Image Data Resource
Names
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Image Data Resource
metasource: Fairsharing.org
version: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
IDR
metasource: Fairsharing.org
version: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
Image Data Resource
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
IDR
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
Names
More detailed information about this field from each metasource.
Image Data Resource
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
IDR
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
IDR is a prototype platform for publishing, mining and integrating bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy using the OMERO and Bio-Formats open source software built by the Open Microscopy Environment. Deployed on an OpenStack cloud running on the EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology.
Description
More detailed information about this field from each metasource.
IDR is a prototype platform for publishing, mining and integrating bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy using the OMERO and Bio-Formats open source software built by the Open Microscopy Environment. Deployed on an OpenStack cloud running on the EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology.
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
The IDR makes datasets that have never previously been accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing data promotes the validation of experimental methods and scientific conclusions, the comparison with new data obtained by the global scientific community, and enables data reuse by developers of new analysis and processing tools.
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
Webpage:
https://idr.openmicroscopy.orgWebpage
More detailed information about this field from each metasource.
https://idr.openmicroscopy.org
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
https://idr.openmicroscopy.org/about/
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
Licence:
Name: CCLicence name
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CC
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
Licence URL
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https://creativecommons.org/licenses/by/4.0/
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
Publications:
Publications
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The Image Data Resource: A Bioimage Data Integration and Publication Platform
PMID: 28775673
metasource: Fairsharing.org
version: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
The Image Data Resource: A Bioimage Data Integration and Publication Platform
PMID: 28775673
metasource: Fairsharing.org
version: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
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The Image Data Resource: A Bioimage Data Integration and Publication Platform
PubMed citations: 73.
73 articles citing: The Image Data Resource: A Bioimage Data Integration and Publication Platform
Label-free cell tracking enables collective motion phenotyping in epithelial monolayers. PMID:35856018
Single-molecule localization microscopy. PMID:35663461
Serum metabolomics strategy for understanding the therapeutic effects of Yin-Chen-Hao-Tang against Yanghuang syndrome. PMID:35539139
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
A collaborative semantic-based provenance management platform for reproducibility. PMID:35494870
Deep learning -- promises for 3D nuclear imaging: a guide for biologists. PMID:35420128
WashU Epigenome Browser update 2022. PMID:35412637
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
User-Accessible Machine Learning Approaches for Cell Segmentation and Analysis in Tissue. PMID:35360226
Three-dimensional structured illumination microscopy data of mitochondria and lysosomes in cardiomyoblasts under normal and galactose-adapted conditions. PMID:35322035
Can super-resolution microscopy become a standard characterization technique for materials chemistry? PMID:35310478
MITI minimum information guidelines for highly multiplexed tissue images. PMID:35277708
Pooled genetic perturbation screens with image-based phenotypes. PMID:35022620
End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach. PMID:34991705
Unbox the black-box for the medical explainable AI via multi-modal and multi-centre data fusion: A mini-review, two showcases and beyond. PMID:34980946
BioProfiling.jl: Profiling biological perturbations with high-content imaging in single cells and heterogeneous populations. PMID:34935929
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. PMID:34862503
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. PMID:34862501
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies. PMID:34845388
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. PMID:34811556
Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. PMID:34750536
The importance of adherence to international standards for depositing open data in public repositories. PMID:34727971
Avoiding a replication crisis in deep-learning-based bioimage analysis. PMID:34608322
Image-based deep learning reveals the responses of human motor neurons to stress and VCP-related ALS. PMID:34595747
Subcellular proteomics. PMID:34549195
Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations. PMID:34139168
Interpretable deep learning uncovers cellular properties in label-free live cell images that are predictive of highly metastatic melanoma. PMID:34077708
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. PMID:34021280
Data science in cell imaging. PMID:33795377
Creating clear and informative image-based figures for scientific publications. PMID:33788834
Effective image visualization for publications - a workflow using open access tools and concepts. PMID:33708381
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. PMID:33627808
Nuisance compounds in cellular assays. PMID:33592188
A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. PMID:33575256
Predicting cell health phenotypes using image-based morphology profiling. PMID:33534641
In situ genome sequencing resolves DNA sequence and structure in intact biological samples. PMID:33384301
Pancreatlas: Applying an Adaptable Framework to Map the Human Pancreas in Health and Disease. PMID:33294866
BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows. PMID:33205108
OpSeF: Open Source Python Framework for Collaborative Instance Segmentation of Bioimages. PMID:33117778
MarrowQuant Across Aging and Aplasia: A Digital Pathology Workflow for Quantification of Bone Marrow Compartments in Histological Sections. PMID:33071956
An extensible big data software architecture managing a research resource of real-world clinical radiology data linked to other health data from the whole Scottish population. PMID:32990744
TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects. PMID:32934016
Biobanks in the era of big data: objectives, challenges, perspectives, and innovations for predictive, preventive, and personalised medicine. PMID:32849924
Community standards for open cell migration data. PMID:32396199
Immune monitoring using mass cytometry and related high-dimensional imaging approaches. PMID:31892734
Open Practices and Resources for Collaborative Digital Pathology. PMID:31799253
Mapping the perturbome network of cellular perturbations. PMID:31723137
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. PMID:31701143
Key challenges facing data-driven multicellular systems biology. PMID:31648301
Bringing Open Data to Whole Slide Imaging. PMID:31579322
Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures. PMID:31398189
IA-Lab: A MATLAB framework for efficient microscopy image analysis development, applied to quantifying intracellular transport of internalized peptide-drug conjugate. PMID:31369634
Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images. PMID:31313519
Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes. PMID:31278301
From observing to predicting single-cell structure and function with high-throughput/high-content microscopy. PMID:31243141
Securing the future of research computing in the biosciences. PMID:31095554
Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline: Data architecture, artificial intelligence, automated processing, containerization, and clusters orchestration ease the transition from data acquisition to insights in medium-to-large datasets. PMID:31094000
Multicolor multiscale brain imaging with chromatic multiphoton serial microscopy. PMID:30971684
Evaluating reproducibility of AI algorithms in digital pathology with DAPPER. PMID:30917113
Designing a rigorous microscopy experiment: Validating methods and avoiding bias. PMID:30894402
Enhancing the Value of Histopathological Assessment of Allograft Biopsy Monitoring. PMID:30768568
Super-resolution microscopy demystified. PMID:30602772
A call for public archives for biological image data. PMID:30377375
A beginner's guide to rigor and reproducibility in fluorescence imaging experiments. PMID:29953344
Sharing and reusing cell image data. PMID:29851565
A deep-learning classifier identifies patients with clinical heart failure using whole-slide images of H&E tissue. PMID:29614076
NGLview-interactive molecular graphics for Jupyter notebooks. PMID:29236954
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes. PMID:29087936
The BioStudies database-one stop shop for all data supporting a life sciences study. PMID:29069414
Data-analysis strategies for image-based cell profiling. PMID:28858338
Challenges for visualizing three-dimensional data in genomic browsers. PMID:28771695
A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay. PMID:28327978
Tags:
Tags
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biological imaging
metasource: Fairsharing.org
version: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
high-content screen
metasource: Fairsharing.org
version: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
super-resolution microscopy
metasource: Fairsharing.org
version: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
bioimage
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
digital pathology
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
gene networks
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
high-content screening
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
multi-dimensional microscopy
metasource: re3data.org
version: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
Tags
More detailed information about this field from each metasource.
biological imaging
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
high-content screen
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
super-resolution microscopy
metasource: Fairsharing.orgversion: FAIRsharing.org: IDR; Image Data Resource; DOI: https://doi.org/10.25504/FAIRsharing.6wf1zw; Last edited: June 30, 2021, 10:17 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
bioimage
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
digital pathology
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
gene networks
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
high-content screening
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
multi-dimensional microscopy
metasource: re3data.orgversion: re3data.org: Image Data Resource; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XR0R last accessed: 2022-11-04
biological imaging high-content screen super-resolution microscopy bioimage digital pathology gene networks high-content screening multi-dimensional microscopy
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