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Seminars and Colloquia


The Image Data Resource: a platform for publishing, integrating and mining biological imaging data at scale 
Tue, Sep 12, 2017,   12:00 PM to 01:00 PM at Seminar Room 34, 2nd Floor, Main Building

Prof. Jason Swedlow
University of Dundee, Dundee

Much of the published research in the life sciences is based on image datasets that sample 3D space, time, and the spectral characteristics of detected signal to provide quantitative measures of cell, tissue and organismal processes and structures.

To address this challenge, we have built a next-generation imaging resource, the I mage D ata R esource (IDR; http://idr.openmicroscopy.org ) – an added value resource that combines data from multiple independent imaging experiments and from many different imaging modalities, integrates them into a single resource, and makes the data available for re-analysis in a convenient, scalable form. IDR provides, for the first time, a prototyped resource that supports browsing, search, visualisation and computational processing within and across datasets acquired from a wide variety of imaging domains. IDR stores, publishes and integrates >50 TB of super-resolution, high content screening, timelapse and histological whole slide imaging data with metadata related to experimental design, image acquisition, downstream analysis and interpretation. Data from >35 studies are available for search and query through a user-friendly web interface. Wherever possible, we have mapped the reagents, methods and phenotypes to published common ontologies. IDR is available at http://idr.openmicroscopy.org .

By mining IDR data, we have demonstrated that control of cell elongation involves the Set1B histone methyltransferase in fission yeast and human cells, suggesting a conserved mechanism controlling cell shape based individual cells. To promote re-use of IDR data, we have built a virtual analysis environment using JupyterHub and Docker, so researchers can analyse and mine IDR data and metadata using cloud-based computational resources. Notebooks for mining IDR metadata and image features are available at https://github.com/IDR/idr-notebooks . Users can deploy their own IDR using Ansible-based tools available at https://github.com/IDR/deployment .