April 2024 OME workshops

The OME Team gave two practical sessions on OMERO, OME-NGFF and IDR as a part of the Microscopy data analysis course at EMBL-EBI.

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Organisers: EMBL-EBI

Location: held remotely

Practical on Day 4: Image data resource – practical

Date: 25 April 2024

Duration: 3 hours

Practical on Day 5: Distributed/Cloud computing - practical

Date: 26 April 2024

Duration: 3 hours

The usage of Image Data Resource (IDR) was explored and it was demonstrated how to access the IDR data using the Python API, to fetch image data and metadata from IDR study associated with a publication. A workflow involving programmatical harvesting of data from multiple Data resources (HumanMine and IDR) was shown. Further, re-analysis of data using an alternative segmentation tool to the one used by the publication authors was performed. The analytical packages used included Cellpose, StarDist and CellProfiler. In the second workshop on the following day, the Distributed/Cloud computing workshop introduced an emerging cloud-optimized imaging format OME-NGFF currently used by the BioImage Archive and the IDR. It was shown how it can be used to access cloud-hosted imaging data and how it facilitates analysis in parallel, how to convert other formats into OME-NGFF and how to upload and download OME-NGFF images to and from S3 storage. The image analysis examples included workflows involving Cellpose and StarDist.

Resources available:

The repository with jupyter notebooks and scripts and five selected workflows published on WorkflowHub.

  1. Load Image with labels from IDR, re-analyze using Cellpose
  2. Load Image with labels from IDR, re-analyze using StarDist
  3. Load ome.zarr Image with labels from public S3 repositories, analyze in parallel using Cellpose and compare results
  4. Load ome.zarr Image with labels from a public S3 repository, analyze using StarDist and compare results
  5. Use Public Resources to answer a biological question

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