IDR – Image Data Resource
Image data resource – Lecture
Trainer: Jason Swedlow
Overview: IDR links data from several imaging modalities, including high-content screening, multi-dimensional microscopy and digital pathology, with public genetic or chemical databases and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable reanalysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open-source platform for publishing imaging data. Thus IDR provides an online resource and a software infrastructure that promotes and extends publication and reanalysis of scientific image data. (Segment from the abstract at Nature methods)
Learning outcomes
By the end of this session you will be able to:
- List IDRs benefits and services
- Identify the importance of FAIR principles in bioimaging data
Materials:
- Presentation slides
- Article – Image Data Resource: a bioimage data integration and publication platform
- IDR home page
Image data resource – Lecture
Trainer: Frances Wong
Overview: The Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access high quality bio-image data. The lecture will focus on data submission and curation in IDR. This will include the IDR submission workflow, IDR submission process, how to fill in IDR metadata templates and metadata curation in IDR.
Learning outcomes
By the end of this session you will be able to:
- Find more information about IDR
- Submit data to IDR
Materials:
Image data resource – Practical
Trainer: Jean Marie Burel
Overview: In this section you will explore the web-based graphical interface of IDR showing the browsing and data and metadata layout and searches inside IDR. This section will also demonstrate how to connect imaging software packages to analyse images and metadata hosted in IDR using OMERO APIs.
Learning outcomes
By the end of this session you will be able to:
- Browse through IDR’s web-based interface to locate data and metadata
- Practice basic connections to IDR to some software packages for bioimage analysis through OMERO’s APIs
Materials:
- A particular video with very similar content to the one shown in practical during the course
- Notebooks for the second part of the practical – to demonstrate how to access the images and metadata from the Image Data Resource (IDR), including features and all descriptive tags
- Omero-guides containing other notebooks used in the practical – The OMERO guide offers step-by-step instructions on how to use components of the OMERO platform.