a/resources/nfdi4bioimage.yml b/resources/nfdi4bioimage.yml index e521d3b8..56be4017 100644 --- a/resources/nfdi4bioimage.yml +++ b/resources/nfdi4bioimage.yml @@ -3513,7 +3513,7 @@ resources: - Vanessa Fuchs - Aphaia Fiona - Jens Wendt - - Maximilian Müller + - "Maximilian M\xFCller" - Mohsen Ahmadi - Riccardo Massei - Cornelia Wetzker @@ -4164,24 +4164,30 @@ resources: url: - https://zenodo.org/records/13506641 - https://doi.org/10.5281/zenodo.13506641 - -- authors: - - Matúš Kalaš et al. - description: EDAM-bioimaging is an extension of the EDAM ontology, dedicated to bioimage analysis, bioimage informatics, and bioimaging. +- authors: + - "Matu\u0301s\u030C Kalas\u030C et al." + description: EDAM-bioimaging is an extension of the EDAM ontology, dedicated to + bioimage analysis, bioimage informatics, and bioimaging. license: CC-BY-4.0 - name: EDAM-bioimaging - The ontology of bioimage informatics operations, topics, data, and formats + name: EDAM-bioimaging - The ontology of bioimage informatics operations, topics, + data, and formats tags: - Ontology - Bioimage Analysis type: - Poster - url: https://hal.science/hal-02267597/document + url: https://hal.science/hal-02267597/document - authors: - Geert van Geest - Yann Haefliger - Monique Zahn-Zabal - Patricia M. Palagi - description: 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. + description: 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. license: CC-BY-4.0 name: Using Glittr.org to find, compare and re-use online training materials tags: @@ -4194,7 +4200,9 @@ resources: url: https://www.biorxiv.org/content/10.1101/2024.08.20.608021v1 - authors: - Johannes Soltwedel - description: This repository contains a collection of tools for working with OMERO. Such tools can be working with the OMERO command line interface to transfer datasets between repositories, etc. + description: This repository contains a collection of tools for working with OMERO. + Such tools can be working with the OMERO command line interface to transfer datasets + between repositories, etc. license: CC-BY-4.0 name: Omero-tools tags: @@ -4202,16 +4210,17 @@ resources: - Bioimage Analysis type: - Github Repository - url: https://biapol.github.io/omero-tools/ + url: https://biapol.github.io/omero-tools/ - authors: - Manan Lalit - Joran Deschamps - Florian Jug - Ajinkya Kulkarni - description: Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images + description: Code Implementation for EmbedSeg, an Instance Segmentation Method for + Microscopy Images license: CC-BY-NC-4.0 name: EmbedSeg Repository - tags: + tags: - Bioimage Analysis - Instance Segmentation type: @@ -4219,8 +4228,9 @@ resources: url: https://github.com/juglab/EmbedSeg - authors: - Pauli Virtanen et al. - description: This is a conversion and second life of SciPy Cookbook as a bunch of Ipython notebooks. - license: bsd 3-clause + description: This is a conversion and second life of SciPy Cookbook as a bunch of + Ipython notebooks. + license: BSD-3-CLAUSE name: Scipy Cookbook tags: - Bioimage Analysis @@ -4230,27 +4240,28 @@ resources: - authors: - Ziv Yaniv et al. description: Jupyter notebooks for learning how to use SimpleITK - license: Apache-2.0 license + license: APACHE-2.0 LICENSE name: SimpleITK-Notebooks tags: - Bioimage Analysis - - SimpleITK + - Simpleitk type: - Github Repository - url: https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks + url: https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks - authors: - Juan Nunez-Iglesias et al. - description: skimage-tutorials - a collection of tutorials for the scikit-image package. - license: CC0 1.0 Universal + description: skimage-tutorials - a collection of tutorials for the scikit-image + package. + license: CC0 1.0 UNIVERSAL name: skimage-tutorials tags: - Bioimage Analysis - - Scikit-image + - Scikit-Image type: - Github Repository url: https://github.com/scikit-image/skimage-tutorials - authors: - - Loïc Estève et al. + - "Lo\xEFc Est\xE8ve et al." description: Machine learning in Python with scikit-learn MOOC license: CC-BY-4.0 name: scikit-learn MOOC @@ -4263,7 +4274,7 @@ resources: - authors: - Yandex School of Data Analysis description: YSDA course in Natural Language Processing - license: MIT license + license: MIT name: NLP Course tags: - Natural Language Processing @@ -4272,8 +4283,14 @@ resources: url: https://github.com/yandexdataschool/nlp_course - authors: - Beth Cimini et al. - description: 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. - license: BSD License + description: 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. + license: BSD LICENSE name: Community-developed checklists for publishing images and image analyses tags: - Bioimage Analysis @@ -4281,11 +4298,12 @@ resources: type: - Notebook - Collection - url: https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html + url: https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html - authors: - EMBL-EBI - description: Online tutorial and webinar library, designed and delivered by EMBL-EBI experts - license: CC0 (mostly, but can differ depending on resource) + description: Online tutorial and webinar library, designed and delivered by EMBL-EBI + experts + license: CC0 (MOSTLY, BUT CAN DIFFER DEPENDING ON RESOURCE) name: EMBL-EBI material collection tags: - Bioinformatics @@ -4293,115 +4311,117 @@ resources: type: - Collection url: https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query= - - authors: - Vanessa Fuchs - Fiona Aphaia - Christian Schmidt - Tom Boissonnet description: '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. - + 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 structured metadata annotations in the image data management platform OMERO (OME Remote Objects) to optimize their data handling. This strategy helps both with organizing data for easier processing and analysis and for the preparation of data publication in journal manuscripts and in public repositories such as the BioImage Archive. Participants learn the - principles of leveraging object-oriented data organization in OMERO to enhance findability - and usability of their data, also in collaborative settings. The integration of - OMERO with image analysis tools, in particular ImageJ/Fiji, will be trained. Moreover, - users learn about community-accepted metadata checklists (REMBI) to enrich the value - of their data toward reproducibility and reusability. In this workshop, we will - provide hands-on training and recommendations on: - - + principles of leveraging object-oriented data organization in OMERO to enhance + findability and usability of their data, also in collaborative settings. The integration + of OMERO with image analysis tools, in particular ImageJ/Fiji, will be trained. + Moreover, users learn about community-accepted metadata checklists (REMBI) to + enrich the value of their data toward reproducibility and reusability. In this + workshop, we will provide hands-on training and recommendations on: + + Structured metadata annotation features in OMERO and how to use them - - Types of metadata in bioimaging: Technical metadata, sample metadata, analysis metadata - + + Types of metadata in bioimaging: Technical metadata, sample metadata, analysis + metadata + The use of ontologies and terminologies for metadata annotation - + REMBI, the recommended metadata for biological images - + Metadata-assisted image analysis streamlining - + Tools for metadata annotation in OMERO - - + + The target group for this workshop - - This workshop is directed at researchers at all career levels who have started using - 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. - + + This workshop is directed at researchers at all career levels who have started + using 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. + Who are the trainers (see trainer description below for more details) - - + + Dr. Vanessa Fuchs (NFDI4BIOIMAGE Data Steward, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) - + Dr. Tom Boissonnet (OMERO admin and image metadata specialist, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) - + Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg) - - + + Material Description - + Published here are the presentation slides that were used for input from the trainers - during the different sessions of the programme. Additionally, a Fiji Macro is published - that depends on the OMERO Extensions Plugin by Pouchin et al, 2022, F100Research, - https://doi.org/10.12688/f1000research.110385.2  - + during the different sessions of the programme. Additionally, a Fiji Macro is + published that depends on the OMERO Extensions Plugin by Pouchin et al, 2022, + F100Research, https://doi.org/10.12688/f1000research.110385.2  + Programme Overview - + Day 1 - April 29th, 2024 09.00 a.m. to 10.00 a.m.: Session 1 - Welcome and Introduction - + 10.00 a.m. to 10.30 a.m.:  Session 2 - Introduction to the FAIR principles & data annotation - + 10:30 a.m. to 10:45 a.m.: Coffee break - + 10.45 a.m. to 12.00 a.m.: Session 3 - Data structure (datasets in OMERO) and organization with Tags  - + 12.00 a.m. to 1.00 p.m.:  Lunch Break - - 1.00 p.m. to 2.00 p.m.:  Session 4 - REMBI, Key-Value pair annotations in bioimaging - + + 1.00 p.m. to 2.00 p.m.:  Session 4 - REMBI, Key-Value pair annotations in + bioimaging + 2:00 p.m. to 2.30 p.m.:  Session 5 - Ontologies for Key-Value Pairs in OMERO - + 2:30 p.m. to 2:45 p.m. Coffee break - + 2.45 p.m. to 3.45 p.m.:  Wrap-up, discussion, outlook on day 2 - + Day 2 - April 30th, 2024 - + 09.00 a.m. to 09.30 a.m.:  Arrival and Start into day 2 - + 09.30 a.m. to 11.30 a.m.:  Session 6 - Hands-on : REMBI-based Key-Value Pair annotation in OMERO - + 11.30 a.m. to 12.30 a.m.:  Lunch Break - + 12.30 a.m. to 1.15 p.m.: Session 7 - OMERO and OMERO.plugins - + 1.15 p.m. to 2.00 p.m.: Session 8 - Loading OMERO-hosted data into Fiji - + 2.00 p.m. to 2.15 p.m.: Coffee break  - + 2.15 p.m. to 3.00 p.m.: Discussion, Outlook' license: CC-BY-4.0 name: '[Workshop] FAIR data handling for microscopy: Structured metadata annotation @@ -4411,11 +4431,10 @@ resources: url: - https://zenodo.org/records/11109616 - https://doi.org/10.5281/zenodo.11109616 - - -- authors: Massei, Riccardo +- authors: + - Riccardo Massei description: 'YMIA python event 2024 - + Presentation :  "Getting started with Python: intro and set-up a conda environment with Dr. Riccardo Massei"' license: CC-BY-4.0 @@ -4425,11 +4444,12 @@ resources: url: - https://zenodo.org/records/13908480 - https://doi.org/10.5281/zenodo.13908480 -- authors: Haase, Robert +- authors: + - Robert Haase description: In this presentation I introduce bia-bob, an AI-based code generator that integrates into Jupyter Lab and allows for easy generation of Bio-Image Analysis - Python code. It highlights how to get started with using large language models and - prompt engineering to get high-quality bio-image analysis code. + Python code. It highlights how to get started with using large language models + and prompt engineering to get high-quality bio-image analysis code. license: CC-BY-4.0 name: Bio-image Analysis Code Generation using bia-bob num_downloads: 101 @@ -4437,18 +4457,24 @@ resources: url: - https://zenodo.org/records/13908108 - https://doi.org/10.5281/zenodo.13908108 - -- authors: University of Ghent - description: 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. +- authors: + - University of Ghent + description: 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. license: UNKNOWN name: Ghent University Research Data Management (RDM) - policy and support tags: - Research Data Management - type: + type: - Website url: https://www.ugent.be/en/research/openscience/datamanagement -- authors: GO FAIR - description: 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. +- authors: + - GO FAIR + description: 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. license: CC-BY-4.0 name: RDM Starter Kit tags: @@ -4456,24 +4482,29 @@ resources: type: - Website url: https://www.go-fair.org/resources/rdm-starter-kit/ -- authors: Haase, Robert - description: Overview about decision making and how to influence decisions in the bio-image analysis software context. +- authors: + - Robert Haase + description: Overview about decision making and how to influence decisions in the + bio-image analysis software context. license: CC-BY-4.0 name: Hitchhiking through a diverse Bio-image Analysis Software Universe - tags: + tags: - Bioimage Analysis type: - Slide - Presentation num_downloads: 86 publication_date: '2022-07-22' - url: + url: - https://f1000research.com/slides/11-746 - https://doi.org/10.7490/f1000research.1119026.1 -- authors: Costantino Thanos - description: This article discusses various aspects of data reusability in the context of scientific research, including technological, legal, and policy frameworks. +- authors: + - Costantino Thanos + description: This article discusses various aspects of data reusability in the context + of scientific research, including technological, legal, and policy frameworks. license: CC-BY-4.0 - name: Research Data Reusability - Conceptual Foundations, Barriers and Enabling Technologies + name: Research Data Reusability - Conceptual Foundations, Barriers and Enabling + Technologies tags: - Research Data Management - Open Science @@ -4482,14 +4513,16 @@ resources: - Publication publication_date: '2017-01-09' url: https://www.mdpi.com/2304-6775/5/1/2 -- authors: - - Mark D. Wilkinson - - Michel Dumontier - - IJsbrand Jan Aalbersberg - - Gabrielle Appleton - - Myles Axton - - et. al - description: This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community. +- authors: + - Mark D. Wilkinson + - Michel Dumontier + - IJsbrand Jan Aalbersberg + - Gabrielle Appleton + - Myles Axton + - et. al + description: This Comment is the first formal publication of the FAIR Principles, + and includes the rationale behind them, and some exemplar implementations in the + community. license: CC-BY-4.0 name: The FAIR Guiding Principles for scientific data management and stewardship tags: @@ -4498,17 +4531,21 @@ resources: type: - Publication publication_date: '2016-03-15' - url: + url: - https://www.nature.com/articles/sdata201618 - https://doi.org/10.1038/sdata.2016.18 -- authors: +- authors: - Mark A Musen - Martin J O'Connor - Erik Schultes - - Marcos Martínez-Romero + - "Marcos Mart\xEDnez-Romero" - Josef Hardi - John Graybeal - description: The authors have developed a model for scientific metadata, and they have made that model usable by both CEDAR and FAIRware. The approach shows that a formal metadata model can standardize reporting guidelines and that it can enable separate software systems to assist (1) in the authoring of standards-adherent metadata and (2) in the evaluation of existing metadata. + description: The authors have developed a model for scientific metadata, and they + have made that model usable by both CEDAR and FAIRware. The approach shows that + a formal metadata model can standardize reporting guidelines and that it can enable + separate software systems to assist (1) in the authoring of standards-adherent + metadata and (2) in the evaluation of existing metadata. license: CC-BY-4.0 name: Modeling community standards for metadata as templates makes data FAIR tags: @@ -4518,19 +4555,24 @@ resources: type: - Publication publication_date: '2022-11-12' - url: + url: - https://pubmed.ncbi.nlm.nih.gov/36371407/ - https://www.nature.com/articles/s41597-022-01815-3 -- authors: +- authors: - Mathias Hammer - Maximiliaan Huisman - Alessandro Rigano - Ulrike Boehm - James J. Chambers - et al. - description: Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata specifications that extend the OME data model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments. + description: Rigorous record-keeping and quality control are required to ensure + the quality, reproducibility and value of imaging data. The 4DN Initiative and + BINA here propose light Microscopy Metadata specifications that extend the OME + data model, scale with experimental intent and complexity, and make it possible + for scientists to create comprehensive records of imaging experiments. license: UNKNOWN - name: Towards community-driven metadata standards for light microscopy - tiered specifications extending the OME model + name: Towards community-driven metadata standards for light microscopy - tiered + specifications extending the OME model tags: - Reproducibility - Microscopy Image Analysis @@ -4549,9 +4591,13 @@ resources: - Jan Ellenberg - David Grunwald - et al. - description: 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. + description: 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. license: UNKNOWN - name: REMBI - Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology + name: "REMBI - Recommended Metadata for Biological Images\u2014enabling reuse of\ + \ microscopy data in biology" tags: - Metadata - Bioimage Data @@ -4560,18 +4606,20 @@ resources: type: - Publication publication_date: '2021-05-21' - url: + url: - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015/ - https://www.nature.com/articles/s41592-021-01166-8 - https://doi.org/10.1038/s41592-021-01166-8 -- authors: +- authors: - Philippa C. Griffin - Jyoti Khadake - Kate S. LeMay - Suzanna E. Lewis - - Sandra Orchard + - Sandra Orchard - et al. - description: 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. + description: "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 \u2018omics\u2019 datasets and computer-based data processing and analysis." license: UNKNOWN name: Best practice data life cycle approaches for the life sciences tags: @@ -4585,12 +4633,14 @@ resources: num_downloads: 1615 publication_date: '2018-06-04' url: https://doi.org/10.12688/f1000research.12344.2 -- authors: - - Schmidt, Christian - - Ferrando-May, Elisa - description: Align existing and establish novel services & solutions for data management tasks throughout the bioimage data lifecycle. - license: ccy-by-sa-4.0 - name: NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data +- authors: + - Christian Schmidt + - Elisa Ferrando-May + description: Align existing and establish novel services & solutions for data management + tasks throughout the bioimage data lifecycle. + license: CCY-BY-SA-4.0 + name: NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure + for Microscopy Data tags: - Nfdi4Bioimage - Image Data Management @@ -4599,10 +4649,12 @@ resources: type: - Conference Abstract - Slide - publication_date: '2021-04-29' + publication_date: '2021-04-29' url: https://doi.org/10.11588/heidok.00029489 -- authors: ELIXIR (2021) Research Data Management Kit - description: In this section, information is organised according to the stages of the research data life cycle. +- authors: + - ELIXIR (2021) Research Data Management Kit + description: In this section, information is organised according to the stages of + the research data life cycle. license: CC-BY-4.0 name: Data life cycle tags: @@ -4621,28 +4673,33 @@ resources: type: - Collection url: https://tess.elixir-europe.org/search?q=data+life+cycle#materials -- authors: +- authors: - Uli Hahn - Kerstin Helbig - Gerald Jagusch - Jessica Rex - description: Die vorliegende Empfehlung sowie die zugehörigen Erfahrungsberichte geben einen Überblick über die verschiedenen Möglichkeiten der Gestaltung einer Forschungsdatenmanagement Policy sowie Wege zu deren Erstellung. + description: "Die vorliegende Empfehlung sowie die zugeh\xF6rigen Erfahrungsberichte\ + \ geben einen \xDCberblick \xFCber die verschiedenen M\xF6glichkeiten der Gestaltung\ + \ einer Forschungsdatenmanagement Policy sowie Wege zu deren Erstellung." license: CC-BY-4.0 - name: Erstellung und Realisierung einer institutionellen Forschungsdaten-Policy + name: Erstellung und Realisierung einer institutionellen Forschungsdaten-Policy tags: - - Research Data Management + - Research Data Management type: - Publication - publication_date: ' 2018-10-22' - url: + publication_date: ' 2018-10-22' + url: - https://bausteine-fdm.de/article/view/7945 - - https://doi.org/10.17192/bfdm.2018.1.7945 -- authors: + - https://doi.org/10.17192/bfdm.2018.1.7945 +- authors: - Bea Hiemenz - Monika Kuberek - description: As a methodological approach, research data policies of German universities are collected and evaluated, and compared to international recommendations on research data policies. + description: As a methodological approach, research data policies of German universities + are collected and evaluated, and compared to international recommendations on + research data policies. license: CC-BY-4.0 - name: Leitlinie? Grundsätze? Policy? Richtlinie? – Forschungsdaten-Policies an deutschen Universitäten + name: "Leitlinie? Grunds\xE4tze? Policy? Richtlinie? \u2013 Forschungsdaten-Policies\ + \ an deutschen Universit\xE4ten" tags: - Research Data Management - FAIR-Principles @@ -4650,7 +4707,9 @@ resources: - Publication publication_date: '2018-07-13' url: https://www.o-bib.de/bib/article/view/2018H2S1-13 -- description: 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. +- description: 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. license: CC-BY-4.0 name: Guidance for Developing a Research Data Management (RDM) Policy tags: @@ -4659,10 +4718,11 @@ resources: - Book num_downloads: 545 publication_date: '2017' - url: + url: - https://discovery.ucl.ac.uk/id/eprint/1546596/1/26_Learn_Guidance_137-140.pdf - https://doi.org/10.14324/000.learn.27 -- description: Leading open-source platform for collaborative and living data management plans. +- description: Leading open-source platform for collaborative and living data management + plans. license: UNKOWN name: Data Stewardship Wizard tags: @@ -4674,7 +4734,8 @@ resources: - Website - Online Tutorial url: https://ds-wizard.org/ -- description: Der Research Data Management Organiser (RDMO) unterstützt Forschungsprojekte bei der Planung, Umsetzung und Verwaltung aller Aufgaben des Forschungsdatenmanagements. +- description: "Der Research Data Management Organiser (RDMO) unterst\xFCtzt Forschungsprojekte\ + \ bei der Planung, Umsetzung und Verwaltung aller Aufgaben des Forschungsdatenmanagements." license: UNKNOWN name: RDMO - Research Data Management Organiser tags: @@ -4684,8 +4745,11 @@ resources: - Website - Online Tutorial url: https://rdmorganiser.github.io/ -- authors: Robert Haase - description: 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. +- authors: + - Robert Haase + description: 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. license: CC-BY-4.0 name: Creating a Research Data Management Plan using chatGPT tags: @@ -4696,12 +4760,21 @@ resources: - Blog publication_date: '2023-11-06' url: https://focalplane.biologists.com/2023/11/06/creating-a-research-data-management-plan-using-chatgpt/ -- authors: +- authors: - Till Kreutzer - Henning Lahmann - description: Die Digitalisierung ermöglicht eine offene Wissenschaft (Open Science). Diese hat viele Aspekte, insbesondere den freien Zugang zu wissenschaftlichen Veröffentlichungen und Materialien (Open Access), transparente Begutachtungsverfahren (Open Peer Review) oder quelloffene Technologien (Open Source). Das Programm Hamburg Open Science (Laufzeit 2018–2020) unterstützt unter anderem den Kulturwandel in der Wissenschaft. In diesem Kontext entstand der nun vorliegende Leitfaden, der das rechtliche Umfeld greifbar machen soll. Der Leitfaden erarbeitet die betroffenen Rechtsgebiete zunächst systematisch. Im zweiten Teil werden rechtliche Fragen zu Open Science beantwortet, die direkt aus den Universitäten und Bibliotheken kommen. - license: CC-BY-4.0 - name: Rechtsfragen bei Open Science - Ein Leitfaden + description: "Die Digitalisierung erm\xF6glicht eine offene Wissenschaft (Open Science).\ + \ Diese hat viele Aspekte, insbesondere den freien Zugang zu wissenschaftlichen\ + \ Ver\xF6ffentlichungen und Materialien (Open Access), transparente Begutachtungsverfahren\ + \ (Open Peer Review) oder quelloffene Technologien (Open Source). Das Programm\ + \ Hamburg Open Science (Laufzeit 2018\u20132020) unterst\xFCtzt unter anderem\ + \ den Kulturwandel in der Wissenschaft. In diesem Kontext entstand der nun vorliegende\ + \ Leitfaden, der das rechtliche Umfeld greifbar machen soll. Der Leitfaden erarbeitet\ + \ die betroffenen Rechtsgebiete zun\xE4chst systematisch. Im zweiten Teil werden\ + \ rechtliche Fragen zu Open Science beantwortet, die direkt aus den Universit\xE4\ + ten und Bibliotheken kommen." + license: CC-BY-4.0 + name: Rechtsfragen bei Open Science - Ein Leitfaden tags: - Open Science - Open Access @@ -4709,8 +4782,9 @@ resources: type: - Book publication_date: '2021-05-25' - url: https://hup.sub.uni-hamburg.de/oa-pub/catalog/book/205 -- description: Fiji is a popular free open-source image processing package based on ImageJ. + url: https://hup.sub.uni-hamburg.de/oa-pub/catalog/book/205 +- description: Fiji is a popular free open-source image processing package based on + ImageJ. license: BSD-2-CLAUSE name: Fiji tags: @@ -4718,11 +4792,12 @@ resources: - OMERO type: - Online Tutorial - url: https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html -- authors: Christian Schmidt + url: https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html +- authors: + - Christian Schmidt description: A Microscopy Research Data Management Resource. license: UNKNOWN - name: I3D bio – Information Infrastructure for BioImage Data - Bioimage Metadata + name: "I3D bio \u2013 Information Infrastructure for BioImage Data - Bioimage Metadata" tags: - Metadata - I3Dbio @@ -4730,9 +4805,10 @@ resources: - Bioimage Data type: - Collection - url: + url: - https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/ -- description: The key-value pairs are annotations in OMERO useful to describe thoroughly the data and can be added & edited via the OMERO.web interface. +- description: The key-value pairs are annotations in OMERO useful to describe thoroughly + the data and can be added & edited via the OMERO.web interface. license: UNKNOWN name: Key-Value pairs scripts tags: @@ -4741,35 +4817,41 @@ resources: - Documentation - Collection url: https://guide-kvpairs-scripts.readthedocs.io/en/latest/ -- authors: +- authors: - Ilya G. Goldberg - Chris Allan - Jean-Marie Burel - Doug Creager - Andrea Falconi - et. al - description: The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. + description: The Open Microscopy Environment (OME) defines a data model and a software + implementation to serve as an informatics framework for imaging in biological + microscopy experiments, including representation of acquisition parameters, annotations + and image analysis results. license: CC-BY-4.0 - name: The Open Microscopy Environment (OME) Data Model and XML file - open tools for informatics and quantitative analysis in biological imaging + name: The Open Microscopy Environment (OME) Data Model and XML file - open tools + for informatics and quantitative analysis in biological imaging tags: - Microscopy Image Analysis - Bioimage Analysis type: - Publication publication_date: '2005-05-03' - url: + url: - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47 - https://doi.org/10.1186/gb-2005-6-5-r47 - authors: - - Marie-Hélène Bourget + - "Marie-H\xE9l\xE8ne Bourget" - Lee Kamentsky - Satrajit S. Ghosh - Giacomo Mazzamuto - Alberto Lazari - et al. - description: The Brain Imaging Data Structure (BIDS) is a specification for organizing, sharing, and archiving neuroimaging data and metadata in a reusable way. + description: The Brain Imaging Data Structure (BIDS) is a specification for organizing, + sharing, and archiving neuroimaging data and metadata in a reusable way. license: CC-BY-4.0 - name: Microscopy-BIDS - An Extension to the Brain Imaging Data Structure for Microscopy Data + name: Microscopy-BIDS - An Extension to the Brain Imaging Data Structure for Microscopy + Data tags: - Research Data Management - Image Data Management @@ -4779,7 +4861,8 @@ resources: num_downloads: 768 publication_date: '2022-04-19' url: https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2022.871228/full -- description: Recommended Metadata for Biological Images (REMBI) provides guidelines for metadata for biological images to enable the FAIR sharing of scientific data. +- description: Recommended Metadata for Biological Images (REMBI) provides guidelines + for metadata for biological images to enable the FAIR sharing of scientific data. license: CC0-1.0 name: REMBI Overview tags: @@ -4791,14 +4874,18 @@ resources: type: - Collection url: https://www.ebi.ac.uk/bioimage-archive/rembi-help-overview/ -- authors: +- authors: - Rohola Hosseini - Matthijs Vlasveld - Joost Willemse - Bob van de Water - - Sylvia E. Le Dévédec - - Katherine J. Wolstencroft - description: 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. + - "Sylvia E. Le D\xE9v\xE9dec" + - Katherine J. Wolstencroft + description: 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. license: CC-BY-4.0 name: FAIR High Content Screening in Bioimaging tags: @@ -4811,10 +4898,12 @@ resources: - Publication publication_date: '2023-07-17' url: https://www.nature.com/articles/s41597-023-02367-w -- authors: +- authors: - Lienhard Wegewitz - - F. Strauß - description: 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. + - "F. Strau\xDF" + description: 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. license: AGPL-3.0 name: Dokumentation und Anleitung zum elektronischen Laborbuch (eLabFTW) tags: @@ -4824,17 +4913,18 @@ resources: - Document - Tutorial publication_date: '2020-03-23' - url: + url: - https://www.fdm.tu-clausthal.de/fileadmin/FDM/documents/Manual_eLab_v0.3_20200323.pdf - https://www.elabftw.net/ -- authors: +- authors: - Daniel Dietrich - Jonathan Gray - Tim McNamara - Antti Poikola - Rufus Pollock - et al. - description: This handbook is about open data but what exactly is it? In particular what makes open data open, and what sorts of data are we talking about? + description: This handbook is about open data but what exactly is it? In particular + what makes open data open, and what sorts of data are we talking about? license: CC-BY-4.0 name: What is Open Data? tags: @@ -4842,7 +4932,9 @@ resources: type: - Collection url: http://opendatahandbook.org/guide/en/what-is-open-data/ -- description: Sharing your data can benefit your career in some interesting ways. In this post, read why you should be making more of your research data openly available. +- description: Sharing your data can benefit your career in some interesting ways. + In this post, read why you should be making more of your research data openly + available. license: UNKNOWN name: Five great reasons to share your research data tags: @@ -4852,9 +4944,12 @@ resources: - Blog publication_date: '2022-03-18' url: https://web.library.uq.edu.au/blog/2022/03/five-great-reasons-share-your-research-data -- description: The website offers detailed advice on publishing research data, focusing on key issues like data management, FAIR data principles, legal considerations, and repository selection. +- description: The website offers detailed advice on publishing research data, focusing + on key issues like data management, FAIR data principles, legal considerations, + and repository selection. license: UNKNOWN - name: Research data - what are the key issues to consider when publishing this kind of material? + name: Research data - what are the key issues to consider when publishing this kind + of material? tags: - Research Data Management - FAIR-Principles @@ -4862,8 +4957,11 @@ resources: type: - Tutorial url: https://www.publisso.de/en/advice/publishing-advice-faqs/research-data -- authors: Christian Schmidt - description: 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? +- authors: + - Christian Schmidt + description: 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? license: UNKNOWN name: Finding and Choosing a Data Repository tags: @@ -4873,7 +4971,10 @@ resources: - Tutorial publication_date: '2023-07-01' url: https://gerbi-gmb.de/2023/06/01/finding-and-choosing-a-repository/ -- description: 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. +- description: 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. license: CC-BY-4.0 name: re3data.org - registry of Research Data Repositories tags: @@ -4881,7 +4982,10 @@ resources: type: - Website url: https://www.re3data.org/ -- description: 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. +- description: "In 2016, the \u2018FAIR Guiding Principles for scientific data management\ + \ and stewardship\u2019 were published in Scientific Data. The authors intended\ + \ to provide guidelines to improve the Findability, Accessibility, Interoperability,\ + \ and Reuse of digital assets." license: CC-BY-4.0 name: FAIR Priciples tags: @@ -4891,7 +4995,9 @@ resources: type: - Collection url: https://www.go-fair.org/fair-principles/ -- description: 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. +- description: "To submit, you\u2019ll 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." license: CC0-1.0 name: Submitting data to the BioImage Archive tags: @@ -4902,16 +5008,18 @@ resources: - Tutorial - Video url: https://www.ebi.ac.uk/bioimage-archive/submit/ -- authors: - - Matthew Hartley - - Gerard J. Kleywegt - - Ardan Patwardhan - - Ugis Sarkans - - Jason R. Swedlow - - Alvis Brazma - description: The BioImage Archive is a new archival data resource at the European Bioinformatics Institute (EMBL-EBI). +- authors: + - Matthew Hartley + - Gerard J. Kleywegt + - Ardan Patwardhan + - Ugis Sarkans + - Jason R. Swedlow + - Alvis Brazma + description: The BioImage Archive is a new archival data resource at the European + Bioinformatics Institute (EMBL-EBI). license: UNKNOWN - name: The BioImage Archive – Building a Home for Life-Sciences Microscopy Data + name: "The BioImage Archive \u2013 Building a Home for Life-Sciences Microscopy\ + \ Data" tags: - Image Data Management - Research Data Management @@ -4919,26 +5027,31 @@ resources: type: - Publication publication_date: '2022-06-22' - url: + url: - https://www.sciencedirect.com/science/article/pii/S0022283622000791?via%3Dihub - https://doi.org/10.1016/j.jmb.2022.167505 -- description: 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. +- description: "Schritt f\xFCr Schritt verbessern wir die Nutzungsm\xF6glichkeiten\ + \ von Daten f\xFCr Wissenschaft und Gesellschaft. Durch unser Zusammenwirken im\ + \ NFDI-Verein entsteht eine Dachorganisation f\xFCr das Forschungsdatenmanagement\ + \ in allen Wissenschaftszweigen." license: UNKNOWN - name: NFDI - Daten als gemeinsames Gut für exzellente Forschung, organisiert durch die Wissenschaft in Deutschland. + name: "NFDI - Daten als gemeinsames Gut f\xFCr exzellente Forschung, organisiert\ + \ durch die Wissenschaft in Deutschland." tags: - Nfdi4Bioimage - Research Data Management type: - Website - url: https://www.nfdi.de/ -- authors: + url: https://www.nfdi.de/ +- authors: - Leyla Garcia - - Bérénice Batut + - "B\xE9r\xE9nice Batut" - Melissa L. Burke - Mateusz Kuzak - Fotis Psomopoulos - et al. - description: The authors offer trainers some simple rules, to help make their training materials FAIR, enabling others to find, (re)use, and adapt them. + description: The authors offer trainers some simple rules, to help make their training + materials FAIR, enabling others to find, (re)use, and adapt them. license: CC-BY-4.0 name: Ten simple rules for making training materials FAIR tags: @@ -4951,11 +5064,14 @@ resources: num_downloads: 4311 publication_date: '2020-05-21' url: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854 -- authors: +- authors: - Martin Boeckhout - Gerhard A. Zielhuis - - Annelien L. Bredenoord - description: The FAIR guiding principles for research data stewardship (findability, accessibility, interoperability, and reusability) look set to become a cornerstone of research in the life sciences. A critical appraisal of these principles in light of ongoing discussions and developments about data sharing is in order. + - Annelien L. Bredenoord + description: The FAIR guiding principles for research data stewardship (findability, + accessibility, interoperability, and reusability) look set to become a cornerstone + of research in the life sciences. A critical appraisal of these principles in + light of ongoing discussions and developments about data sharing is in order. license: CC-BY-4.0 name: The FAIR guiding principles for data stewardship - fair enough? tags: @@ -4978,7 +5094,9 @@ resources: - Presentation publication_date: '2023-07-05' url: https://omero-fbi.fr/slides/elmi23_cfd/main.html#/title-slide -- description: 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. +- description: 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. license: CC-BY-4.0 name: DataPLANT knowledge base tags: @@ -4989,23 +5107,26 @@ resources: - Collection publication_date: '2022-12-14' url: https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html -- description: An easy to use and open source converter for bioimaging data. NGFF-Converter is a GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF. +- description: An easy to use and open source converter for bioimaging data. NGFF-Converter + is a GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation + File Format) or OME-TIFF. license: GPL-2.0 - name: NGFF Converter + name: NGFF Converter tags: - Bioimage Data - Open Source Software type: - Application - url: https://www.glencoesoftware.com/products/ngff-converter/ + url: https://www.glencoesoftware.com/products/ngff-converter/ - authors: - Melissa Linkert - Chris Allan - Josh Moore - - Sébastien Besson + - "S\xE9bastien Besson" - David Gault - et al. - description: Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification. + description: Java application to convert image file formats, including .mrxs, to + an intermediate Zarr structure compatible with the OME-NGFF specification. license: GPL-2.0 name: bioformats2raw Converter tags: @@ -5018,9 +5139,10 @@ resources: - authors: - Melissa Linkert - Chris Allan - - Sébastien Besson + - "S\xE9bastien Besson" - Josh Moore - description: Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion. + description: Java application to convert a directory of tiles to an OME-TIFF pyramid. + This is the second half of iSyntax/.mrxs => OME-TIFF conversion. license: GPL-2.0 name: raw2ometiff Converter tags: @@ -5030,19 +5152,24 @@ resources: - Application - Github Repository url: https://github.com/glencoesoftware/raw2ometiff -- description: This Focus issue features a series of papers offering guidelines and tools for improving the tracking and reporting of microscopy metadata with an emphasis on reproducibility and data re-use. +- description: This Focus issue features a series of papers offering guidelines and + tools for improving the tracking and reporting of microscopy metadata with an + emphasis on reproducibility and data re-use. license: UNKNOWN name: Reporting and reproducibility in microscopy tags: - Reproducibility - - Meta Data + - Metadata - Bioimage Data type: - Collection publication_date: '2021-12-03' - url: https://www.nature.com/collections/djiciihhjh -- authors: Christopher Schmied - description: In this paper we introduce two sets of checklists. One is concerned with the publication of images. The other one gives instructions for the publication of image analysis. + url: https://www.nature.com/collections/djiciihhjh +- authors: + - Christopher Schmied + description: In this paper we introduce two sets of checklists. One is concerned + with the publication of images. The other one gives instructions for the publication + of image analysis. license: CC0-1.0 name: Checklists for publishing images and image analysis tags: @@ -5051,15 +5178,16 @@ resources: type: - Forum Post publication_date: '2023-09-14' - url: https://forum.image.sc/t/checklists-for-publishing-images-and-image-analysis/86304 -- authors: - - Stian Soiland-Reyes + url: https://forum.image.sc/t/checklists-for-publishing-images-and-image-analysis/86304 +- authors: + - Stian Soiland-Reyes - Finn Bacall - Bert Droesbeke - Alan R Williams - Johan Gustafsson - et al. - description: A registry for describing, sharing and publishing scientific computational workflows. + description: A registry for describing, sharing and publishing scientific computational + workflows. license: BSD-3-CLAUSE name: WorkflowHub tags: @@ -5070,7 +5198,7 @@ resources: - R type: - Collection - url: https://workflowhub.eu/ + url: https://workflowhub.eu/ - license: CC-BY-4.0 name: Creating Workflows and Advanced Workflow Options tags: @@ -5078,8 +5206,11 @@ resources: type: - Tutorial - Online Tutorial - url: https://galaxyproject.org/learn/advanced-workflow/ -- description: A workflow is a chain of analysis steps. In Galaxy, we can create a workflow from an existing analysis history, or we can create one visually by adding tools to a canvas. This tutorial covers building a workflow to analyse a bacterial genome, from input FASTQ sequencing reads to assembly, annotation, and visualization. + url: https://galaxyproject.org/learn/advanced-workflow/ +- description: A workflow is a chain of analysis steps. In Galaxy, we can create a + workflow from an existing analysis history, or we can create one visually by adding + tools to a canvas. This tutorial covers building a workflow to analyse a bacterial + genome, from input FASTQ sequencing reads to assembly, annotation, and visualization. license: CC0-1.0 name: Galaxy workflows tags: @@ -5087,8 +5218,9 @@ resources: type: - Online Tutorial - Tutorial - url: https://galaxy-au-training.github.io/tutorials/modules/workflows/ -- description: Collection of tutorials developed and maintained by the worldwide Galaxy community. + url: https://galaxy-au-training.github.io/tutorials/modules/workflows/ +- description: Collection of tutorials developed and maintained by the worldwide Galaxy + community. license: CC-BY-4.0 name: Galaxy Training tags: @@ -5097,12 +5229,15 @@ resources: type: - Collection - Tutorial - num_downloads: - publication_date: - url: https://training.galaxyproject.org/ -- authors: - description: The KNIME Image Processing Extension allows you to read in more than 140 different kinds of images and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME. - license: GPLv3 + num_downloads: null + publication_date: null + url: https://training.galaxyproject.org/ +- authors: null + description: The KNIME Image Processing Extension allows you to read in more than + 140 different kinds of images and to apply well known methods on images, like + preprocessing. segmentation, feature extraction, tracking and classification in + KNIME. + license: GPLV3 name: KNIME Image Processing tags: - Imagej @@ -5113,8 +5248,9 @@ resources: - Tutorial - Online Tutorial - Documentation - url: https://www.knime.com/community/image-processing -- description: The NFDI Basic Service DMP4NFDI supports consortia in developing and providing data management plans (DMP) services for their community. + url: https://www.knime.com/community/image-processing +- description: The NFDI Basic Service DMP4NFDI supports consortia in developing and + providing data management plans (DMP) services for their community. license: CC-BY-4.0 name: Abstract - NFDI Basic Service for Data Management Plans tags: @@ -5122,7 +5258,8 @@ resources: type: - Document url: https://base4nfdi.de/images/AbstractDMP4NFDI.pdf -- description: OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data +- description: OME develops open-source software and data format standards for the + storage and manipulation of biological microscopy data license: CC-BY-4.0 name: Open Micoscropy Environment (OME) Youtube Channel tags: @@ -5132,14 +5269,15 @@ resources: type: - Video - Collection - num_downloads: - publication_date: - url: https://www.youtube.com/@OpenMicroscopyEnvironment -- authors: + num_downloads: null + publication_date: null + url: https://www.youtube.com/@OpenMicroscopyEnvironment +- authors: - SciPy - Erick Martins Ratamero - license: Youttube Standard License - name: Erick Martins Ratamero - Expanding the OME ecosystem for imaging data management | SciPy 2024 + license: YOUTTUBE STANDARD LICENSE + name: Erick Martins Ratamero - Expanding the OME ecosystem for imaging data management + | SciPy 2024 tags: - Image Data Management - OMERO @@ -5148,15 +5286,16 @@ resources: - Video - Presentation publication_date: '2024-08-19' - url: https://www.youtube.com/watch?v=GmhyDNm1RsM -- authors: - - Pierre Pouchin + url: https://www.youtube.com/watch?v=GmhyDNm1RsM +- authors: + - Pierre Pouchin - Rdornier - - kekunn - - Jean-Marie Burel - description: A wrapper library which can be called from scripts in Fiji, but can mostly be used in Maven projects to wrap calls to the underlying OMERO Java Gateway. + - kekunn + - Jean-Marie Burel + description: A wrapper library which can be called from scripts in Fiji, but can + mostly be used in Maven projects to wrap calls to the underlying OMERO Java Gateway. license: GPL-2.0 - name: Plugin "simple-omero-client" + name: Plugin "simple-omero-client" tags: - OMERO - Github @@ -5164,7 +5303,8 @@ resources: type: - Github Repository url: https://github.com/GReD-Clermont/simple-omero-client -- description: An ImageJ plugin to run a script or macro on a batch of images from/to OMERO. +- description: An ImageJ plugin to run a script or macro on a batch of images from/to + OMERO. license: GPL-2.0 name: Plugin "omero-batch-plugin" tags: @@ -5175,13 +5315,15 @@ resources: type: - Github Repository url: https://github.com/GReD-Clermont/omero_batch-plugin -- authors: +- authors: - Torec T. Luik - - Rodrigo Rosas-Bertolini - - Eric A.J. Reits - - Ron A. Hoebe - - Przemek M. Krawczyk - description: The authors introduce BIOMERO (bioimage analysis in OMERO), a bridge connecting OMERO, a renowned bioimaging data management platform, FAIR workflows, and high-performance computing (HPC) environments. + - Rodrigo Rosas-Bertolini + - Eric A.J. Reits + - Ron A. Hoebe + - Przemek M. Krawczyk + description: The authors introduce BIOMERO (bioimage analysis in OMERO), a bridge + connecting OMERO, a renowned bioimaging data management platform, FAIR workflows, + and high-performance computing (HPC) environments. license: CC-BY-4.0 name: BIOMERO - A scalable and extensible image analysis framework tags: @@ -5191,14 +5333,16 @@ resources: - Image Data Management type: - Publication - num_downloads: - publication_date: - url: https://doi.org/10.1016/j.patter.2024.101024 -- authors: + num_downloads: null + publication_date: null + url: https://doi.org/10.1016/j.patter.2024.101024 +- authors: - Torec Luik - Johannes Soltwedel - description: The BIOMERO framework, for BioImage analysis in OMERO, allows you to run (FAIR) bioimage analysis workflows directly from OMERO on a high-performance compute (HPC) cluster, remotely through SSH. - license: Apache-2.0 + description: The BIOMERO framework, for BioImage analysis in OMERO, allows you to + run (FAIR) bioimage analysis workflows directly from OMERO on a high-performance + compute (HPC) cluster, remotely through SSH. + license: APACHE-2.0 name: Biomero tags: - OMERO @@ -5208,13 +5352,14 @@ resources: publication_date: '2024-07-24' url: https://github.com/NL-BioImaging/biomero - authors: - - Erick Martins Ratamero - - Jean-Marie Burel - - Will Moore - - Guillaume Gay - - Christoph Moehl + - Erick Martins Ratamero + - Jean-Marie Burel + - Will Moore + - Guillaume Gay + - Christoph Moehl - et al. - description: An OMERO CLI plugin for creating and using transfer packets between OMERO servers. + description: An OMERO CLI plugin for creating and using transfer packets between + OMERO servers. license: GPL-2.0 name: Plugin "omero-cli-transfer" tags: @@ -5222,12 +5367,12 @@ resources: type: - Github Repository publication_date: '2024-09-14' - url: https://github.com/ome/omero-cli-transfer -- authors: + url: https://github.com/ome/omero-cli-transfer +- authors: - Will Moore - Josh Moore - Yaroslav Halchenko - - Sébastien Besson + - "S\xE9bastien Besson" description: Web page for validating OME-NGFF files. license: BSD-2-CLAUSE name: ome-ngff-validator @@ -5237,10 +5382,12 @@ resources: - Github Repository - Application publication_date: '2022-09-29' - url: + url: - https://ome.github.io/ome-ngff-validator/ - - https://github.com/ome/ome-ngff-validator -- description: Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. There are several scripts for using Bio-Formats on the command line, which are listed here. + - https://github.com/ome/ome-ngff-validator +- description: Bio-Formats is a standalone Java library for reading and writing life + sciences image file formats. There are several scripts for using Bio-Formats on + the command line, which are listed here. license: CC-BY-4.0 name: BioFormats Command line (CLI) tools tags: @@ -5249,24 +5396,23 @@ resources: - Documentation publication_date: '2024-10-24' url: https://bio-formats.readthedocs.io/en/v8.0.0/users/comlinetools/index.html - - -- authors: Haase, Robert +- authors: + - Robert Haase description: The integration of Large Language Models (LLMs) in scientific research - presents both opportunities and challenges for life scientists. Key challenges include - ensuring transparency in AI-generated content and facilitating efficient knowledge - exchange among researchers. These issues arise from the in-transparent nature of - AI-driven code generation and the informal sharing of AI insights, which may hinder - reproducibility and collaboration. This paper introduces git-bob, an innovative - AI-assistant designed to address these challenges by fostering an interactive and - transparent collaboration platform within GitHub. By enabling seamless dialogue + presents both opportunities and challenges for life scientists. Key challenges + include ensuring transparency in AI-generated content and facilitating efficient + knowledge exchange among researchers. These issues arise from the in-transparent + nature of AI-driven code generation and the informal sharing of AI insights, which + may hinder reproducibility and collaboration. This paper introduces git-bob, an + innovative AI-assistant designed to address these challenges by fostering an interactive + and transparent collaboration platform within GitHub. By enabling seamless dialogue between humans and AI, git-bob ensures that AI contributions are transparent and reproducible. Moreover, it supports collaborative knowledge exchange, enhancing the interdisciplinary dialogue necessary for cutting-edge life sciences research. The open-source nature of git-bob further promotes accessibility and customization, positioning it as a vital tool in employing LLMs responsibly and effectively within scientific communities. - license: cc-by-4.0 + license: CC-BY-4.0 name: Towards Transparency and Knowledge Exchange in AI-assisted Data Analysis Code Generation num_downloads: 13 @@ -5274,20 +5420,24 @@ resources: url: - https://zenodo.org/records/13928832 - https://doi.org/10.5281/zenodo.13928832 - -- authors: Fazeli, Elnaz, Robert, Haase, Michael, Doube, Kota, Miura, David, Legland +- authors: + - Elnaz Fazeli + - Haase Robert + - Doube Michael + - Miura Kota + - Legland David description: Bioimaging has transformed our understanding of biological processes, yet extracting meaningful information from complex datasets remains a challenge, particularly for early career scientists. This paper proposes a simplified, systematic approach to bioimage analysis, focusing on categorizing commonly - observed structures and shapes, and providing relevant analysis methods. Our - approach includes illustrative examples and a visual flowchart, enabling researchers - to define analysis objectives clearly. By understanding the diversity of bioimage - structures and aligning them with appropriate analysis approaches, the framework - empowers researchers to navigate bioimage datasets more efficiently. It also - aims to foster a common language between researchers and analysts, thereby - enhancing mutual understanding and facilitating effective communication. - license: cc-by-4.0 + observed structures and shapes, and providing relevant analysis methods. + Our approach includes illustrative examples and a visual flowchart, enabling + researchers to define analysis objectives clearly. By understanding the diversity + of bioimage structures and aligning them with appropriate analysis approaches, + the framework empowers researchers to navigate bioimage datasets more efficiently. + It also aims to foster a common language between researchers and analysts, + thereby enhancing mutual understanding and facilitating effective communication. + license: CC-BY-4.0 name: 'From Cells to Pixels: Bridging Biologists and Image Analysts Through a Common Language' num_downloads: 324 @@ -5295,21 +5445,20 @@ resources: url: - https://zenodo.org/records/13331351 - https://doi.org/10.5281/zenodo.13331351 - -- authors: 'Rémy Jean Daniel Dornier' +- authors: + - "R\xE9my Jean Daniel Dornier" license: - CC-BY-NC-SA-4.0 name: OMERO - QuPath - description: OMERO-RAW extension for QuPath allows to directly access to the raw pixels - of images. All types of images (RGB, fluorescence, ...) are supported with this - extension. + description: OMERO-RAW extension for QuPath allows to directly access to the raw + pixels of images. All types of images (RGB, fluorescence, ...) are supported with + this extension. tags: - Bioimage Analysis - OMERO type: - Online Tutorial url: https://wiki-biop.epfl.ch/en/data-management/omero/qupath - - authors: - Shanghang Zhang - Gaole Dai @@ -5317,40 +5466,46 @@ resources: - Jianxu Chen license: - CC-BY-NC-SA - description: Multimodal large language models have been recognized as a historical milestone in the field of artificial intelligence and have demonstrated revolutionary potentials not only in commercial applications, but also for many scientific fields. Here we give a brief overview of multimodal large language models through the lens of bioimage analysis and discuss how we could build these models as a community to facilitate biology research + description: Multimodal large language models have been recognized as a historical + milestone in the field of artificial intelligence and have demonstrated revolutionary + potentials not only in commercial applications, but also for many scientific fields. + Here we give a brief overview of multimodal large language models through the + lens of bioimage analysis and discuss how we could build these models as a community + to facilitate biology research name: Multimodal large language models for bioimage analysis tags: - Bioimage Analysis - Large Language Models - - Fair-Principles + - FAIR-Principles - Workflow type: - Publication url: - https://www.nature.com/articles/s41592-024-02334-2 - https://arxiv.org/abs/2407.19778 - -- authors: Haase, Robert +- authors: + - Robert Haase description: 'Large Language Models are changing the way we interact with computers, especially how we write code. In this tutorial, we will generate bio-image analysis code using two LLM-based code generators, bia-bob and git-bob. - + https://github.com/haesleinhuepf/bia-bob - + https://github.com/haesleinhuepf/git-bob - +  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Bio-image Analysis Code Generation num_downloads: 4 publication_date: '2024-10-28' url: - https://zenodo.org/records/14001044 - https://doi.org/10.5281/zenodo.14001044 -- authors: +- authors: - Alan O'Callaghan - - Léo Leplat - description: These are the notebooks and associated files for the i2k 2024 QuPath for Python programmers workshop. + - "L\xE9o Leplat" + description: These are the notebooks and associated files for the i2k 2024 QuPath + for Python programmers workshop. tags: - Python - Notebooks @@ -5364,8 +5519,7 @@ resources: name: QuPath for Python programmers publication_date: '2024-10-23' url: https://github.com/qupath/i2k-qupath-for-python-programmers - -- authors: +- authors: - Stephan Saalfeld - Tobias Pietzsch tags: @@ -5374,16 +5528,16 @@ resources: - Workshop - Notebook - Github Repository - license: Apache-2.0 - name: I2K2024 workshop material - Lazy Parallel Processing and Visualization of Large Data with ImgLib2, BigDataViewer, the N5-API, and Spark - num_downloads: - publication_date: - url: + license: APACHE-2.0 + name: I2K2024 workshop material - Lazy Parallel Processing and Visualization of + Large Data with ImgLib2, BigDataViewer, the N5-API, and Spark + num_downloads: null + publication_date: null + url: - https://saalfeldlab.github.io/i2k2024-lazy-workshop/ - https://github.com/saalfeldlab/i2k2024-lazy-workshop - -- authors: - - Jordão Bragantini +- authors: + - "Jord\xE3o Bragantini" - Teun Huijben tags: - Segmentation @@ -5395,16 +5549,16 @@ resources: - Tutorial license: BSD3-CLAUSE name: Ultrack I2K 2024 Workshop Materials - url: + url: - https://github.com/royerlab/ultrack-i2k2024 - https://royerlab.github.io/ultrack-i2k2024/ - -- authors: - - Agustín Andrés Corbat +- authors: + - "Agust\xEDn Andr\xE9s Corbat" - OmFrederic - Jonas Windhager - - Kristína Lidayová - description: Material for the I2K 2024 "Multiplexed tissue imaging - tools and approaches" workshop + - "Krist\xEDna Lidayov\xE1" + description: Material for the I2K 2024 "Multiplexed tissue imaging - tools and approaches" + workshop tags: - Bioimage Analysis - Microscopy Image Analysis @@ -5414,12 +5568,14 @@ resources: - Workshop license: CC-BY-4.0 name: Multiplexed tissue imaging - tools and approaches - url: + url: - https://github.com/BIIFSweden/I2K2024-MTIWorkshop - https://docs.google.com/presentation/d/1R9-4lXAmTYuyFZpTMDR85SjnLsPZhVZ8/edit#slide=id.p1 - -- authors: Robert Haase - description: This repository contains training materials for the Tutorial "Bio-Image Analysis Code Generation" at the From Images To Knowledge (I2K) Conference (virtual) October 28th-30th 2024. +- authors: + - Robert Haase + description: This repository contains training materials for the Tutorial "Bio-Image + Analysis Code Generation" at the From Images To Knowledge (I2K) Conference (virtual) + October 28th-30th 2024. tags: - Bioimage Analysis - Notebooks @@ -5431,9 +5587,10 @@ resources: license: BSD-3-CLAUSE name: I2K2024(virtual) - Bio-Image Analysis Code Generation url: https://github.com/haesleinhuepf/i2k2024-ai-code-generation - -- authors: Joanna Pylvänäinen - description: I2K 2024 workshop materials for "Object Tracking and Track Analysis using TrackMate and CellTracksColab" +- authors: + - "Joanna Pylv\xE4n\xE4inen" + description: I2K 2024 workshop materials for "Object Tracking and Track Analysis + using TrackMate and CellTracksColab" tags: - Bioimage Analysis - Training @@ -5444,14 +5601,16 @@ resources: - Slides license: GPL-3.0 name: Object Tracking and Track Analysis using TrackMate and CellTracksColab - num_downloads: - publication_date: + num_downloads: null + publication_date: null url: https://github.com/CellMigrationLab/I2K_2024 - -- authors: +- authors: - Stephane Rigaud - Robert Haase - description: Course and material for the clEsperanto workshop presented at I2K 2024 @ Human Technopol (Milan, Italy). The workshop is an hands-on demo of the clesperanto project, focussing on how to use the library for users who want use GPU-acceleration for their Image Processing pipeline. + description: Course and material for the clEsperanto workshop presented at I2K 2024 + @ Human Technopol (Milan, Italy). The workshop is an hands-on demo of the clesperanto + project, focussing on how to use the library for users who want use GPU-acceleration + for their Image Processing pipeline. tags: - Clesperanto - Training @@ -5464,11 +5623,14 @@ resources: - Tutorial - Notebook license: BSD-3-CLAUSE - name: "I2K 2024: clEsperanto - GPU-Accelerated Image Processing Library" + name: 'I2K 2024: clEsperanto - GPU-Accelerated Image Processing Library' url: https://github.com/StRigaud/clesperanto_workshop_I2K24?tab=readme-ov-file - -- authors: Tim Monko - description: Napari-ndev is a collection of widgets intended to serve any person seeking to process microscopy images from start to finish. The goal of this example pipeline is to get the user familiar with working with napari-ndev for batch processing and reproducibility (view Image Utilities and Workflow Widget). +- authors: + - Tim Monko + description: Napari-ndev is a collection of widgets intended to serve any person + seeking to process microscopy images from start to finish. The goal of this example + pipeline is to get the user familiar with working with napari-ndev for batch processing + and reproducibility (view Image Utilities and Workflow Widget). tags: - Napari - Microscopy Image Analysis @@ -5480,13 +5642,14 @@ resources: license: BSD-3-CLAUSE name: Example Pipeline Tutorial publication_date: '2024-10-28' - url: + url: - https://timmonko.github.io/napari-ndev/tutorial/01_example_pipeline/ - - https://github.com/timmonko/napari-ndev -- authors: Moore, Josh + - https://github.com/timmonko/napari-ndev +- authors: + - Josh Moore description: Presented at https://globalbioimaging.org/exchange-of-experience/exchange-of-experience-ix in Okazaki, Japan. - license: cc-by-4.0 + license: CC-BY-4.0 name: "[GBI EoE IX] NFDI4BIOIMAGE\nNational Research Data Infrastructure \nfor Microscopy\ \ and BioImage Analysis" num_downloads: 23 @@ -5494,51 +5657,52 @@ resources: url: - https://zenodo.org/records/14001388 - https://doi.org/10.5281/zenodo.14001388 - -- authors: Moore, Josh +- authors: + - Josh Moore description: Presented at https://www.bioimagingnorthamerica.org/events/bina-2024-community-congress/ - license: cc-by-4.0 + license: CC-BY-4.0 name: '[BINA CC] Scalable strategies for a next-generation of FAIR bioimaging' num_downloads: 37 publication_date: '2024-09-24' url: - https://zenodo.org/records/13831274 - https://doi.org/10.5281/zenodo.13831274 - -- authors: Moore, Josh +- authors: + - Josh Moore description: 'or, "OME-Zarr: ''even a talk on formats [can be] interesting''" - + Presented at https://events.humantechnopole.it/event/1/' - license: cc-by-4.0 + license: CC-BY-4.0 name: '[I2K] Scalable strategies for a next-generation of FAIR bioimaging' num_downloads: 279 publication_date: '2024-10-25' url: - https://zenodo.org/records/13991322 - https://doi.org/10.5281/zenodo.13991322 - -- authors: Zobel, Thomas, Wendt, Jens +- authors: + - Thomas Zobel + - Jens Wendt description: 'This Excel Workbook contains some simple Macros to help with the generation - of a .csv in the necessary format for Key-Value pair annotations of images in OMERO. - + of a .csv in the necessary format for Key-Value pair annotations of images in + OMERO. + The format is tailored for the OMERO.web script "KeyVal_from_csv.py"  (from the version <=5.8.3 of the core omero-scripts). - + Attached is also a video of Thomas Zobel, the head of the imaging core facility Uni Münster, showcasing the use of the Excel workbook.The video uses a slightly older version of the workbook and OMERO, but the core functionality remains unchanged. - + Please keep in mind, that the OMERO.web script(s) to handle Key-Value Pairs from/to .csv files will undergo a major change very soon.This might break the compatibility with the format used now for the generated .csv from the workbook.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Excel template for adding Key-Value Pairs to images num_downloads: 30 publication_date: '2024-10-30' url: - https://zenodo.org/records/14014252 - https://doi.org/10.5281/zenodo.14014252 - - authors: - Chris Allan - Emil Rozbicki @@ -5553,7 +5717,6 @@ resources: license: UNKNOWN name: Glencoe Software Webinars url: https://www.glencoesoftware.com/media/webinars/ - - authors: - Christian Schmidt - Janina Hanne @@ -5561,7 +5724,9 @@ resources: - Christian Meesters - Elisa Ferrando-May - et al. - description: 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. + description: As an initiative within Germany's National Research Data Infrastructure, + the authors conducted this community survey in summer 2021 to assess the state + of the art of bioimaging RDM and the community needs. tags: - Research Data Management - Image Data Management @@ -5569,34 +5734,39 @@ resources: type: - Publication license: CC-BY-4.0 - name: Research data management for bioimaging - the 2021 NFDI4BIOIMAGE community survey + name: Research data management for bioimaging - the 2021 NFDI4BIOIMAGE community + survey num_downloads: 321 publication_date: '2022-09-20' url: https://f1000research.com/articles/11-638/v2 - - - author: Marvin Albert - description: Repository accompanying the multiview-stitcher tutorial for Virtual I2K - 2024 - license: BSD 3-Clause "New" or "Revised" License + description: Repository accompanying the multiview-stitcher tutorial for Virtual + I2K 2024 + license: BSD-3-CLAUSE name: Virtual-I2K-2024-multiview-stitcher publication_date: '2024-10-30T07:38:11+00:00' tags: - Big Data - - BioImageAnalysis - type: - - GitHub Repository + - Bioimageanalysis + type: + - Github Repository - Tutorial - url: + url: - https://github.com/m-albert/Virtual-I2K-2024-multiview-stitcher - -- authors: Steuerungsgremium Allianz-Schwerpunkt, Alexander von Humboldt Foundation, - Deutsche Forschungsgemeinschaft, Fraunhofer Society, German Rectors' Conference, - Leibniz Association, German National Academy of Sciences Leopoldina, German Academic - Exchange Service, Helmholtz Association of German Research Centres, Max Planck Society +- authors: + - Steuerungsgremium Allianz-Schwerpunkt + - Alexander von Humboldt Foundation + - Deutsche Forschungsgemeinschaft + - Fraunhofer Society + - German Rectors' Conference + - Leibniz Association + - German National Academy of Sciences Leopoldina + - German Academic Exchange Service + - Helmholtz Association of German Research Centres + - Max Planck Society description: Arbeitspapier des Steuerungsgremiums des Allianz-Schwerpunkts "Digitalität in der Wissenschaft" - license: cc-by-4.0 + license: CC-BY-4.0 name: "Forschungsdatenmanagement zukunftsfest gestalten \u2013 Impulse f\xFCr die\ \ Strukturevaluation der Nationalen Forschungsdateninfrastruktur (NFDI)" num_downloads: 237 @@ -5604,48 +5774,54 @@ resources: url: - https://zenodo.org/records/14032908 - https://doi.org/10.5281/zenodo.14032908 - -- authors: Haase, Robert +- authors: + - Robert Haase description: 'This is a dataset of PNG images of [Bio-Image Data Science teaching - slides](https://zenodo.org/records/12623730). The png_umap.yml file contains a list - of all images and a dimensionality reduced embedding (Uniform Manifold Approximation + slides](https://zenodo.org/records/12623730). The png_umap.yml file contains a + list of all images and a dimensionality reduced embedding (Uniform Manifold Approximation Projection, UMAP) made using OpenAI''s text-embedding-ada-002 model. - + A notebook for visualizing this data is published here: https://github.com/haesleinhuepf/stackview/blob/main/docs/sliceplot.ipynb' - license: cc-by-4.0 + license: CC-BY-4.0 name: Stackview sliceplot example data num_downloads: 3 publication_date: '2024-11-03' url: - https://zenodo.org/records/14030307 - https://doi.org/10.5281/zenodo.14030307 - - author: Isra Mekki description: '' - license: MIT License + license: MIT name: Prompt-Engineering-LLMs-Course publication_date: '2024-09-11T07:45:30+00:00' tags: - - LLMs + - Llms - Prompt Engineering - Code Generation - type: - - GitHub Repository + type: + - Github Repository - Tutorial url: https://github.com/HelmholtzAI-Consultants-Munich/Prompt-Engineering-LLMs-Course - -- authors: Massei, Riccardo, Berndt, Matthias, Serrano-Solano, Beatriz, Busch, Wibke, - Scholz, Stefan, Bohring, Hannes, Nyffeler, Jo, Reger, Luise, Bumberger, Jan, Lopez-Delisle, - Lucille +- authors: + - Riccardo Massei + - Matthias Berndt + - Beatriz Serrano-Solano + - Wibke Busch + - Stefan Scholz + - Hannes Bohring + - Jo Nyffeler + - Luise Reger + - Jan Bumberger + - Lucille Lopez-Delisle description: 'Imaging is crucial across various scientific disciplines, particularly in life sciences, where it plays a key role in studies ranging from single molecules to whole organisms. However, the complexity and sheer volume of image data, especially from high-content screening (HCS) experiments involving cell lines or other organisms, present significant challenges. Managing and analysing this data efficiently requires - well-defined image processing tools and analysis pipelines that align with the FAIR - principles—ensuring they are findable, accessible, interoperable, and reusable - across different domains. - + well-defined image processing tools and analysis pipelines that align with the + FAIR principles—ensuring they are findable, accessible, interoperable, and + reusable across different domains. + In the frame of NFDI4BioImaging (the National Research Data Infrastructure focusing on bioimaging in Germany), we want to find viable solutions for storing, processing, analysing, and sharing HCS data. In particular, we want to develop solutions to @@ -5654,31 +5830,32 @@ resources: supporting reproducibility, and enabling interdisciplinary collaboration. These tools can be used by different users to retrieve images based on specific attributes as well as support quality control by identifying appropriate metadata. - - Galaxy, an open-source, web-based platform for data-intensive research, offers a - solution by enabling the construction of reproducible pipelines for image analysis. - By integrating popular analysis software like CellProfiler and connecting with cloud - services such as OMERO and IDR, Galaxy facilitates the seamless access and management - of image data. This capability is particularly valuable in bioimaging, where automated - pipelines can streamline the handling of complex metadata, ensuring data integrity - and fostering interdisciplinary collaboration. This approach not only increases - the efficiency of HCS bioimaging but also contributes to the broader scientific - community''s efforts to embrace FAIR principles, ultimately advancing scientific - discovery and innovation. - - In the present study, we proposed an automated analysis pipeline for storing, processing, - analysing, and sharing HCS bioimaging data. The (semi)automatic workflow was developed - by taking as a case study a dataset of zebrafish larvae and cell lines images previously - obtained from an automated imaging system generating data in an HCS fashion. In - our workflows, images are automatically enriched with metadata (i.e. key-value pairs, - tags, raw data, regions of interest) and uploaded to the UFZ-OME Remote Objects - (OMERO) server using a novel OMERO tool suite developed with GALAXY. Workflows give - the possibility to the user to intuitively fetch images from the local server and - perform image analysis (i.e. annotation) or even more complex toxicological analyses - (dose response modelling). Furthermore, we want to improve the FAIRness of the protocol - by adding a direct upload link to the Image Data Resource (IDR) repository to automatically - prepare the data for publication and sharing.' - license: cc-by-4.0 + + Galaxy, an open-source, web-based platform for data-intensive research, offers + a solution by enabling the construction of reproducible pipelines for image analysis. + By integrating popular analysis software like CellProfiler and connecting with + cloud services such as OMERO and IDR, Galaxy facilitates the seamless access and + management of image data. This capability is particularly valuable in bioimaging, + where automated pipelines can streamline the handling of complex metadata, ensuring + data integrity and fostering interdisciplinary collaboration. This approach not + only increases the efficiency of HCS bioimaging but also contributes to the broader + scientific community''s efforts to embrace FAIR principles, ultimately advancing + scientific discovery and innovation. + + In the present study, we proposed an automated analysis pipeline for storing, + processing, analysing, and sharing HCS bioimaging data. The (semi)automatic workflow + was developed by taking as a case study a dataset of zebrafish larvae and cell + lines images previously obtained from an automated imaging system generating data + in an HCS fashion. In our workflows, images are automatically enriched with metadata + (i.e. key-value pairs, tags, raw data, regions of interest) and uploaded to the + UFZ-OME Remote Objects (OMERO) server using a novel OMERO tool suite developed + with GALAXY. Workflows give the possibility to the user to intuitively fetch images + from the local server and perform image analysis (i.e. annotation) or even more + complex toxicological analyses (dose response modelling). Furthermore, we want + to improve the FAIRness of the protocol by adding a direct upload link to the + Image Data Resource (IDR) repository to automatically prepare the data for publication + and sharing.' + license: CC-BY-4.0 name: Building FAIR image analysis pipelines for high-content-screening (HCS) data using Galaxy num_downloads: 1 @@ -5687,42 +5864,47 @@ resources: - https://zenodo.org/records/14044640 - https://doi.org/10.5281/zenodo.14044640 - https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/ - - -- authors: Bruna Piereck, Alexander Botzki +- authors: + - Bruna Piereck + - Alexander Botzki description: Course repository for Strategic Use of Generative AI - license: Creative Commons Attribution 4.0 International + license: CC-BY-4.0 name: introduction-to-generative-ai publication_date: '2024-09-27T14:38:51+00:00' tags: - - artificial intelligence - type: - - GitHub Repository + - Artificial Intelligence + type: + - Github Repository - Tutorial - url: + url: - https://github.com/vibbits/introduction-to-generative-ai - https://liascript.github.io/course/?https://raw.githubusercontent.com/vibbits/introduction-to-generative-ai/refs/heads/main/README.md - -- authors: Tuur Muyldermans, Kris Davie, Alexander, Nicolas Vannieuwkerke, Kobe Lavaerts, - Marcel Ribeiro-Dantas, Bruna Piereck, Steff Taelman +- authors: + - Tuur Muyldermans + - Kris Davie + - Alexander + - Nicolas Vannieuwkerke + - Kobe Lavaerts + - Marcel Ribeiro-Dantas + - Bruna Piereck + - Steff Taelman description: Nextflow workshop materials March 2023 - license: cc-by-4.0 + license: CC-BY-4.0 name: nextflow-workshop publication_date: '2023-03-29T10:40:04+00:00' - tags: - - workflow - - nextflow - type: - - GitHub Repository + tags: + - Workflow + - Nextflow + type: + - Github Repository - Tutorial - url: + url: - https://github.com/vibbits/nextflow-workshop - https://liascript.github.io/course/?https://raw.githubusercontent.com/vibbits/nextflow-workshop/main/README.md#1 - - authors: - Curtis Rueden - Albane de la Villegeorges - - Simon F. Nørrelykke + - "Simon F. N\xF8rrelykke" - Romain Guiet - Olivier Burri - et al. @@ -5737,15 +5919,15 @@ resources: - Forum Post - Workshop url: https://forum.image.sc/t/upcoming-image-analysis-events/60018/67 - - authors: - Riccardo Massei - Robert Haase - ENicolay - description: This repository offer access to teaching material and useful resources for the YMIA - Python-Based Event Series. - license: MIT License + description: This repository offer access to teaching material and useful resources + for the YMIA - Python-Based Event Series. + license: MIT name: YMIA - Python-Based Event Series Training Material - publication_date: + publication_date: null tags: - Python - Large Language Models @@ -5757,10 +5939,10 @@ resources: - Github Repository - Slides url: https://github.com/rmassei/ymia_python_event_series_material - - -- authors: SaibotMagd - description: This tool is intended to link different research data management platforms with each other. +- authors: + - SaibotMagd + description: This tool is intended to link different research data management platforms + with each other. license: UNKNOWN name: RDM_system_connector tags: @@ -5769,9 +5951,13 @@ resources: type: - Github Repository url: https://github.com/SaibotMagd/RDM_system_connector - -- authors: Anna Swan - description: Sharing knowledge and data in the life sciences allows us to learn from each other and built on what others have discovered. This collection of online courses brings together a variety of training, covering topics such as biocuration, open data, restricted access data and finding publicly available data, to help you discover and make the most of publicly available data in the life sciences. +- authors: + - Anna Swan + description: Sharing knowledge and data in the life sciences allows us to learn + from each other and built on what others have discovered. This collection of online + courses brings together a variety of training, covering topics such as biocuration, + open data, restricted access data and finding publicly available data, to help + you discover and make the most of publicly available data in the life sciences. license: CC-BY-4.0 name: Finding and using publicly available data publication_date: '2024-01-01' @@ -5784,86 +5970,89 @@ resources: - Tutorial - Videos url: https://www.ebi.ac.uk/training/online/courses/finding-using-public-data/ - -- authors: Boissonnet, Tom, Hagen, Bettina, Kunis, Susanne, Schmidt, Christian, Weidtkamp-Peters, - Stefanie +- authors: + - Tom Boissonnet + - Bettina Hagen + - Susanne Kunis + - Christian Schmidt + - Stefanie Weidtkamp-Peters description: '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: - - + 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 - + + Learn how to train users, establish sustainability strategies, and foster FAIR + RDM for bioimaging at your institution + ' - license: cc-by-4.0 + license: CC-BY-4.0 name: '[Workshop Material] Fit for OMERO - How imaging facilities and IT departments work together to enable RDM for bioimaging, October 16-17, 2024, Heidelberg' num_downloads: 101 @@ -5871,32 +6060,64 @@ resources: url: - https://zenodo.org/records/14013026 - https://doi.org/10.5281/zenodo.14013026 - -- authors: "Carl Herrmann, annavonbachmann, David Hoksza, Martin Schätz, Dario Malchiodi, jnguyenvan, Britta Velten, Elodie Laine, JanaBraunger, barwil" +- authors: + - Carl Herrmann + - annavonbachmann + - David Hoksza + - "Martin Sch\xE4tz" + - Dario Malchiodi + - jnguyenvan + - Britta Velten + - Elodie Laine + - JanaBraunger + - barwil name: Lecture-materials of the DeepLife course publication_date: '2023-12-06' license: UNKNOWN - tags: - - bioinformatics - type: - - GitHub Repository + tags: + - Bioinformatics + type: + - Github Repository - Slides - Notebook url: https://github.com/deeplife4eu/Lecture-materials/ - - -- authors: "Christian Tischer, Antonio Politi, Toby Hodges, maulakhan, grinic, bugraoezdemir, Tim-Oliver Buchholz, Elnaz Fazeli, Aliaksandr Halavatyi, Dominik Kutra, Stefania Marcotti, AnniekStok, Felix, jhennies, Severina Klaus, Martin Schorb, Nima Vakili, Sebastian Gonzalez Tirado, Stefan Helfrich, Yi Sun, Ziqiang Huang, Jan Eglinger, Constantin Pape, Joel Lüthi, Matt McCormick, Oane Gros" +- authors: + - Christian Tischer + - Antonio Politi + - Toby Hodges + - maulakhan + - grinic + - bugraoezdemir + - Tim-Oliver Buchholz + - Elnaz Fazeli + - Aliaksandr Halavatyi + - Dominik Kutra + - Stefania Marcotti + - AnniekStok + - Felix + - jhennies + - Severina Klaus + - Martin Schorb + - Nima Vakili + - Sebastian Gonzalez Tirado + - Stefan Helfrich + - Yi Sun + - Ziqiang Huang + - Jan Eglinger + - Constantin Pape + - "Joel L\xFCthi" + - Matt McCormick + - Oane Gros description: Resources for teaching/preparing to teach bioimage analysis - license: cc-by-4.0 + license: CC-BY-4.0 name: training-resources publication_date: '2020-04-23T07:51:38+00:00' - tags: - - BioImageAnalysis + tags: + - Bioimageanalysis - Neurobias - type: - - GitHub Repository + type: + - Github Repository url: https://github.com/NEUBIAS/training-resources - - authors: - Arif Khan - Christian Tischer @@ -5904,8 +6125,8 @@ resources: - Dominik Kutra - Felix Schneider - et al. - license: MIT License - name: cba-support-template + license: MIT + name: cba-support-template publication_date: '2021-12-01' tags: - Workflow @@ -5913,9 +6134,10 @@ resources: type: - Tutorial url: https://git.embl.de/grp-cba/cba-support-template - -- authors: Bret Fisher - description: In this course you will learn how to use Docker, Compose and Kubernetes on your machine for better software building and testing. +- authors: + - Bret Fisher + description: In this course you will learn how to use Docker, Compose and Kubernetes + on your machine for better software building and testing. license: UNKNOWN name: Docker Mastery - with Kubernetes + Swarm from a Docker Captain tags: @@ -5926,8 +6148,9 @@ resources: - Tutorial - Online Course url: https://www.udemy.com/course/docker-mastery/?srsltid=AfmBOornR5gRqOg-4v8Nsap1z24CaPPUPxg8JzyqEGZ6MvW_dh-sf4Af&couponCode=ST2MT110724BNEW - -- description: Computational skills training at the UCL Sainsbury Wellcome Centre and Gatsby Computational Neuroscience Unit, delivered by members of the Neuroinformatics Unit. +- description: Computational skills training at the UCL Sainsbury Wellcome Centre + and Gatsby Computational Neuroscience Unit, delivered by members of the Neuroinformatics + Unit. license: CC-BY-4.0 name: SWC/GCNU Software Skills tags: @@ -5938,28 +6161,31 @@ resources: - Videos - Tutorial url: https://software-skills.neuroinformatics.dev/index.html - -- authors: Daniele Procida - description: Diátaxis is a systematic framework for technical documentation that organizes content into four types—tutorials, how-to guides, technical reference, and explanations—to address distinct user needs, enhancing both user understanding and the documentation process. +- authors: + - Daniele Procida + description: "Di\xE1taxis is a systematic framework for technical documentation\ + \ that organizes content into four types\u2014tutorials, how-to guides, technical\ + \ reference, and explanations\u2014to address distinct user needs, enhancing both\ + \ user understanding and the documentation process." license: CC-BY-SA-4.0 - name: Diátaxis - A systematic approach to technical documentation authoring. + name: "Di\xE1taxis - A systematic approach to technical documentation authoring." tags: - Documentation type: - Website - Tutorial - Workflow - url: + url: - https://www.diataxis.fr/ - - authors: - Mark Meysenburg - - Toby Hodges - - Dominik Kutra - - Erin Becker + - Toby Hodges + - Dominik Kutra + - Erin Becker - David Palmquist - et al. - description: This lesson shows how to use Python and scikit-image to do basic image processing. + description: This lesson shows how to use Python and scikit-image to do basic image + processing. license: CC-BY-4.0 name: Image Processing with Python tags: @@ -5967,148 +6193,150 @@ resources: - Bioimage Analysis - Training - Python - - Scikit-image + - Scikit-Image - Image Segmentation type: - Tutorial - Workflow url: https://datacarpentry.org/image-processing/key-points.html - -- authors: Nicolas Chiaruttini +- authors: + - Nicolas Chiaruttini description: 'The files contained in this repository are confocal images taken with the Evident FV 4000 of a sample containing DAPI and mCherry stains, excited with a 405 nm laser and a 561 nm laser - - + + individual tiles are named `tiling-sample-brain-section_A01_G001_{i}.oir` - + The stiched image is named `Stitch_A01_G001` and contains an extra file `Stitch_A01_G001_00001` - + Some metadata like the tiles positions are stored in the extra files (omp2info) - - + +  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Evident OIR sample files tiles + stitched image - FV 4000 num_downloads: 154 publication_date: '2024-09-04' url: - https://zenodo.org/records/13680725 - https://doi.org/10.5281/zenodo.13680725 - - -- authors: Romain Guiet, Nicolas Chiaruttini - description: "Mouse duodenum fixed in 4% PFA overnight at 4°C, processed for paraffin\ - \ infiltration using a standard histology procedure and cut at 4 microns were dewaxed,\ - \ rehydrated, permeabilized with 0.5% Triton X-100 in PBS 1x and stained with Azide\ - \ - Alexa Fluor 555 (Thermo Fisher) to detect EdU and DAPI for nuclei. The images\ - \ were taken using a Leica DM5500 microscope with a 40X N.A.1 objective (black&white\ - \ camera: DFC350FXR2, pixel dimension: 0.161 microns). Next, the slide was unmounted\ - \ and stained using the fully automated Ventana Discovery xT autostainer (Roche\ - \ Diagnostics, Rotkreuz, Switzerland). All steps were performed on automate with\ - \ Ventana solutions. Sections were pretreated with heat using the CC1 solution under\ - \ mild conditions. The primary rat anti BrDU (clone: BU1/75 (ICR1), Serotec, diluted\ - \ 1:300) was incubated 1 hour at 37°C. After incubation with a donkey anti rat\ - \ biotin diluted 1:200 (Jackson ImmunoResearch Laboratories), chromogenic revelation\ - \ was performed with DabMap kit. The section was counterstained with Harris hematoxylin\ - \ (J.T. Baker) before a second round of imaging on DM5500 PL Fluotar 40X N.A.1.0\ - \ oil (color camera: DFC 320 R2, pixel dimension: 0.1725 microns). Before acquisition,\ - \ a white-balance as well as a shading correction is performed according to Leica\ - \ LAS software wizard. The fluorescence and DAB images were converted in ome.tiff\ - \ multiresolution file with the kheops Fiji Plugin.\n\nSampled prepared in the EPFL\ - \ histology core facility by Nathalie Müller and Gian-Filippo Mancini.\n\n\ - Associated documents:\n\n\n\thttps://c4science.ch/w/bioimaging_and_optics_platform_biop/teaching/dab-intensity/\n\ +- authors: + - Romain Guiet + - Nicolas Chiaruttini + description: "Mouse duodenum fixed in 4% PFA overnight at 4°C, processed for\ + \ paraffin infiltration using a standard histology procedure and cut at 4 microns\ + \ were dewaxed, rehydrated, permeabilized with 0.5% Triton X-100 in PBS 1x and\ + \ stained with Azide - Alexa Fluor 555 (Thermo Fisher) to detect EdU and DAPI\ + \ for nuclei. The images were taken using a Leica DM5500 microscope with a 40X\ + \ N.A.1 objective (black&white camera: DFC350FXR2, pixel dimension: 0.161\ + \ microns). Next, the slide was unmounted and stained using the fully automated\ + \ Ventana Discovery xT autostainer (Roche Diagnostics, Rotkreuz, Switzerland).\ + \ All steps were performed on automate with Ventana solutions. Sections were pretreated\ + \ with heat using the CC1 solution under mild conditions. The primary rat anti\ + \ BrDU (clone: BU1/75 (ICR1), Serotec, diluted 1:300) was incubated 1 hour at\ + \ 37°C. After incubation with a donkey anti rat biotin diluted 1:200 (Jackson\ + \ ImmunoResearch Laboratories), chromogenic revelation was performed with DabMap\ + \ kit. The section was counterstained with Harris hematoxylin (J.T. Baker) before\ + \ a second round of imaging on DM5500 PL Fluotar 40X N.A.1.0 oil (color camera:\ + \ DFC 320 R2, pixel dimension: 0.1725 microns). Before acquisition, a white-balance\ + \ as well as a shading correction is performed according to Leica LAS software\ + \ wizard. The fluorescence and DAB images were converted in ome.tiff multiresolution\ + \ file with the kheops Fiji Plugin.\n\nSampled prepared in the EPFL histology\ + \ core facility by Nathalie Müller and Gian-Filippo Mancini.\n\nAssociated\ + \ documents:\n\n\n\thttps://c4science.ch/w/bioimaging_and_optics_platform_biop/teaching/dab-intensity/\n\ \thttps://imagej.net/plugins/bdv/warpy/warpy\n\n\nThis document contains a full\ \ QuPath project with an example of registered image.\n\n " - license: cc-by-4.0 + license: CC-BY-4.0 name: Test Dataset for Whole Slide Image Registration num_downloads: 1001 publication_date: '2021-04-12' url: - https://zenodo.org/records/5675686 - - https://doi.org/10.5281/zenodo.5675686 - -- authors: Nicolas Chiaruttini + - https://doi.org/10.5281/zenodo.5675686 +- authors: + - Nicolas Chiaruttini description: 'This is a microscopy image dataset generated by the Perkin Elmer Operetta HCS microscope by of the user of the PTBIOP EPFL facility. - - + + As of the 17th of July 2023, opening this file in ImageJ/Fiji using the BioFormats 6.14 library, this dataset generates a Null Pointer Exception. - - + + A post on forum.image.sc is linked to this issue: - - + + https://forum.image.sc/t/null-pointer-exception-in-perkin-elmer-operetta-dataset-with-bio-formats-6-14/83784 - - + +   - - + +  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Example Operetta Dataset num_downloads: 3 publication_date: '2023-07-17' url: - https://zenodo.org/records/8153907 - https://doi.org/10.5281/zenodo.8153907 +- authors: + - Nicolas Chiaruttini + description: 'A set of public CZI files. These can be used for testing CZI readers. -- authors: Nicolas Chiaruttini - description: 'A set of public CZI files. These can be used for testing CZI readers. - - - Demo LISH 4x8 15pct 647.czi: A cleared mouse brain acquired with a Zeiss LightSheet Z1 with 32 tiles. Courtesy of the Carl Petersen lab LSENS (https://www.epfl.ch/labs/lsens). Sampled prepared by Yanqi Liu an imaged by Olivier Burri. - - - test_gray.czi: a synthetically generated CZI file without metadata, made by Sebastian - Rhode - - + + - test_gray.czi: a synthetically generated CZI file without metadata, made by + Sebastian Rhode + + - Image_1_2023_08_18__14_32_31_964.czi: an example multi-part CZI file, containing only camera noise - - + + - a xt scan, xz scan, xzt scan - a set of multi angle, multi illumination, mutli tile acquisition, taken on the LightSheet Z1 microscope of the PTBIOP by Lorenzo Talà' - license: cc-by-4.0 + license: CC-BY-4.0 name: CZI file examples num_downloads: 1192 publication_date: '2023-08-18' url: - https://zenodo.org/records/8305531 - https://doi.org/10.5281/zenodo.8305531 - - -- authors: Sarah Machado, Vincent Mercier, Nicolas Chiaruttini +- authors: + - Sarah Machado + - Vincent Mercier + - Nicolas Chiaruttini description: "Image datasets from the publication : LimeSeg: A coarse-grained\ \ lipid membrane simulation for 3D image segmentation\n\n\n\tVesicles.tif: spinning-disc\ - \ confocal images of giant unilamellar vesicles\n\tHelaCell-FIBSEM.tif: a 3D\ - \ Electron Microscopy (EM) dataset of nearly isotropic sections of a Hela\ - \ cell, acquired with a focused ion beam scanning electron microscope (FIB-SEM).\ + \ confocal images of giant unilamellar vesicles\n\tHelaCell-FIBSEM.tif: a\ + \ 3D Electron Microscopy (EM) dataset of nearly isotropic sections of\ + \ a Hela cell, acquired with a focused ion beam scanning electron microscope (FIB-SEM).\ \ Sections are aligned with TrackEm2 (doi: ), without additional preprocessing.\n\ - \tDrosophilaEggChamber.tif: point scanning confocal images of a Drosophila egg chamber.\ - \ Channel 1: cell nuclei  stained with DAPI. Channel 2: cell membranes\ - \ visualized with fused membrane proteins Nrg::GFP and Bsg::GFP. \n\n\nImage\ - \ metadata contains extra information including voxel sizes.\n\n " - license: cc-by-4.0 + \tDrosophilaEggChamber.tif: point scanning confocal images of a Drosophila egg\ + \ chamber. Channel 1: cell nuclei  stained with DAPI. Channel 2: cell\ + \ membranes visualized with fused membrane proteins Nrg::GFP and Bsg::GFP. \n\ + \n\nImage metadata contains extra information including voxel sizes.\n\n " + license: CC-BY-4.0 name: LimeSeg Test Datasets num_downloads: 174 publication_date: '2018-10-27' url: - https://zenodo.org/records/1472859 - https://doi.org/10.5281/zenodo.1472859 - -- authors: Yannick KREMPP - description: A review of the tools, methods and concepts useful for biologists and life scientists as well as bioimage analysts. +- authors: + - Yannick KREMPP + description: A review of the tools, methods and concepts useful for biologists and + life scientists as well as bioimage analysts. license: UNKNOWN - name: AI ML DL in Bioimage Analysis - Webinar + name: AI ML DL in Bioimage Analysis - Webinar publication_date: '2024-11-14' tags: - Deep Learning @@ -6121,11 +6349,18 @@ resources: - Slides - Webinar url: https://www.youtube.com/watch?v=TJXNMIWtdac - -- authors: Guillaume Jacquemet - description: Leukocyte extravasation is a critical component of the innate immune response, while circulating tumour cell extravasation is a crucial step in metastasis formation. Despite their importance, these extravasation mechanisms remain incompletely understood. In this talk, Guillaume Jacquemet presents a novel imaging framework that integrates microfluidics with high-speed, label-free imaging to study the arrest of pancreatic cancer cells (PDAC) on human endothelial layers under physiological flow conditions. +- authors: + - Guillaume Jacquemet + description: Leukocyte extravasation is a critical component of the innate immune + response, while circulating tumour cell extravasation is a crucial step in metastasis + formation. Despite their importance, these extravasation mechanisms remain incompletely + understood. In this talk, Guillaume Jacquemet presents a novel imaging framework + that integrates microfluidics with high-speed, label-free imaging to study the + arrest of pancreatic cancer cells (PDAC) on human endothelial layers under physiological + flow conditions. license: UNKNOWN - name: Dr Guillaume Jacquemet on studying cancer cell metastasis in the era of deep learning for microscopy + name: Dr Guillaume Jacquemet on studying cancer cell metastasis in the era of deep + learning for microscopy publication_date: '2024-10-24' tags: - Deep Learning @@ -6134,8 +6369,10 @@ resources: - Youtube Video - Slides url: https://www.youtube.com/watch?v=KTdZBgSCYJQ - -- description: The mission of Metrics Reloaded is to guide researchers in the selection of appropriate performance metrics for biomedical image analysis problems, as well as provide a comprehensive online resource for metric-related information and pitfalls +- description: The mission of Metrics Reloaded is to guide researchers in the selection + of appropriate performance metrics for biomedical image analysis problems, as + well as provide a comprehensive online resource for metric-related information + and pitfalls license: UNKNOWN name: Metrics Reloaded - A framework for trustworthy image analysis validation tags: @@ -6146,45 +6383,62 @@ resources: - Website - Collection url: https://metrics-reloaded.dkfz.de/ - - - submission_date: '2024-11-12T10:17:25.985725' - authors: Wendt Jens + authors: + - Wendt Jens description: Short presentation given at at PoL BioImage Analysis Symposium Dresden 2023 - license: cc-by-4.0 + license: CC-BY-4.0 name: Metadata Annotation Workflow for OMERO with Tabbles num_downloads: 131 publication_date: '2023-09-04' url: - https://zenodo.org/records/8314968 - https://doi.org/10.5281/zenodo.8314968 - -- authors: Kemmer, Isabel, Romdhane, Feriel, Euro-BioImaging ERIC +- authors: + - Kemmer + - Isabel + - Romdhane + - Feriel + - Euro-BioImaging ERIC description: 'Depositing data in quality data repositories is one crucial step towards FAIR (Findable, Accessible, Interoperable, and Reusable) data. Accordingly, Euro-BioImaging strongly encourages sharing scientific imaging data in established, thematic repositories.  - - To guide you in the selection of appropriate repositories, we have created an overview - of available repositories for different types of image data, including their scope - and requirements. This decision tree guides you through questions about your data - and directs you to the correct repository, and/or provides instructions for further - processing to meet the critera of the repositories.  - - Three seperate trees are provided for different classes of imaging data: open bioimage - data, preclinical data, and human imaging data. ' - license: cc-by-4.0 + + To guide you in the selection of appropriate repositories, we have created an + overview of available repositories for different types of image data, including + their scope and requirements. This decision tree guides you through questions + about your data and directs you to the correct repository, and/or provides instructions + for further processing to meet the critera of the repositories.  + + Three seperate trees are provided for different classes of imaging data: open + bioimage data, preclinical data, and human imaging data. ' + license: CC-BY-4.0 name: Image Repository Decision Tree - Where do I deposit my imaging data num_downloads: 129 publication_date: '2024-10-22' url: - https://zenodo.org/records/13945179 - https://doi.org/10.5281/zenodo.13945179 - -- authors: Alessandro Rigano, Ulrike Boehm, Claire M. Brown, Joel Ryan, James J. Chambers, - Robert A. Coleman, Orestis Faklaris, Thomas Guilbert, Michelle S. Itano, Judith - Lacoste, Alex Laude, Marco Marcello, Paula Montero-Llopis, Glyn Nelson, Roland Nitschke, - Jaime A. Pimentel, Stefanie Weidtkamp-Peters, Caterina Strambio-De-Castillia +- authors: + - Alessandro Rigano + - Ulrike Boehm + - Claire M. Brown + - Joel Ryan + - James J. Chambers + - Robert A. Coleman + - Orestis Faklaris + - Thomas Guilbert + - Michelle S. Itano + - Judith Lacoste + - Alex Laude + - Marco Marcello + - Paula Montero-Llopis + - Glyn Nelson + - Roland Nitschke + - Jaime A. Pimentel + - Stefanie Weidtkamp-Peters + - Caterina Strambio-De-Castillia description: "Example Microscopy Metadata (Microscope.JSON and Settings.JSON) files\ \ produced using Micro-Meta App to document the Hardware Specifications of example\ \ Microscopes and the Image Acquisition Settings utilized to acquire example images\ @@ -6192,103 +6446,104 @@ resources: \ JSON files:\n\n\n\tMicroscope.JSON file (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json)\n\ \tSettings.JSON file (indicated with the name of the image and with the _AS suffix)\n\ \n\n\nMicro-Meta App was developed as part of a global community initiative including\ - \ the 4D Nucleome (4DN) Imaging Working Group, BioImaging North America (BINA) Quality\ - \ Control and Data Management Working Group, and QUAlity and REProducibility for\ - \ Instrument and Images in Light Microscopy (QUAREP-LiMi), to extend the Open Microscopy\ - \ Environment (OME) data model.\n\n\nThe works of this global community effort resulted\ - \ in multiple publications featured on a recent Nature Methods FOCUS ISSUE dedicated\ - \ to Reporting and reproducibility in microscopy.\n\n\n\nLearn More! For a thorough\ - \ description of Micro-Meta App consult our recent Nature Methods and BioRxiv.org\ - \ publications!\n\n\n \n\n\n\t\n\t\t\n\t\t\tNr.\n\t\t\tManufacturer\n\t\t\t\ - Model\n\t\t\tTier\n\t\t\tΕxperiment Type\n\t\t\tFacility Name\n\t\t\tDepartment\ - \ and Institution\n\t\t\tURL\n\t\t\tReferences\n\t\t\n\t\t\n\t\t\t1\n\t\t\tCarl\ - \ Zeiss Microscopy\n\t\t\tAxio Observer Z1 (with LSM 710 scan head)\n\t\t\t1\n\t\ - \t\t3D visualization of superhydrophobic polymer-nanoparticles\n\t\t\tCentre for\ - \ Cell Imaging (CCI)\n\t\t\tUniversity of Liverpool\n\t\t\thttps://cci.liv.ac.uk/equipment_710.html\n\ - \t\t\tUpton et al., 2020\n\t\t\n\t\t\n\t\t\t2\n\t\t\tCarl Zeiss Microscopy\n\t\t\ - \tAxio Observer (Axiovert 200M)\n\t\t\t2\n\t\t\tΜeasurement of illumination stability\ - \ on Chinese Hamster Ovary cells expressing Paxillin-EGFP\n\t\t\tAdvanced BioImaging\ - \ Facility (ABIF).\n\t\t\tMcGill University\n\t\t\thttps://www.mcgill.ca/abif/equipment/axiovert-1\n\ - \t\t\tKiepas et al., 2020\n\t\t\n\t\t\n\t\t\t3\n\t\t\tCarl Zeiss Microscopy\n\t\t\ - \tAxio Observer Z1 (with Spinning Disk)\n\t\t\t2\n\t\t\tImmunofluorescence imaging\ + \ the 4D Nucleome (4DN) Imaging Working Group, BioImaging North America (BINA)\ + \ Quality Control and Data Management Working Group, and QUAlity and REProducibility\ + \ for Instrument and Images in Light Microscopy (QUAREP-LiMi), to extend the Open\ + \ Microscopy Environment (OME) data model.\n\n\nThe works of this global community\ + \ effort resulted in multiple publications featured on a recent Nature Methods\ + \ FOCUS ISSUE dedicated to Reporting and reproducibility in microscopy.\n\n\n\n\ + Learn More! For a thorough description of Micro-Meta App consult our recent Nature\ + \ Methods and BioRxiv.org publications!\n\n\n \n\n\n\t\n\t\t\n\t\t\tNr.\n\ + \t\t\tManufacturer\n\t\t\tModel\n\t\t\tTier\n\t\t\tΕxperiment Type\n\t\ + \t\tFacility Name\n\t\t\tDepartment and Institution\n\t\t\tURL\n\t\t\tReferences\n\ + \t\t\n\t\t\n\t\t\t1\n\t\t\tCarl Zeiss Microscopy\n\t\t\tAxio Observer Z1 (with\ + \ LSM 710 scan head)\n\t\t\t1\n\t\t\t3D visualization of superhydrophobic polymer-nanoparticles\n\ + \t\t\tCentre for Cell Imaging (CCI)\n\t\t\tUniversity of Liverpool\n\t\t\thttps://cci.liv.ac.uk/equipment_710.html\n\ + \t\t\tUpton et al., 2020\n\t\t\n\t\t\n\t\t\t2\n\t\t\tCarl Zeiss Microscopy\n\t\ + \t\tAxio Observer (Axiovert 200M)\n\t\t\t2\n\t\t\tΜeasurement of illumination\ + \ stability on Chinese Hamster Ovary cells expressing Paxillin-EGFP\n\t\t\tAdvanced\ + \ BioImaging Facility (ABIF).\n\t\t\tMcGill University\n\t\t\thttps://www.mcgill.ca/abif/equipment/axiovert-1\n\ + \t\t\tKiepas et al., 2020\n\t\t\n\t\t\n\t\t\t3\n\t\t\tCarl Zeiss Microscopy\n\t\ + \t\tAxio Observer Z1 (with Spinning Disk)\n\t\t\t2\n\t\t\tImmunofluorescence imaging\ \ of cryosection of Mouse kidney\n\t\t\tImagerie Cellulaire; Quality Control managed\ \ by Miacellavie (https://miacellavie.com/)\n\t\t\tCentre de recherche du Centre\ \ Hospitalier Université de Montréal (CR CHUM), University of Montreal\n\ - \t\t\thttps://www.chumontreal.qc.ca/crchum/plateformes-et-services  (the web\ - \ site is for all core facilities, not specifically for the core facility hosting\ - \ this microscope)\n\t\t\tPilliod et al., 2020\n\t\t\n\t\t\n\t\t\t4\n\t\t\tCarl\ - \ Zeiss Microscopy\n\t\t\tAxio Imager Z2 (with Apotome)\n\t\t\t2\n\t\t\tImmunofluorescence\ - \ imaging of mitotic division in Hela cells using  \n\t\t\tBioimaging\ - \ Unit\n\t\t\tNewcastle University\n\t\t\thttps://www.ncl.ac.uk/bioimaging/\n\t\t\ - \tWatson et al., 2020\n\t\t\n\t\t\n\t\t\t5\n\t\t\tCarl Zeiss Microscopy\n\t\t\t\ - Axio Observer Z1\n\t\t\t2\n\t\t\tFluorescence microscopy of human skin fibroblasts\ - \ from Glycogen Storage Disease patients.\n\t\t\tLife Imaging Center (LIC)\n\t\t\ - \tCentre for Integrative Signalling Analysis (CISA), University of Freiburg\n\t\t\ - \thttps://miap.eu/equipments/sd-i-abl/\n\t\t\tHannibal et al., 2020\n\t\t\n\t\t\n\ - \t\t\t6\n\t\t\tLeica Microsystems\n\t\t\tDMI6000B\n\t\t\t2\n\t\t\t3D immunofluorescence\ + \t\t\thttps://www.chumontreal.qc.ca/crchum/plateformes-et-services  (the\ + \ web site is for all core facilities, not specifically for the core facility\ + \ hosting this microscope)\n\t\t\tPilliod et al., 2020\n\t\t\n\t\t\n\t\t\t4\n\t\ + \t\tCarl Zeiss Microscopy\n\t\t\tAxio Imager Z2 (with Apotome)\n\t\t\t2\n\t\t\t\ + Immunofluorescence imaging of mitotic division in Hela cells using  \n\ + \t\t\tBioimaging Unit\n\t\t\tNewcastle University\n\t\t\thttps://www.ncl.ac.uk/bioimaging/\n\ + \t\t\tWatson et al., 2020\n\t\t\n\t\t\n\t\t\t5\n\t\t\tCarl Zeiss Microscopy\n\t\ + \t\tAxio Observer Z1\n\t\t\t2\n\t\t\tFluorescence microscopy of human skin fibroblasts\ + \ from Glycogen Storage Disease patients.\n\t\t\tLife Imaging Center (LIC)\n\t\ + \t\tCentre for Integrative Signalling Analysis (CISA), University of Freiburg\n\ + \t\t\thttps://miap.eu/equipments/sd-i-abl/\n\t\t\tHannibal et al., 2020\n\t\t\n\ + \t\t\n\t\t\t6\n\t\t\tLeica Microsystems\n\t\t\tDMI6000B\n\t\t\t2\n\t\t\t3D immunofluorescence\ \ imaging  rhinovirus infected macrophages \n\t\t\tIMAG'IC Confocal\ - \ Microscopy Facility\n\t\t\tInstitut Cochin, CNRS, INSERM, Université de\ - \ Paris\n\t\t\thttps://www.institutcochin.fr/core_facilities/confocal-microscopy/cochin-imaging-photonic-microscopy/organigram_team/10054/view\n\ - \t\t\tJubrail et al., 2020\n\t\t\n\t\t\n\t\t\t7\n\t\t\tLeica Microsystems\n\t\t\t\ - DM5500B\n\t\t\t2\n\t\t\tImmunofluorescence analysis of the colocalization of PML\ - \ bodies with DNA double-strand breaks\n\t\t\tBioimaging Unit\n\t\t\tEdwardson Building\ - \ on the Campus for Ageing and Vitality, Newcastle University\n\t\t\thttps://www.ncl.ac.uk/bioimaging/equipment/leica-dm5500/#overview\n\ - \t\t\tda Silva et al., 2019; Nelson et al., 2012\n\t\t\t  \n\t\t\n\t\t\ - \n\t\t\t8\n\t\t\tLeica Microsystems\n\t\t\tDMI8-CS (with TCS SP8 STED 3X)\n\t\t\t\ - 2\n\t\t\tLive-cell imaging of N. benthamiana leaves cells-derived protoplasts\n\t\ - \t\tCenter for Advanced Imaging (CAi)\n\t\t\tSchool of Mathematics/Natural Sciences,\ - \ Heinrich-Heine-Universität Düsseldorf\n\t\t\thttps://www.cai.hhu.de/en/equipment/super-resolution-microscopy/leica-tcs-sp8-sted-3x\n\ - \t\t\tSinger et al., 2017; Hänsch et al., 2020\n\t\t\n\t\t\n\t\t\t9\n\t\t\t\ - Nikon Instruments\n\t\t\tEclipse Ti\n\t\t\t2\n\t\t\tImmunofluorescence analysis\ + \ Microscopy Facility\n\t\t\tInstitut Cochin, CNRS, INSERM, Université\ + \ de Paris\n\t\t\thttps://www.institutcochin.fr/core_facilities/confocal-microscopy/cochin-imaging-photonic-microscopy/organigram_team/10054/view\n\ + \t\t\tJubrail et al., 2020\n\t\t\n\t\t\n\t\t\t7\n\t\t\tLeica Microsystems\n\t\t\ + \tDM5500B\n\t\t\t2\n\t\t\tImmunofluorescence analysis of the colocalization of\ + \ PML bodies with DNA double-strand breaks\n\t\t\tBioimaging Unit\n\t\t\tEdwardson\ + \ Building on the Campus for Ageing and Vitality, Newcastle University\n\t\t\t\ + https://www.ncl.ac.uk/bioimaging/equipment/leica-dm5500/#overview\n\t\t\tda Silva\ + \ et al., 2019; Nelson et al., 2012\n\t\t\t  \n\t\t\n\t\t\n\t\t\t8\n\ + \t\t\tLeica Microsystems\n\t\t\tDMI8-CS (with TCS SP8 STED 3X)\n\t\t\t2\n\t\t\t\ + Live-cell imaging of N. benthamiana leaves cells-derived protoplasts\n\t\t\tCenter\ + \ for Advanced Imaging (CAi)\n\t\t\tSchool of Mathematics/Natural Sciences, Heinrich-Heine-Universität\ + \ Düsseldorf\n\t\t\thttps://www.cai.hhu.de/en/equipment/super-resolution-microscopy/leica-tcs-sp8-sted-3x\n\ + \t\t\tSinger et al., 2017; Hänsch et al., 2020\n\t\t\n\t\t\n\t\t\t9\n\t\t\ + \tNikon Instruments\n\t\t\tEclipse Ti\n\t\t\t2\n\t\t\tImmunofluorescence analysis\ \ of the cytoskeleton structure in COS cells\n\t\t\tAdvanced Imaging Center (AIC)\n\ \t\t\tJanelia Research Campus, Howard Hughes Medical Institute\n\t\t\thttps://www.janelia.org/support-team/light-microscopy/equipment\n\ - \t\t\tAbdelfattah et al., 2019; Qian et al., 2019; Grimm et al., 2020\n\t\t\n\t\t\ - \n\t\t\t10\n\t\t\tNikon Instruments\n\t\t\tEclipse Ti-E (HCA)\n\t\t\t2\n\t\t\tΤime-lapse\ - \ analysis of the bursting behavior of amine-functionalized vesicular assemblies\n\ - \t\t\tLight Microscopy Facility (IALS-LIF)\n\t\t\tInstitute for Applied Life Sciences,\ - \ University of Massachusetts at Amherst\n\t\t\thttps://www.umass.edu/ials/light-microscopy\n\ + \t\t\tAbdelfattah et al., 2019; Qian et al., 2019; Grimm et al., 2020\n\t\t\n\t\ + \t\n\t\t\t10\n\t\t\tNikon Instruments\n\t\t\tEclipse Ti-E (HCA)\n\t\t\t2\n\t\t\ + \tΤime-lapse analysis of the bursting behavior of amine-functionalized vesicular\ + \ assemblies\n\t\t\tLight Microscopy Facility (IALS-LIF)\n\t\t\tInstitute for\ + \ Applied Life Sciences, University of Massachusetts at Amherst\n\t\t\thttps://www.umass.edu/ials/light-microscopy\n\ \t\t\tFernandez et al., 2020\n\t\t\n\t\t\n\t\t\t11\n\t\t\tNikon Instruments/Coleman\ \ laboratory (customized)\n\t\t\tTIRF HILO Epifluorescence light Microscope (THEM)/\ \ Eclipse Ti\n\t\t\t2\n\t\t\tSingle-particle tracking of Halo-tagged PCNA in Lox\ \ cells\n\t\t\tColeman laboratory\n\t\t\tAnatomy and Structural Biology Department,\ \ The Albert Einstein College of Medicine\n\t\t\thttps://einsteinmed.org/faculty/12252/robert-coleman/\n\ - \t\t\tDrosopoulos et al., 2020\n\t\t\n\t\t\n\t\t\t12\n\t\t\tNikon Instruments\n\t\ - \t\tEclipse Ti (with Andor Dragon Fly Spinning Disk)\n\t\t\t2\n\t\t\tInvestigation\ + \t\t\tDrosopoulos et al., 2020\n\t\t\n\t\t\n\t\t\t12\n\t\t\tNikon Instruments\n\ + \t\t\tEclipse Ti (with Andor Dragon Fly Spinning Disk)\n\t\t\t2\n\t\t\tInvestigation\ \ of the 3D structure of cerebral organoids\n\t\t\tMontpellier Resources Imagerie\n\ \t\t\tCentre de Recherche de Biologie cellulaire de Montpellier (MRI-CRBM), CNRS,\ \ Univerity of Montpellier\n\t\t\thttps://www.mri.cnrs.fr/en/optical-imaging/our-facilities/mri-crbm.html\n\ - \t\t\tAyala-Nunez et al., 2019\n\t\t\n\t\t\n\t\t\t13\n\t\t\tNikon Instruments\n\t\ - \t\tEclipse Ti2\n\t\t\t2\n\t\t\tΙmmunofluorescence imaging of cryosections\ - \ of mouse hearth myocardium \n\t\t\tNeuroscience Center Microscopy Core\n\t\ - \t\tNeuroscience Center, University of North Carolina\n\t\t\thttps://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/\n\ - \t\t\tAghajanian et al., 2021\n\t\t\n\t\t\n\t\t\t14\n\t\t\tNikon Instruments\n\t\ - \t\tEclipse Ti2\n\t\t\t2\n\t\t\tLive-cell imaging of bacterial cells expressing\ + \t\t\tAyala-Nunez et al., 2019\n\t\t\n\t\t\n\t\t\t13\n\t\t\tNikon Instruments\n\ + \t\t\tEclipse Ti2\n\t\t\t2\n\t\t\tΙmmunofluorescence imaging of cryosections\ + \ of mouse hearth myocardium \n\t\t\tNeuroscience Center Microscopy Core\n\ + \t\t\tNeuroscience Center, University of North Carolina\n\t\t\thttps://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/\n\ + \t\t\tAghajanian et al., 2021\n\t\t\n\t\t\n\t\t\t14\n\t\t\tNikon Instruments\n\ + \t\t\tEclipse Ti2\n\t\t\t2\n\t\t\tLive-cell imaging of bacterial cells expressing\ \ GFP-PopZ\n\t\t\tMicroscopy Resources on the North Quad (MicRoN)\n\t\t\tHarvard\ \ Medical School \n\t\t\thttps://micron.hms.harvard.edu/\n\t\t\tLim and Bernhardt\ \ 2019; Lim et al., 2019\n\t\t\n\t\t\n\t\t\t15\n\t\t\tOlympus/Biomedical Imaging\ \ Group (customized)\n\t\t\tTIRF Epifluorescence Structured light Microscope (TESM)/IX71\n\ - \t\t\t3\n\t\t\t3D distribution of HIV-1 in the nucleus of human cells\n\t\t\tBiomedical\ - \ Imaging Group\n\t\t\tProgram in Molecular Medicine, University of Massachusetts\ + \t\t\t3\n\t\t\t3D distribution of HIV-1 in the nucleus of human cells\n\t\t\t\ + Biomedical Imaging Group\n\t\t\tProgram in Molecular Medicine, University of Massachusetts\ \ Medical School\n\t\t\thttps://trello.com/b/BQ8zCcQC/tirf-epi-fluorescence-structured-light-microscope\n\ \t\t\tNavaroli et al., 2012\n\t\t\n\t\t\n\t\t\t16\n\t\t\tOlympus/Computer Vision\ - \ Laboratory (customized)\n\t\t\t3D BrightField Scanner/IX71\n\t\t\t3\n\t\t\tTransmitted\ - \ light brightfield visualization of swimming spermatocytes\n\t\t\tLaboratorio Nacional\ - \ de Microscopia Avanzada (LNMA) and Computer Vision Laboratory of the Institute\ - \ of Biotechnology\n\t\t\tUniversidad Nacional Autonoma de Mexico (UNAM)\n\t\t\t\ - https://lnma.unam.mx/wp/\n\t\t\tPimentel et al., 2012; Silva-Villalobos et al.,\ - \ 2014\n\t\t\n\t\n\n\nGetting started\n\nUse these videos to get started with using\ - \ Micro-Meta App after installation into OMERO and downloading the example data\ - \ files:\n\n\n\tVideo 1\n\tVideo 2\n\n\nMore information\n\n\nFor full information\ - \ on how to use Micro-Meta App please utilize the following resources:\n\n\n\tMicro-Meta\ - \ App website\n\tFull documentation\n\tInstallation instructions\n\tStep-by-Step\ - \ Instructions\n\tTutorial Videos\n\n\n\nBackground\n\nIf you want to learn more\ - \ about the importance of metadata and quality control to ensure full reproducibility,\ - \ quality and scientific value in light microscopy, please take a look at our recent\ - \ publications describing the development of community-driven light 4DN-BINA-OME\ - \ Microscopy Metadata specifications Nature Methods and BioRxiv.org and our overview\ - \ manuscript entitled A perspective on Microscopy Metadata: data provenance and\ - \ quality control.\n\n \n\n " - license: cc-by-4.0 + \ Laboratory (customized)\n\t\t\t3D BrightField Scanner/IX71\n\t\t\t3\n\t\t\t\ + Transmitted light brightfield visualization of swimming spermatocytes\n\t\t\t\ + Laboratorio Nacional de Microscopia Avanzada (LNMA) and Computer Vision Laboratory\ + \ of the Institute of Biotechnology\n\t\t\tUniversidad Nacional Autonoma de Mexico\ + \ (UNAM)\n\t\t\thttps://lnma.unam.mx/wp/\n\t\t\tPimentel et al., 2012; Silva-Villalobos\ + \ et al., 2014\n\t\t\n\t\n\n\nGetting started\n\nUse these videos to get started\ + \ with using Micro-Meta App after installation into OMERO and downloading the\ + \ example data files:\n\n\n\tVideo 1\n\tVideo 2\n\n\nMore information\n\n\nFor\ + \ full information on how to use Micro-Meta App please utilize the following resources:\n\ + \n\n\tMicro-Meta App website\n\tFull documentation\n\tInstallation instructions\n\ + \tStep-by-Step Instructions\n\tTutorial Videos\n\n\n\nBackground\n\nIf you want\ + \ to learn more about the importance of metadata and quality control to ensure\ + \ full reproducibility, quality and scientific value in light microscopy, please\ + \ take a look at our recent publications describing the development of community-driven\ + \ light 4DN-BINA-OME Microscopy Metadata specifications Nature Methods and BioRxiv.org\ + \ and our overview manuscript entitled A perspective on Microscopy Metadata: data\ + \ provenance and quality control.\n\n \n\n " + license: CC-BY-4.0 name: Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities num_downloads: 1053 @@ -6296,82 +6551,110 @@ resources: url: - https://zenodo.org/records/5847477 - https://doi.org/10.5281/zenodo.5847477 - -- authors: "Ahmadi, Mohsen, Wagner, Robert, Mattern, Philipp, Plathe, Nick, Bekeschus,\ - \ Sander, Becker, Markus M., St\xF6ter, Torsten, Weidtkamp-Peters, Stefanie" +- authors: + - Ahmadi + - Mohsen + - Wagner + - Robert + - Mattern + - Philipp + - Plathe + - Nick + - Bekeschus + - Sander + - Becker + - Markus M. + - "St\xF6ter" + - Torsten + - Weidtkamp-Peters + - Stefanie description: A more detailed understanding of the effect of plasmas on biological systems can be fostered by combining data from different imaging modalities, such - as optical imaging, fluorescence imaging, and mass spectrometry imaging. This, however, - requires the implementation and use of sophisticated research data management (RDM) - solutions to incorporate the influence of plasma parameters and treatment procedures - as well as the effects of plasma on the treated targets. In order to address this, - RDM activities on different levels and from different perspectives are started and - brought together within the framework of the NFDI consortium NFDI4BIOIMAGE. - license: cc-by-4.0 - name: Data stewardship and research data management tools for multimodal linking of - imaging data in plasma medicine + as optical imaging, fluorescence imaging, and mass spectrometry imaging. This, + however, requires the implementation and use of sophisticated research data management + (RDM) solutions to incorporate the influence of plasma parameters and treatment + procedures as well as the effects of plasma on the treated targets. In order to + address this, RDM activities on different levels and from different perspectives + are started and brought together within the framework of the NFDI consortium NFDI4BIOIMAGE. + license: CC-BY-4.0 + name: Data stewardship and research data management tools for multimodal linking + of imaging data in plasma medicine num_downloads: 68 publication_date: '2023-11-03' url: - https://zenodo.org/records/10069368 - https://doi.org/10.5281/zenodo.10069368 - -- authors: "Heber, Maximilian, Jakob, Moritz, Landwehr, Matthias, Leendertse, Jan, M\xFC\ - ller, Maximilian, Schneider, Gabriel, von Suchodoletz, Dirk, Ulrich, Robert" +- authors: + - Heber + - Maximilian + - Jakob + - Moritz + - Landwehr + - Matthias + - Leendertse + - Jan + - "M\xFCller" + - Maximilian + - Schneider + - Gabriel + - von Suchodoletz + - Dirk + - Ulrich + - Robert description: "Im Zuge der stetig wachsenden Brisanz des Forschungsdatenmanagements\ - \ fallen immer größere Mengen an Forschungsdaten an. Diese an sich begrüßenswerte\ - \ Entwicklung führt zu technischen und organisatorischen Herausforderungen\ - \ nicht nur im Bereich der Speicherung von Forschungsdaten, sondern in allen Phasen\ - \ des Forschungsdatenlebenszyklus. Der vorliegende Beitrag erläutert vor diesem\ - \ Hintergrund mögliche Motivationen hinter digitaler Datensparsamkeit mit Blick\ - \ auf organisatorische, technische und ethische Kriterien, Datenschutz und Nachhaltigkeit.\ - \ Anschließend werden vor dem Hintergrund zentraler Herausforderungen Umsetzungsvorschläge\ - \ für das Vorfeld sowie den Verlauf eines Forschungsvorhabens gemacht. Zudem\ - \ werden grundlegende Empfehlungen zur digitalen Datensparsamkeit ausgesprochen.\n\ - Eine kürzere Ausgabe des Leitfadens ist im Mai 2024 in der Zeitschrift o |\ - \ bib erschienen: https://doi.org/10.5282/o-bib/6036 \nDiese Ausgabe enthält\ - \ ein zusätzliches Kapitel (4.2) mit konkreten Praxisbeispielen.\nDieser Artikel\ - \ wurde ins Englische übersetzt:\nHeber, M., Jakob, M., Landwehr, M., Leendertse,\ - \ J., Müller, M., Schneider, G., von Suchodoletz, D., & Ulrich, R. (2024).\ - \ A Users' Guide to Economical Digital Data Usage. Zenodo. https://doi.org/10.5281/zenodo.13752220" - license: cc-by-4.0 + \ fallen immer größere Mengen an Forschungsdaten an. Diese an sich\ + \ begrüßenswerte Entwicklung führt zu technischen und organisatorischen\ + \ Herausforderungen nicht nur im Bereich der Speicherung von Forschungsdaten,\ + \ sondern in allen Phasen des Forschungsdatenlebenszyklus. Der vorliegende Beitrag\ + \ erläutert vor diesem Hintergrund mögliche Motivationen hinter digitaler\ + \ Datensparsamkeit mit Blick auf organisatorische, technische und ethische Kriterien,\ + \ Datenschutz und Nachhaltigkeit. Anschließend werden vor dem Hintergrund\ + \ zentraler Herausforderungen Umsetzungsvorschläge für das Vorfeld sowie\ + \ den Verlauf eines Forschungsvorhabens gemacht. Zudem werden grundlegende Empfehlungen\ + \ zur digitalen Datensparsamkeit ausgesprochen.\nEine kürzere Ausgabe des\ + \ Leitfadens ist im Mai 2024 in der Zeitschrift o | bib erschienen: https://doi.org/10.5282/o-bib/6036\ + \ \nDiese Ausgabe enthält ein zusätzliches Kapitel (4.2) mit konkreten\ + \ Praxisbeispielen.\nDieser Artikel wurde ins Englische übersetzt:\nHeber,\ + \ M., Jakob, M., Landwehr, M., Leendertse, J., Müller, M., Schneider, G.,\ + \ von Suchodoletz, D., & Ulrich, R. (2024). A Users' Guide to Economical Digital\ + \ Data Usage. Zenodo. https://doi.org/10.5281/zenodo.13752220" + license: CC-BY-4.0 name: Leitfaden zur digitalen Datensparsamkeit (mit Praxisbeispielen) num_downloads: 255 publication_date: '2024-06-03' url: - https://zenodo.org/records/11445843 - https://doi.org/10.5281/zenodo.11445843 - -- authors: C. Li +- authors: + - C. Li description: 'Online R learning for applied statistics ' - license: Creative Commons Zero v1.0 Universal + license: CC0-1.0 name: Online_R_learning publication_date: '2023-07-09T06:27:14+00:00' - tags: - - statistics - type: - - GitHub Repository + tags: + - Statistics + type: + - Github Repository url: https://github.com/cxli233/Online_R_learning - -- authors: C. Li +- authors: + - C. Li description: 'Friends don''t let friends make certain types of data visualization - What are they and why are they bad. ' - license: MIT License + license: MIT name: FriendsDontLetFriends publication_date: '2024-03-10T15:34:07+00:00' - tags: + tags: - Visualization - type: GitHub Repository + type: + - Github Repository url: https://github.com/cxli233/FriendsDontLetFriends - - - submission_date: '2024-11-18T14:39:37.692470' authors: - - Boissonnet, Tom - - Hagen, Bettina - - Kunis, Susanne - - Schmidt, Christian - - Weidtkamp-Peters, Stefanie + - Tom Boissonnet + - Bettina Hagen + - Susanne Kunis + - Christian Schmidt + - Stefanie Weidtkamp-Peters description: 'Fit for OMERO: How imaging facilities and IT departments work together to enable RDM for bioimaging @@ -6448,7 +6731,7 @@ resources: RDM for bioimaging at your institution ' - license: cc-by-4.0 + license: CC-BY-4.0 name: '[Workshop Material] Fit for OMERO - How imaging facilities and IT departments work together to enable RDM for bioimaging, October 16-17, 2024, Heidelberg' num_downloads: 144 @@ -6458,7 +6741,7 @@ resources: - https://doi.org/10.5281/zenodo.14178789 - submission_date: '2024-11-18T14:39:38.611036' authors: - - Wetzker, Cornelia + - Cornelia Wetzker description: 'The poster introduces the consortium NFDI4BIOIMAGE with its central objectives, provides an overview of challenges in bioimage data handling, sharing and analysis and lists support options by the consortium through its data stewardship @@ -6468,7 +6751,7 @@ resources: Forschungsgemeinschaft (DFG grant number NFDI 46/1, project number 501864659) and has been presented at the conference FDM@Campus held in Göttingen September 23-25, 2024.' - license: cc-by-4.0 + license: CC-BY-4.0 name: 'New Kid on the (NFDI) Block: NFDI4BIOIMAGE - A National Initiative for FAIR Data Management in Bioimaging and Bioimage Analysis' num_downloads: 29 @@ -6478,10 +6761,10 @@ resources: - https://doi.org/10.5281/zenodo.14006558 - submission_date: '2024-11-18T14:39:39.787873' authors: - - "J\xFCngst, Christian" - - Zentis, Peter + - "Christian J\xFCngst" + - Peter Zentis description: Raw microscopy image from the NFDI4Bioimage calendar October 2024 - license: cc-by-4.0 + license: CC-BY-4.0 name: NFDI4Bioimage Calendar 2024 October; original image num_downloads: 8 publication_date: '2024-09-25' @@ -6490,8 +6773,8 @@ resources: - https://doi.org/10.5281/zenodo.13837146 - submission_date: '2024-11-18T14:39:41.141377' authors: - - Dvoretskii, Stefan - license: cc-by-4.0 + - Stefan Dvoretskii + license: CC-BY-4.0 name: Insights from Acquiring Open Medical Imaging Datasets for Foundation Model Development num_downloads: 41 @@ -6501,12 +6784,12 @@ resources: - https://doi.org/10.5281/zenodo.11503289 - submission_date: '2024-11-18T14:39:41.489967' authors: - - Wetzker, Cornelia - - Schlierf, Michael + - Cornelia Wetzker + - Michael Schlierf description: The poster is part of the work of the German consortium NFDI4BIOIMAGE funded by the Deutsche Forschungsgemeinschaft (DFG grant number NFDI 46/1, project number 501864659). - license: cc-by-4.0 + license: CC-BY-4.0 name: RESEARCH DATA MANAGEMENT on Campus and in NFDI4BIOIMAGE num_downloads: 32 publication_date: '2024-08-29' @@ -6515,7 +6798,7 @@ resources: - https://doi.org/10.5281/zenodo.13684187 - submission_date: '2024-11-18T14:39:41.946082' authors: - - Haase, Robert + - Robert Haase description: 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 @@ -6524,7 +6807,7 @@ resources: 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. - license: cc-by-4.0 + license: CC-BY-4.0 name: Towards Preservation of Life Science Data with NFDI4BIOIMAGE num_downloads: 228 publication_date: '2024-09-03' @@ -6533,8 +6816,8 @@ resources: - https://doi.org/10.5281/zenodo.13640979 - submission_date: '2024-11-18T14:39:42.386226' authors: - - Dvoretskii, Stefan - license: cc-by-4.0 + - Stefan Dvoretskii + license: CC-BY-4.0 name: Insights from Acquiring Open Medical Imaging Datasets for Foundation Model Development num_downloads: 46 @@ -6544,10 +6827,10 @@ resources: - https://doi.org/10.5281/zenodo.13380289 - submission_date: '2024-11-18T14:39:43.407105' authors: - - Habinger, Sophie - - Heber, Maximilian - - Kralj, Sonja - - Mikautsch, Emilia + - Sophie Habinger + - Maximilian Heber + - Sonja Kralj + - Emilia Mikautsch description: 'The rise of Open Science (OS) and the academic community’s needs that come with it bring about a range of challenges for academic libraries. To face these challenges, the University of Konstanz has created a competence unit @@ -6594,7 +6877,7 @@ resources: other OS professionals from the European Reform University Alliance (ERUA) and the European University for Well-Being (EUniWell), establishing formats for best practice exchange, such as monthly OS Meet-Ups.' - license: cc-by-4.0 + license: CC-BY-4.0 name: 'Institutionalization and Collaboration as a Way of Addressing the Challenges Open Science Presents to Libraries: The University of Konstanz as a National Pioneer' num_downloads: 119 @@ -6604,14 +6887,14 @@ resources: - https://doi.org/10.5281/zenodo.12699637 - submission_date: '2024-11-18T14:39:44.756942' authors: - - Massei, Riccardo - - Schmidt, Christian - - Bortolomeazzi, Michele - - Thoennissen, Julia - - Bumberger, Jan - - Dickscheid, Timo - - Mallm, Jan-Philipp - - Ferrando-May, Elisa + - Riccardo Massei + - Christian Schmidt + - Michele Bortolomeazzi + - Julia Thoennissen + - Jan Bumberger + - Timo Dickscheid + - Jan-Philipp Mallm + - Elisa Ferrando-May description: 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, @@ -6627,7 +6910,7 @@ resources: 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 - license: cc-by-4.0 + license: CC-BY-4.0 name: The role of Helmholtz Centers in NFDI4BIOIMAGE - A national consortium enhancing FAIR data management for microscopy and bioimage analysis num_downloads: 54 @@ -6637,9 +6920,9 @@ resources: - https://doi.org/10.5281/zenodo.11501662 - submission_date: '2024-11-18T14:39:45.213893' authors: - - Massei, Riccardo - - Bortolomeazzi, Michele - - Schmidt, Christian + - Riccardo Massei + - Michele Bortolomeazzi + - Christian Schmidt description: 'Here we share the material used in a workshop held on May 13th, 2024, at the German Cancer Research Center in Heidelberg (on-premise) @@ -6691,7 +6974,7 @@ resources: Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg, Project Coordinator of the NFDI4BIOIMAGE project)' - license: cc-by-4.0 + license: CC-BY-4.0 name: '[Workshop] Bioimage data management and analysis with OMERO' num_downloads: 211 publication_date: '2024-05-13' @@ -6700,11 +6983,11 @@ resources: - https://doi.org/10.5281/zenodo.11350689 - submission_date: '2024-11-18T14:39:45.586962' authors: - - Moore, Josh - - Kunis, Susanne + - Josh Moore + - Susanne Kunis description: Poster presented at the European Light Microscopy Initiative meeting in Liverpool (https://www.elmi2024.org/) - license: cc-by-4.0 + license: CC-BY-4.0 name: '[ELMI 2024] AI''s Dirty Little Secret: Without FAIR Data, It''s Just Fancy Math' @@ -6715,9 +6998,10 @@ resources: - https://doi.org/10.5281/zenodo.11235513 - submission_date: '2024-11-18T14:39:45.979235' authors: - - Escobar Diaz Guerrero, Rodrigo + - Escobar Diaz Guerrero + - Rodrigo description: First updates of LEO (Linking ELN with OMERO) - license: cc-by-4.0 + license: CC-BY-4.0 name: 'LEO: Linking ELN with OMERO' num_downloads: 3 publication_date: '2024-05-08' @@ -6726,9 +7010,9 @@ resources: - https://doi.org/10.5281/zenodo.11146807 - submission_date: '2024-11-18T14:39:46.762148' authors: - - Fortmann-Grote, Carsten + - Carsten Fortmann-Grote description: This presentation was given at the 2nd MPG-NFDI Workshop on April 18th. - license: cc-by-4.0 + license: CC-BY-4.0 name: NFDI4BIOIMAGE num_downloads: 81 publication_date: '2024-04-22' @@ -6737,11 +7021,11 @@ resources: - https://doi.org/10.5281/zenodo.11031747 - submission_date: '2024-11-18T14:39:47.147338' authors: - - Schmidt, Christian + - Christian Schmidt description: Short Talk about the NFDI4BIOIMAGE consortium presented at the RDM in (Bio-)Medicine Information Event on April 10th, 2024, organized C³RDM & ZB MED. - license: cc-by-4.0 + license: CC-BY-4.0 name: '[Short Talk] NFDI4BIOIMAGE - A consortium in the National Research Data Infrastructure' num_downloads: 47 publication_date: '2024-04-10' @@ -6750,16 +7034,16 @@ resources: - https://doi.org/10.5281/zenodo.10939520 - submission_date: '2024-11-18T14:39:47.561518' authors: - - Margineanu, Anca - - Stringari, Chiara - - Zoccoler, Marcelo - - Wetzker, Cornelia + - Anca Margineanu + - Chiara Stringari + - Marcelo Zoccoler + - Cornelia Wetzker description: The presentations introduce open-source software to read in, visualize and analyse fluorescence lifetime imaging microscopy (FLIM) raw data developed for life scientists. The slides were presented at German Bioimaging (GerBI) FLIM Workshop held February 26 to 29 2024 at the Biomedical Center of LMU München by Anca Margineanu, Chiara Stringari and Conni Wetzker.  - license: cc-by-4.0 + license: CC-BY-4.0 name: A Glimpse of the Open-Source FLIM Analysis Software Tools FLIMfit, FLUTE and napari-flim-phasor-plotter num_downloads: 219 @@ -6769,8 +7053,8 @@ resources: - https://doi.org/10.5281/zenodo.10886750 - submission_date: '2024-11-18T14:39:47.946546' authors: - - Fortmann-Grote, Carsten - license: cc-by-4.0 + - Carsten Fortmann-Grote + license: CC-BY-4.0 name: Linked (Open) Data for Microbial Population Biology num_downloads: 121 publication_date: '2024-03-12' @@ -6779,13 +7063,13 @@ resources: - https://doi.org/10.5281/zenodo.10808486 - submission_date: '2024-11-18T14:39:48.292240' authors: - - Massei, Riccardo + - Riccardo Massei description: '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)  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Hackaton Results - Conversion of KNIME image analysis workflows to Galaxy num_downloads: 46 publication_date: '2024-03-07' @@ -6794,31 +7078,32 @@ resources: - https://doi.org/10.5281/zenodo.10793700 - submission_date: '2024-11-18T14:39:48.632022' authors: - - Fuchs, Vanessa Aphaia Fiona - - Wendt, Jens - - "M\xFCller, Maximilian" - - Ahmadi, Mohsen - - Massei, Riccardo - - Wetzker, Cornelia + - Fuchs + - Vanessa Aphaia Fiona + - Jens Wendt + - "Maximilian M\xFCller" + - Mohsen Ahmadi + - Riccardo Massei + - Cornelia Wetzker description: The Data Steward Team of the NFDI4BIOIMAGE consortium presents themselves and the services (including the Helpdesk) that we offer. - license: cc-by-4.0 + license: CC-BY-4.0 name: Who you gonna call? - Data Stewards to the rescue num_downloads: 91 publication_date: '2024-03-01' url: - https://zenodo.org/records/10730424 - https://doi.org/10.5281/zenodo.10730424 - -- authors: - - Jannasch, Anett - - Tulok, Silke - - Fuchs, Vanessa Aphaia Fiona - - Boissonnet, Tom - - Schmidt, Christian - - Bortolomeazzi, Michele - - Fabig, Gunar - - Okafornta, Chukwuebuka +- authors: + - Anett Jannasch + - Silke Tulok + - Fuchs + - Vanessa Aphaia Fiona + - Tom Boissonnet + - Christian Schmidt + - Michele Bortolomeazzi + - Gunar Fabig + - Chukwuebuka Okafornta description: '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 @@ -6827,171 +7112,203 @@ resources: 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 (https://github.com/ome/omero-scripts/blob/develop/omero/annotation_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 + + + 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)' - license: cc-by-4.0 + license: CC-BY-4.0 name: Key-Value pair template for annotation of datasets in OMERO (PERIKLES study) num_downloads: 10 publication_date: '2024-06-26' url: - https://zenodo.org/records/12546808 - - https://doi.org/10.5281/zenodo.12546808 - - - -- authors: Stefanie Weidtkamp-Peters, Janina Hanne, Christian Schmidt + - https://doi.org/10.5281/zenodo.12546808 +- authors: + - Stefanie Weidtkamp-Peters + - Janina Hanne + - Christian Schmidt description: '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 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 + 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.  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: A journey to FAIR microscopy data num_downloads: 68 publication_date: '2023-05-03' url: - https://zenodo.org/records/7890311 - https://doi.org/10.5281/zenodo.7890311 - -- authors: "Tulok, Silke, Fabig, Gunar, Vogelsang, Andy, Kugel, Thomas, M\xFCller-Reichert,\ - \ Thomas" +- authors: + - Silke Tulok + - Gunar Fabig + - Andy Vogelsang + - Thomas Kugel + - "Thomas M\xFCller-Reichert" description: The Core Facility Cellular Imaging (CFCI) at the Faculty of Medicine Carl Gustav Carus (TU Dresden) is currently running a pilot project for testing the use and handling of the OMERO software. This is done together with interested - users of the imaging facility and a research group. Currently, we are pushing forward - this pilot study on a small scale without any data steward. Our experiences argue - so far for giving data management issues into the hands of dedicated personnel not - fully involved in research projects. As funding agencies will ask for higher and - higher standards for implementing FAIRdata principles in the future, this will be - a releva - license: cc-by-4.0 + users of the imaging facility and a research group. Currently, we are pushing + forward this pilot study on a small scale without any data steward. Our experiences + argue so far for giving data management issues into the hands of dedicated personnel + not fully involved in research projects. As funding agencies will ask for higher + and higher standards for implementing FAIRdata principles in the future, this + will be a releva + license: CC-BY-4.0 name: 'Report on a pilot study: Implementation of OMERO for microscopy data management' num_downloads: 80 publication_date: '2023-11-10' url: - https://zenodo.org/records/10103316 - https://doi.org/10.5281/zenodo.10103316 +- authors: + - Fabig + - Gunar + - Jannasch + - Anett + - Okafornta + - Chukwuebuka + - Boissonnet + - Tom + - Schmidt + - Christian + - Bortolomeazzi + - Michele + - Fuchs + - Vanessa Aphaia Fiona + - Koeckert + - Maria + - Poddar + - Aayush + - Vogel + - Martin + - Schwarzbach + - Hanna-Margareta + - Vogelsang + - Andy + - Gerlach + - Michael + - Nobst + - Anja + - "M\xFCller-Reichert" + - Thomas + - Tulok + - Silke + description: 'This are a two Key-Value pair templates used for the annotation of + datasets in OMERO. They are tailored for light- and electron microcopy data for + all research projects of the research group of Prof. T. Mueller-Reichert.  + All members of the Core Facility Cellular Imaging agreed for using these templates + to annotate data in OMERO. Furthermore, there are a corresponding public example + datasets used in the publication "Setting up an institutional OMERO environment + for bioimage data: perspectives from both facility staff and users" and are available + here: -- authors: "Fabig, Gunar, Jannasch, Anett, Okafornta, Chukwuebuka, Boissonnet, Tom,\ - \ Schmidt, Christian, Bortolomeazzi, Michele, Fuchs, Vanessa Aphaia Fiona, Koeckert,\ - \ Maria, Poddar, Aayush, Vogel, Martin, Schwarzbach, Hanna-Margareta, Vogelsang,\ - \ Andy, Gerlach, Michael, Nobst, Anja, M\xFCller-Reichert, Thomas, Tulok, Silke" - description: 'This are a two Key-Value pair templates used for the annotation of datasets - in OMERO. They are tailored for light- and electron microcopy data for all research - projects of the research group of Prof. T. Mueller-Reichert.  All members of - the Core Facility Cellular Imaging agreed for using these templates to annotate - data in OMERO. Furthermore, there are a corresponding public example datasets used - in the publication "Setting up an institutional OMERO environment for bioimage data: - perspectives from both facility staff and users" and are available here: - https://omero.med.tu-dresden.de/webclient/?show=dataset-1552 --> for lattice-light sheet microscopy - + https://omero.med.tu-dresden.de/webclient/?show=dataset-1555--> for electron microscopy data - + That templates are based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015) - and were developed during the PoL-Bio-Image Analysis Symposium in Dresden Aug 28th- - Sept 1st in 2023 and further adapeted during the usage of OMERO.  - + and were developed during the PoL-Bio-Image Analysis Symposium in Dresden Aug + 28th- Sept 1st in 2023 and further adapeted during the usage of OMERO.  + With every template it is possible to create a csv-file, that can be used to annotate a dataset in OMERO using the annotation script (https://github.com/ome/omero-scripts/blob/develop/omero/annotation_scripts/). - + How to use: - - + + fill the template with 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 dataset, which should be annotated in OMERO - + save the new excel sheet in csv-file (comma separated values) format - - + + Examples can be seen in sheet 3 ''csv_TOMO'' and sheet 5 csv_TEM''. - + 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).  - + 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.12546808 Key-Value pair template for annotation of datasets in OMERO (PERIKLES study) - + 10.5281/zenodo.12578084 Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI) - +  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: "Key-Value pair template for annotation of datasets in OMERO for light- and\ \ electron microscopy data within the research group of Prof. M\xFCller-Reichert" num_downloads: 12 @@ -6999,15 +7316,14 @@ resources: url: - https://zenodo.org/records/12547566 - https://doi.org/10.5281/zenodo.12547566 - - submission_date: '2024-11-18T16:34:09.954845' authors: - - Gerlach, Michael + - Michael Gerlach description: 'This upload features a simple model for the creation (Manufacturing/Prototyping) of an abdominal imaging window (AIW) for use in mice intravital microscopy. Manufacture in titanium for chronic implantation. Measures in mm.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Abdominal Imaging Window (AIW) for Intravital Imaging num_downloads: 6 publication_date: '2024-11-15' @@ -7016,12 +7332,13 @@ resources: - https://doi.org/10.5281/zenodo.14168603 - submission_date: '2024-11-18T16:34:10.375459' authors: - - Ishikawa-Ankerhold, Dr. Hellen - - Nobis, Max + - Ishikawa-Ankerhold + - Dr. Hellen + - Max Nobis description: Session 2 of a round table workshop. Features description of image processing methods useful in intravital imaging to compensate for the motion of living tissue. - license: cc-by-4.0 + license: CC-BY-4.0 name: Round Table Workshop 2 - Correction of Drift and Movement num_downloads: 7 publication_date: '2024-11-14' @@ -7030,15 +7347,15 @@ resources: - https://doi.org/10.5281/zenodo.14161633 - submission_date: '2024-11-18T16:34:10.757317' authors: - - Gerlach, Michael - - Fried, Hans-Ulrich - - Peuckert, Christiane + - Michael Gerlach + - Hans-Ulrich Fried + - Christiane Peuckert description: 'Notes from a round table workshop on the 4th Day of Intravital Microscopy in Leuven, Belgium. Contains hands-on tips, tricks and schemes to improve sample stability during various models of Intravital Miroscopy.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Round Table Workshop 1 - Sample Stabilization in intravital Imaging num_downloads: 5 publication_date: '2024-11-14' @@ -7047,12 +7364,13 @@ resources: - https://doi.org/10.5281/zenodo.14161289 - submission_date: '2024-11-18T16:34:11.147252' authors: - - Ishikawa-Ankerhold, Dr. Hellen + - Ishikawa-Ankerhold + - Dr. Hellen description: 'Conference Slides for the presentation of GerBI e.V. at the 4th Day of Intravital Microscopy in Leuven, Belgium. Features Structure, activities and Links to join GerBI e.V.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Conference Slides - 4th Day of Intravital Microscopy num_downloads: 16 publication_date: '2024-11-13' @@ -7061,7 +7379,7 @@ resources: - https://doi.org/10.5281/zenodo.14113714 - submission_date: '2024-11-18T16:34:11.542022' authors: - - Gerlach, Michael + - Michael Gerlach description: 'This video describes the surgical process of implanting an abdominal imaging window (AIW) on the liver of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local @@ -7077,7 +7395,7 @@ resources: to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.' - license: cc-by-nd-4.0 + license: CC-BY-ND-4.0 name: Implantation of abdominal imaging windows on the mouse liver num_downloads: 103 publication_date: '2024-09-04' @@ -7086,7 +7404,7 @@ resources: - https://doi.org/10.5281/zenodo.13683167 - submission_date: '2024-11-18T16:34:11.914727' authors: - - Gerlach, Michael + - Michael Gerlach description: 'This video describes the surgical process of implanting an abdominal imaging window (AIW) on the liver of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local @@ -7102,7 +7420,7 @@ resources: to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.' - license: cc-by-nd-4.0 + license: CC-BY-ND-4.0 name: Implantation of abdominal imaging windows on the mouse liver - short version num_downloads: 26 publication_date: '2024-09-09' @@ -7111,7 +7429,7 @@ resources: - https://doi.org/10.5281/zenodo.13736218 - submission_date: '2024-11-18T16:34:12.275231' authors: - - Gerlach, Michael + - Michael Gerlach description: 'This video describes the surgical process of implanting an abdominal imaging window (AIW) on the kidney of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the @@ -7127,7 +7445,7 @@ resources: license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.' - license: cc-by-nd-4.0 + license: CC-BY-ND-4.0 name: Implantation of abdominal imaging windows on the mouse kidney - short version num_downloads: 50 publication_date: '2024-09-09' @@ -7136,7 +7454,7 @@ resources: - https://doi.org/10.5281/zenodo.13736240 - submission_date: '2024-11-18T16:34:12.641988' authors: - - Gerlach, Michael + - Michael Gerlach description: 'This video describes the surgical process of implanting an abdominal imaging window (AIW) on the kidney of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the @@ -7152,7 +7470,7 @@ resources: to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.' - license: cc-by-nd-4.0 + license: CC-BY-ND-4.0 name: Implantation of abdominal imaging windows on the mouse kidney num_downloads: 36 publication_date: '2024-09-04' @@ -7162,13 +7480,13 @@ resources: - submission_date: '2024-11-18T16:34:13.156773' authors: - Financial & Legal Framework of Core Facilities - - Endl, Elmar - - Hedrich, Jana - - Hoth, Juliane - - Nagy, Julia - - Schauss, Astrid - - Schulze, Nina - - Tulok, Silke + - Elmar Endl + - Jana Hedrich + - Juliane Hoth + - Julia Nagy + - Astrid Schauss + - Nina Schulze + - Silke Tulok description: 'Die GermanBioImaging (GerBI-GMB) - Deutsche Gesellschaft für Mikroskopie und Bildanalyse e.V. bietet über regelmäßig stattfindende Treffen (GerBI-Chats) die Möglichkeit zum aktiven Austausch @@ -7193,7 +7511,7 @@ resources: im Fokus stand, geht es im hier enthaltenen zweiten Teil „Antragsvorbereitung und -fertigstellung: Wie schreibe ich am besten einen Großgeräteantrag?“ um die Beantragung von Forschungsgroßgeräten nach Art. 91b GG.' - license: cc-by-4.0 + license: CC-BY-4.0 name: "GerBI-Chat: Teil 2 - Wie schreibe ich am besten einen Gro\xDFegr\xE4teantrag" num_downloads: 39 publication_date: '2024-10-02' @@ -7203,13 +7521,13 @@ resources: - submission_date: '2024-11-18T16:34:13.609723' authors: - Financial & Legal Framework of Core Facilities - - Endl, Elmar - - Hedrich, Jana - - Hoth, Juliane - - Nagy, Julia - - Schauss, Astrid - - Schulze, Nina - - Tulok, Silke + - Elmar Endl + - Jana Hedrich + - Juliane Hoth + - Julia Nagy + - Astrid Schauss + - Nina Schulze + - Silke Tulok description: 'Die GermanBioImaging (GerBI-GMB) - Deutsche Gesellschaft für Mikroskopie und Bildanalyse e.V. bietet über regelmäßig stattfindende Treffen (GerBI-Chats) die Möglichkeit zum aktiven Austausch der Mitglieder @@ -7234,7 +7552,7 @@ resources: 1 - Von der Bedarfsanmeldung bis zum Beginn der Antragststellung. Die weiteren Stufen der Großgerätebeschaffung werden in nachfolgenden Beiträgen behandelt.' - license: cc-by-4.0 + license: CC-BY-4.0 name: "GerBI-Chat: Teil 1 - Vom Bedarf bis zum Gro\xDFger\xE4teantrag-Schreiben" num_downloads: 367 publication_date: '2024-09-11' @@ -7243,11 +7561,11 @@ resources: - https://doi.org/10.5281/zenodo.13810879 - submission_date: '2024-11-18T16:34:14.668170' authors: - - Tulok, Silke - - Nobst, Anja - - Jannasch, Anett - - Boissonnet, Tom - - Fabig, Gunar + - Silke Tulok + - Anja Nobst + - Anett Jannasch + - Tom Boissonnet + - Gunar Fabig description: '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 @@ -7301,7 +7619,7 @@ resources: 10.5281/zenodo.12546808 Key-Value pair template for annotation of datasets in OMERO (PERIKLES study)' - license: cc-by-4.0 + license: CC-BY-4.0 name: Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI) num_downloads: 12 @@ -7311,14 +7629,14 @@ resources: - https://doi.org/10.5281/zenodo.12578084 - submission_date: '2024-11-18T16:34:15.016548' authors: - - Gerlach, Michael + - Michael Gerlach description: 'A 3D- printable microscope stage adapter for the reproducible accomodation of 6 or 12-well plates at a Zeiss AxioZoom microscope. 4 cylindrical anchors are fixed to the glass plate of the stage. The stage adapter is reversibly placed on these anchors and acommodates a standard Greiner 6- or 12-well plate.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Zeiss AxioZoom Stage Adapter - 12/6Well Plate num_downloads: 2 publication_date: '2024-06-20' @@ -7327,7 +7645,7 @@ resources: - https://doi.org/10.5281/zenodo.7944877 - submission_date: '2024-11-18T16:34:15.354820' authors: - - Gerlach, Michael + - Michael Gerlach description: 'A 3D- printable microscope stage adapter for the reproducible accomodation of samples at a Zeiss AxioZoom stereomicroscope. @@ -7335,7 +7653,7 @@ resources: is reversibly placed on these anchors.  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Zeiss AxioZoom Stage Adapter num_downloads: 1 publication_date: '2024-06-20' @@ -7344,14 +7662,14 @@ resources: - https://doi.org/10.5281/zenodo.7963020 - submission_date: '2024-11-18T16:34:15.720049' authors: - - Gerlach, Michael + - Michael Gerlach description: 'A 3D- printable microscope stage adapter for the reproducible accomodation of EM Blocks at a Zeiss AxioZoom microscope. 4 cylindrical anchors are fixed to the glass plate of the stage. The stage adapter is reversibly placed on these anchors and acommodates 70 standard resin EM blocks.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Zeiss AxioZoom Stage Adapter - EM block holder num_downloads: 3 publication_date: '2024-06-20' @@ -7360,13 +7678,13 @@ resources: - https://doi.org/10.5281/zenodo.7963006 - submission_date: '2024-11-18T16:34:16.060174' authors: - - Gerlach, Michael + - Michael Gerlach description: 'A 3D- printable microscope stage adapter for the reproducible accomodation of microscopic slides at a Zeiss AxioZoom microscope. 4 cylindrical anchors are fixed to the glass plate of the stage. The stage adapter is reversibly placed on these anchors and acommodates 4 standard glass slides.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Zeiss AxioZoom Stage Adapter - Microscope slides num_downloads: 1 publication_date: '2024-06-21' @@ -7375,7 +7693,7 @@ resources: - https://doi.org/10.5281/zenodo.7945018 - submission_date: '2024-11-18T16:34:16.445941' authors: - - Gerlach, Michael + - Michael Gerlach description: 'This is a set of databases containing published use of substances which can be applied to rodents in order to contrast specific structures for optical intravital microscopy. @@ -7394,7 +7712,7 @@ resources: Source publications are listed by DOI.  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Intravital microscopy contrasting agents for application - Database num_downloads: 23 publication_date: '2024-06-19' @@ -7403,10 +7721,10 @@ resources: - https://doi.org/10.5281/zenodo.12166710 - submission_date: '2024-11-18T16:34:16.785479' authors: - - Utz, Nadine - - Reither, Sabine - - Hans, Ruth - - Feldhaus, Christian + - Nadine Utz + - Sabine Reither + - Ruth Hans + - Christian Feldhaus description: 'In bio-medical research we often need to combine a broad range of expertise to run complex experiments and analyse and interpret their results. Also, it is desirable that all stakeholders of a project understand all parts @@ -7425,7 +7743,7 @@ resources: Further use cases for this kit are training courses, demonstrations for imaging newbies when designing an experiment and outreach activities but also basic level prototyping.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Development of a platform for advanced optics education, training and prototyping num_downloads: 12 publication_date: '2023-10-05' @@ -7434,14 +7752,14 @@ resources: - https://doi.org/10.5281/zenodo.10925217 - submission_date: '2024-11-18T16:34:17.179933' authors: - - Weidtkamp-Peters, Stefanie - - Moore, Josh - - Schmidt, Christian - - Nitschke, Roland - - Kunis, Susanne - - Zobel, Thomas + - Stefanie Weidtkamp-Peters + - Josh Moore + - Christian Schmidt + - Roland Nitschke + - Susanne Kunis + - Thomas Zobel description: 'Overview of GerBI RDM projects: why and how?' - license: cc-by-4.0 + license: CC-BY-4.0 name: '[Community Meeting 2024] Supporting and financing RDM projects within GerBI' num_downloads: 58 publication_date: '2024-03-28' @@ -7450,7 +7768,7 @@ resources: - https://doi.org/10.5281/zenodo.10889694 - submission_date: '2024-11-18T16:34:17.925836' authors: - - Stringari, Chiara + - Chiara Stringari description: 'This presentation introduces the open source software to analyze FLIM data: @@ -7468,7 +7786,7 @@ resources: The lecture was part of the short talks on community developed FLIM-software at the German BioImaging workshop on FLIM in Munich.' - license: cc-by-4.0 + license: CC-BY-4.0 name: 'Slides about FLUTE: a Python GUI for interactive phasor analysis of FLIM data' num_downloads: 454 @@ -7478,17 +7796,17 @@ resources: - https://doi.org/10.5281/zenodo.10839310 - submission_date: '2024-11-18T16:34:18.393086' authors: - - Schmidt, Christian - - Bortolomeazzi, Michele - - Boissonnet, Tom - - Dohle, Julia - - Wernet, Tobias - - Hanne, Janina - - Nitschke, Roland - - Kunis, Susanne - - Bernhardt, Karen - - Weidtkamp-Peters, Stefanie - - Ferrando-May, Elisa + - Christian Schmidt + - Michele Bortolomeazzi + - Tom Boissonnet + - Julia Dohle + - Tobias Wernet + - Janina Hanne + - Roland Nitschke + - Susanne Kunis + - Karen Bernhardt + - Stefanie Weidtkamp-Peters + - Elisa Ferrando-May description: 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 @@ -7503,7 +7821,7 @@ resources: 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. - license: cc-by-4.0 + license: CC-BY-4.0 name: The Information Infrastructure for BioImage Data (I3D:bio) project to advance FAIR microscopy data management for the community num_downloads: 44 @@ -7513,13 +7831,13 @@ resources: - https://doi.org/10.5281/zenodo.10805204 - submission_date: '2024-11-18T16:34:18.767636' authors: - - Kunis, Susanne - - Zobel, Thomas + - Susanne Kunis + - Thomas Zobel description: 'Overview of Activities of the Team Image Data Analysis and Management of German BioImaging e.V.  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: '[Community Meeting 2024] Overview Team Image Data Analysis and Management' num_downloads: 52 publication_date: '2024-03-08' @@ -7544,7 +7862,7 @@ resources: Error handling updated for each process ' - license: cc-by-4.0 + license: CC-BY-4.0 name: 'Euro-BioImaging/BatchConvert: v0.0.4' num_downloads: 48 publication_date: '2024-02-19' @@ -7553,65 +7871,71 @@ resources: - https://doi.org/10.5281/zenodo.10679318 - submission_date: '2024-11-18T16:34:22.477169' authors: - - David, Romain - - Rybina, Arina - - Burel, Jean-Marie - - Heriche, Jean-Karim - - Audergon, Pauline - - Boiten, Jan-Willem - - Coppens, Frederik - - Crockett, Sara + - Romain David + - Arina Rybina + - Jean-Marie Burel + - Jean-Karim Heriche + - Pauline Audergon + - Jan-Willem Boiten + - Frederik Coppens + - Sara Crockett - Exter Katrina - - Fahrener, Sven - - Fratelli, Maddalena - - Goble, Carole - - Gormanns, Philipp - - Grantner, Tobias - - Gruning, Bjorn - - Gurwitz, Kim Tamara - - Hancock, John - - Harmse, Henriette - - Holub, Petr - - Juty, Nick - - Karnbach, Geoffrey - - Karoune, Emma - - Keppler, Antje - - Klemeier, Jessica - - Lancelotti, Carla - - Legras, Jean-Luc - - Lister, L. Allyson - - Livio Longo, Dario - - Ludwig, Rebecca - - Madon, Benedicte - - Massimi, Marzia - - Matser, Vera - - Matteoni, Rafaele - - Mayrhofer, Michaela Th. - - Ohmann, Christian - - Panagiotopoulou, Maria - - Parkinson, Helen - - Perseil, Isabelle - - Pfander, Claudia - - Pieruschka, Roland - - Raess, Michael - - Rauber, Andreas - - Richard, Audrey S. - - Romano, Paolo - - Rosato, Antonio - - Sanchez-Pla, Alex - - Sansone, Susanna-Assunta - - Sarkans, Ugis - - Serrano-Solano, Beatriz - - Tang, Jing - - Tanoli, Ziaurrehman - - Tedds, Jonathan - - Wagener, Harald - - Weise, Martin - - Westerhoff, Hans V. - - Wittner, Rudolf - - Ewbank, Jonathan - - Blomberg, Niklas - - Gribbon, Philip + - Sven Fahrener + - Maddalena Fratelli + - Carole Goble + - Philipp Gormanns + - Tobias Grantner + - Bjorn Gruning + - Gurwitz + - Kim Tamara + - John Hancock + - Henriette Harmse + - Petr Holub + - Nick Juty + - Geoffrey Karnbach + - Emma Karoune + - Antje Keppler + - Jessica Klemeier + - Carla Lancelotti + - Jean-Luc Legras + - Lister + - L. Allyson + - Livio Longo + - Dario + - Rebecca Ludwig + - Benedicte Madon + - Marzia Massimi + - Vera Matser + - Rafaele Matteoni + - Mayrhofer + - Michaela Th. + - Christian Ohmann + - Maria Panagiotopoulou + - Helen Parkinson + - Isabelle Perseil + - Claudia Pfander + - Roland Pieruschka + - Michael Raess + - Andreas Rauber + - Richard + - Audrey S. + - Paolo Romano + - Antonio Rosato + - Alex Sanchez-Pla + - Susanna-Assunta Sansone + - Ugis Sarkans + - Beatriz Serrano-Solano + - Jing Tang + - Ziaurrehman Tanoli + - Jonathan Tedds + - Harald Wagener + - Martin Weise + - Westerhoff + - Hans V. + - Rudolf Wittner + - Jonathan Ewbank + - Niklas Blomberg + - Philip Gribbon description: '"Be SURE - Be SUstainable REcommendations"The main goals and challenges for the Life Science (LS) communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially @@ -7631,7 +7955,7 @@ resources: of concepts, semantics and functionalities in the life sciences.IN PRESS EMBO Journal: https://www.embopress.org/journal/14602075 AVAILABLE SOON at : https://doi.org/10.15252/embj.2023115008 ' - license: cc-by-4.0 + license: CC-BY-4.0 name: 'Preprint: "Be Sustainable", Recommendations for FAIR Resources in Life Sciences research: EOSC-Life''s Lessons' num_downloads: 2486 @@ -7645,7 +7969,7 @@ resources: description: Graduation presentation for the 7th cohort of the Open Seeds mentoring & training program for Open Science ambassadors. The project presented is called "Euro-BioImaging  Scientific Ambassadors Program". - license: cc-by-4.0 + license: CC-BY-4.0 name: Euro-BioImaging Scientific Ambassadors Program num_downloads: 25 publication_date: '2023-07-25' @@ -7660,7 +7984,7 @@ resources: on Research Infrastructures (ESFRI). Euro-BioImaging is the gateway to world-class imaging facilities across Europe. This document is the Euro-BioImaging Annual Report for the year 2022. - license: cc-by-4.0 + license: CC-BY-4.0 name: Euro-BioImaging ERIC Annual Report 2022 num_downloads: 83 publication_date: '2023-07-14' @@ -7669,15 +7993,17 @@ resources: - https://doi.org/10.5281/zenodo.8146412 - submission_date: '2024-11-18T16:34:23.860886' authors: - - Kemmer, Isabel - - Keppler, Antje - - Serrano-Solano, Beatriz - - Rybina, Arina - - "\xD6zdemir, Bugra" - - Bischof, Johanna - - El Ghadraoui, Ayoub - - Eriksson, John E. - - Mathur, Aastha + - Isabel Kemmer + - Antje Keppler + - Beatriz Serrano-Solano + - Arina Rybina + - "Bugra \xD6zdemir" + - Johanna Bischof + - El Ghadraoui + - Ayoub + - Eriksson + - John E. + - Aastha Mathur description: Bioimaging has now entered the era of big data with faster than ever development of complex microscopy technologies leading to increasingly complex datasets. This enormous increase in data size and informational complexity within @@ -7689,7 +8015,7 @@ resources: how different actors in the microscopy ecosystem are working together, creating synergies that develop new approaches, and how research infrastructures, such as Euro-BioImaging, are fostering these interactions to shape the field.  - license: cc-by-4.0 + license: CC-BY-4.0 name: Building a FAIR image data ecosystem for microscopy communities num_downloads: 199 publication_date: '2023-03-31' @@ -7698,28 +8024,37 @@ resources: - https://doi.org/10.5281/zenodo.7788899 - submission_date: '2024-11-18T16:34:26.146506' authors: - - Sorensen, Luke - - Saito, Ayame - - Poon, Sabrina - - Noe Han, Myat - - Hamnett, Ryan - - Neckel, Peter - - Humenick, Adam - - Mutunduwe, Keith - - Glennan, Christie - - Mahdavian, Narges - - JH Brookes, Simon - - M McQuade, Rachel - - PP Foong, Jaime - - "G\xF3mez-de-Mariscal, Estibaliz" - - "Mu\xF1oz Barrutia, Arrate" - - Kaltschmidt, Julia A. - - King, Sebastian K. - - Haase, Robert - - Carbone, Simona - - A. Veldhuis, Nicholas - - P. Poole, Daniel - - Rajasekhar, Pradeep + - Luke Sorensen + - Ayame Saito + - Sabrina Poon + - Noe Han + - Myat + - Ryan Hamnett + - Peter Neckel + - Adam Humenick + - Keith Mutunduwe + - Christie Glennan + - Narges Mahdavian + - JH Brookes + - Simon + - M McQuade + - Rachel + - PP Foong + - Jaime + - "Estibaliz G\xF3mez-de-Mariscal" + - "Mu\xF1oz Barrutia" + - Arrate + - Kaltschmidt + - Julia A. + - King + - Sebastian K. + - Robert Haase + - Simona Carbone + - A. Veldhuis + - Nicholas + - P. Poole + - Daniel + - Pradeep Rajasekhar description: 'What''s Changed @@ -7741,7 +8076,7 @@ resources: Full Changelog: https://github.com/pr4deepr/GutAnalysisToolbox/compare/v0.6...v0.7' - license: cc-by-4.0 + license: CC-BY-4.0 name: Gut Analysis Toolbox num_downloads: 77 publication_date: '2024-09-10' @@ -7836,7 +8171,7 @@ resources: \ Nehme, E., Lerche, M., Hernández-Pérez, S., Mattila, P.K., Karinou,\ \ E. and Holden, S., 2021. Democratising deep learning for microscopy with ZeroCostDL4Mic. Nature\ \ communications, 12(1), pp.1-18." - license: cc-by-4.0 + license: CC-BY-4.0 name: 'Gut Analysis Toolbox: Training data and 2D models for segmenting enteric neurons, neuronal subtypes and ganglia' num_downloads: 176 @@ -7854,7 +8189,7 @@ resources: Common licenses, and a sum up of electronic laboratory notebooks. The last two slides go through how all of that works in practice in open access core microscopy facility. - license: cc-by-4.0 + license: CC-BY-4.0 name: Research Data Managemet and how not to get overwhelmed with data num_downloads: 229 publication_date: '2023-09-23' @@ -7866,7 +8201,7 @@ resources: - Romain description: A groovy script to use in Fiji to generate artificial images and labels, with example images. - license: cc-by-4.0 + license: CC-BY-4.0 name: Artificial Blobs and Labels image num_downloads: 25 publication_date: '2023-05-10' @@ -7875,10 +8210,10 @@ resources: - https://doi.org/10.5281/zenodo.7919117 - submission_date: '2024-11-18T16:34:28.513488' authors: - - "Sch\xE4tz, Martin" - - "Rube\u0161ov\xE1, Olga" - - "Mare\u0161, Jan" - - Spark, Alan + - "Martin Sch\xE4tz" + - "Olga Rube\u0161ov\xE1" + - "Jan Mare\u0161" + - Alan Spark description: 'The software tool is developed on demand of Radiological Department of Faculty Hospital of Královské Vinohrady, with the aim to provide a tool to estimate the percentage of pneumonia (or COVID-19 presence) in lungs. @@ -7921,7 +8256,7 @@ resources:  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: ImageJ tool for percentage estimation of pneumonia in lungs num_downloads: 179 publication_date: '2023-05-02' @@ -7944,7 +8279,7 @@ resources: using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV1 num_downloads: 228 @@ -7960,7 +8295,7 @@ resources: - Matthias Lutolf description: This imagej macro analyses the reporter intensity activity and expression domain in EPI aggregates and Gastruloids. - license: cc-by-4.0 + license: CC-BY-4.0 name: Measuring reporter activity domain in EPI aggregates and Gastruloids.ijm num_downloads: 34 publication_date: '2022-12-07' @@ -7970,13 +8305,13 @@ resources: - submission_date: '2024-11-18T16:34:30.357363' authors: - "Martin Sch\xE4tz" - - "Sch\xE4tz, Martin" + - "Martin Sch\xE4tz" description: The slides were presented during the Macro programming with ImageJ workshop (https://www.16mcm.cz/programme/#workshops) which was part of the 16th Multinational Congress on Microscopy. It is a collection and "reshuffle" of slides originally made by Robert Haase on topics from Image Analysis in general up to User-friendly GPU-accelerated bio-image analysis and CLIJ2. - license: cc-by-4.0 + license: CC-BY-4.0 name: Interactive Image Data Flow Graphs num_downloads: 14 publication_date: '2022-10-17' @@ -8023,7 +8358,7 @@ resources: as in subsequent imaging data sets, the algorithm outlines more stable volumes in both cases. Thus, increased contour reproducibility is reached by automation of the delineation process by the proposed algorithm.  - license: cc-by-4.0 + license: CC-BY-4.0 name: Optimisation and Validation of a Swarm Intelligence based Segmentation Algorithm for low Contrast Positron Emission Tomography num_downloads: 170 @@ -8045,7 +8380,7 @@ resources: \ any data with more "advanced" dimensions like AiryScan rawdata,\ \ illumination angles etc. Also no CZI files with pixel type RGB are\ \ included yet.\n\n \n\n \n\n " - license: cc-by-4.0 + license: CC-BY-4.0 name: CZI (Carl Zeiss Image) dataset with artificial test camera images with various dimension for testing libraries reading num_downloads: 676 @@ -8055,7 +8390,7 @@ resources: - https://doi.org/10.5281/zenodo.7015307 - submission_date: '2024-11-18T16:34:31.831739' authors: - - "Sch\xE4tz, Martin" + - "Martin Sch\xE4tz" description: 'SciAugment v0.2.0 has pip installable version, channel-wise augmentation was added, and an option for all augmentations or no augmentation. Examples of how to use the tool are in README and in Google Colab notebooks. Practical examples @@ -8065,7 +8400,7 @@ resources: SciAugment aims to provide an option to create an augmented image set with similar changes in data as the imaging sensor and technique would do.' - license: other-open + license: OTHER-OPEN name: SciAugment num_downloads: 8 publication_date: '2022-07-29' @@ -8074,9 +8409,9 @@ resources: - https://doi.org/10.5281/zenodo.6991106 - submission_date: '2024-11-18T16:34:32.177486' authors: - - "Sch\xE4tz, Martin" - - "Mraz\xEDk, Luk\xE1\u0161" - - "M\xE1hlerova, Karolina" + - "Martin Sch\xE4tz" + - "Luk\xE1\u0161 Mraz\xEDk" + - "Karolina M\xE1hlerova" description: 'The first version contains an example of augmentation of scientific data and object detection with YOLO_v5 on colony counting (2 classes), object counting in blood smears (can be used as semisupervised learning for faster annotation), @@ -8084,7 +8419,7 @@ resources: The project is available on GitHub.' - license: other-open + license: OTHER-OPEN name: 'martinschatz-cz/SciCount: v1.0.0 with reusable example notebooks' num_downloads: 3 publication_date: '2022-08-02' @@ -8093,12 +8428,12 @@ resources: - https://doi.org/10.5281/zenodo.6953610 - submission_date: '2024-11-18T16:34:32.987735' authors: - - Waiger, Daniel + - Daniel Waiger description: 'A simple workflow to detect Soma and neurite paths, from light microscopy datasets. Using open-source tools for beginners.' - license: cc-by-4.0 + license: CC-BY-4.0 name: Morphological analysis of neural cells with WEKA and SNT Fiji plugins num_downloads: 38 publication_date: '2022-07-14' @@ -8132,7 +8467,7 @@ resources: NOTE : Some tiles were annotated and used to train a StarDist3D model (https://doi.org/10.5281/zenodo.6645978   )' - license: cc-by-4.0 + license: CC-BY-4.0 name: Large tiling confocal acquisition (rat brain) num_downloads: 9 publication_date: '2022-06-15' @@ -8184,7 +8519,7 @@ resources:  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: 3D Nuclei annotations and StarDist 3D model(s) (rat brain) num_downloads: 547 publication_date: '2022-06-15' @@ -8202,7 +8537,7 @@ resources: under supervision of Jochen Gehrig. The project was hosted at ACQUIFER Imaging with collaboration of the medical university of Heidelberg, and part of the ImageInLife Horizon2020 ITN (PhD program). ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Multi-Template-Matching for object-detection (slides) num_downloads: 169 publication_date: '2022-05-16' @@ -8248,7 +8583,7 @@ resources: As stated in the presentation, illustrations are copyrighted but can be reproduced provided the original attribution is conserved.' - license: other-at + license: OTHER-AT name: Introduction to light-microscopy / Widefield microscopy num_downloads: 104 publication_date: '2022-05-10' @@ -8299,7 +8634,7 @@ resources: [1] Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Scientific Reports (2017). https://doi.org/10.1038/s41598-017-17204-5' - license: cc-by-4.0 + license: CC-BY-4.0 name: Liver Micrometastases area quantification using QuPath and pixel classifier num_downloads: 168 publication_date: '2022-05-06' @@ -8344,7 +8679,7 @@ resources: \ you delete the “_flow” images that are auto-computed when running\ \ the training. If you do not, then the flows from previous runs will be used\ \ for the new training, which might yield confusing results.\n\n " - license: cc-by-4.0 + license: CC-BY-4.0 name: Cellpose models for Label Prediction from Brightfield and Digital Phase Contrast images num_downloads: 78 @@ -8415,7 +8750,7 @@ resources: NOTE: This dataset was used to train the cellpose models in the following Zenodo entry: https://doi.org/10.5281/zenodo.6140111' - license: cc-by-4.0 + license: CC-BY-4.0 name: HeLa "Kyoto" cells under the scope num_downloads: 309 publication_date: '2022-02-25' @@ -8461,7 +8796,7 @@ resources:  ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Digital Phase Contrast on Primary Dermal Human Fibroblasts cells num_downloads: 101 publication_date: '2022-02-09' @@ -8502,7 +8837,7 @@ resources: python -m cellpose --dir NEW/DATASET/PATH --pretrained_model FULL_MODEL_PATH --chan 0 --chan2 0 --save_tif --no_npy' - license: cc-by-4.0 + license: CC-BY-4.0 name: Cellpose model for Digital Phase Contrast images num_downloads: 66 publication_date: '2022-02-09' @@ -8524,7 +8859,7 @@ resources: Latest tested with Fiji 2.1.0/ImageJ 1.53j' - license: mit-license + license: MIT name: 'LauLauThom/MaskFromRois-Fiji: Masks from ROIs plugins for Fiji - initial release' num_downloads: 36 @@ -8557,7 +8892,7 @@ resources: - PSFgen_WFsquare_WBpsf.tif, is the result of the square operation on PSFgen_WF_WBpsf.tif , to approximate a confocal PSF' - license: cc-by-4.0 + license: CC-BY-4.0 name: Deconvolution Test Dataset num_downloads: 353 publication_date: '2021-07-14' @@ -8568,7 +8903,7 @@ resources: authors: - Cavanagh description: A test data set for troublshooting. no scientific meaning. - license: cc-zero + license: CC-ZERO name: Ink in a dish num_downloads: 3 publication_date: '2024-09-03' @@ -8577,7 +8912,7 @@ resources: - https://doi.org/10.5281/zenodo.13642395 - submission_date: '2024-11-18T16:34:40.260008' authors: - - Chiaruttini, Nicolas + - Nicolas Chiaruttini description: 'The files contained in this repository are confocal images taken with the Evident FV 4000 of a sample containing DAPI and mCherry stains, excited with the 405 nm laser and images for different emission windows (lambda scan). @@ -8600,7 +8935,7 @@ resources: 420 to 630 nm by steps of 50 nm, 4 slices, 3 timepoints ' - license: cc-by-4.0 + license: CC-BY-4.0 name: Evident OIR sample files with lambda scan - FV 4000 num_downloads: 59 publication_date: '2024-07-18' @@ -8644,7 +8979,7 @@ resources: \tat ij.macro.Interpreter.run(Interpreter.java:93)\n\tat ij.macro.MacroRunner.run(MacroRunner.java:146)\n\ \tat java.lang.Thread.run(Thread.java:750)\n\nYou can find one example file at this\ \ link 1.\nThanks for your help !Best,Laurent" - license: cc-by-4.0 + license: CC-BY-4.0 name: ICS/IDS stitched file num_downloads: 16 publication_date: '2024-06-13' @@ -8653,34 +8988,20 @@ resources: - https://doi.org/10.5281/zenodo.11637422 - submission_date: '2024-11-18T16:34:41.460603' authors: - - Garcia, Mario + - Mario Garcia description: Human brain tissue with DAB immunostaining. Image acquired by BF microscopy in  Zeiss Axioscan at 20x.  - license: cc-by-4.0 + license: CC-BY-4.0 name: Human DAB staining Axioscan BF 20x num_downloads: 9 publication_date: '2024-05-21' url: - https://zenodo.org/records/11234863 - https://doi.org/10.5281/zenodo.11234863 - -- authors: Weischer, Sarah, Wendt, Jens, Zobel, Thomas - description: In this workshop a fully integrated data analysis solutions employing - OMERO and commonly applied image analysis tools (e.g., CellProfiler, Fiji) using - existing python interfaces (OMERO Python language bindings, ezOmero, Cellprofiler - Python API) is presented. - license: cc-by-4.0 - name: High throughput & automated data analysis and data management workflow with - Cellprofiler and OMERO - num_downloads: 7 - publication_date: '2023-07-12' - submission_date: '2024-11-19T09:44:04.167272' - url: - - https://zenodo.org/records/8139354 - - https://doi.org/10.5281/zenodo.8139354 - - authors: - - Kunis, Susanne - - Dohle, Julia +- authors: + - Sarah Weischer + - Jens Wendt + - Thomas Zobel description: "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\ @@ -8688,7 +9009,7 @@ resources: \ Data\n\tTools to edit/gather metadata\n\tISA Framework\n\tFDO Framework\n\t\ Ontology\n\tRDF\n\tJSON-LD\n\tSPARQL\n\tKnowledge Graph\n\tLinked Data\n\tSmart\ \ Data\n\t...\n" - license: cc-by-4.0 + license: CC-BY-4.0 name: 'Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data' num_downloads: 704