Completed Cells, Biochemistry & Physiology Computing & AI

The Image Data Resource: Making Biological Imaging Data FAIR

In plain English

AI plain-English summary

The Image Data Resource (IDR) already holds over 45 terabytes of biological image data—more than 37 million individual image planes from 46 published studies—and now needs to scale up. This matters because biological imaging data is notoriously difficult to reuse. A single microscopy experiment can generate terabytes of files, and most published images sit in PDF figures or lab hard drives, inaccessible to other researchers. Without a central, searchable repository, scientists cannot verify results, compare datasets, or apply new computational analyses to old experiments. The IDR solves this by making images findable, accessible, interoperable, and reusable (FAIR). If this project succeeds, the IDR will grow to host more diverse datasets and enable cloud-based computation—allowing researchers anywhere to query and re-analyse images without downloading massive files. The team will also redesign the user interface, working with biologists and image analysts through networks like NEUBIAS and Euro-BioImaging, to make the resource easier to use. For the wider scientific community, this means faster validation of published results, fewer duplicated experiments, and the ability to mine historical data for new discoveries. The infrastructure itself is the impact: a quietly running database that changes how biological evidence is shared and built upon.

View original technical description
We have built the Image Data Resource (IDR; http://idr.openmicroscopy.org; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536224/), an added value database prototype that publishes and integrates scientific image datasets linked to peer-reviewed publications. As of this writing, IDR publishes >45 TB of image data, >1.0 million experiments, and >37 million image planes in 46 published studies. The resource is accessed by more than 1600 unique users per month, generating >1 million hits/month. Under the proposed Biomedical Resource Award, we will continue growing IDR, taking in more and more diverse imaging datasets, and scaling the computational resources that enable online, cloud-based computation, querying and re-analysis of IDR datasets. A major focus of this project is the engagement with a range of biologists, image analysts and computational biologists through our participation in NEUBIAS, Euro-BioImaging and Global BioImaging to test new User Interface and Experience concepts to substantially grow the interaction and accessibility of IDR and its data. We will leverage EMBL-EBI’s extensive community/training resources to hold several user testing and training sessions to achieve this aim.

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Researchers

Jason Swedlow (EPMC Awardee)

Related Research

Grants with similar aims, by meaning.

Building a Next Generation Image Repository: Molecular Annotation and Cloud-based Data Processing and Analysis
BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata, and Value
Intuitive Large-scale Image Processing for Biologists
A2O - Transforming EMPIAR into an Essential Resource for EM Data Spanning Scales from Atoms to Organisms
Open image informatics software for biological microscopy

Original classification

Biomedical Resources Grant

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