IMS pipeline

Input

To run pipeline you need to create a submission file that contains paths to the datasets and some running parameters. Example of submission file is sample_submission.yaml

Output

Output can be found either in the directory where this pipeline was invoked or at the location of cwltool argument --outdir.

• segmentation_mask_stitched.ome.tiff Multichannel segmentation mask produced by Cytokit using nuclei channel.
• ims_combined_multilayer.ome.tiff
  All IMS channels combined together in one OME-TIFF
• mxif_combined_multilayer.ome.tiff
  All MxIF channels combined together in one OME-TIFF
• cytokit_config.yaml
  Configuration file that contain parameters for running Cytokit.
• pipeline_config.yaml
  Runtime parameters that were used in the pipeline.

Requirements

cwltool that can run containers with access to GPU: https://github.com/hubmapconsortium/cwltool/tree/docker-gpu

Docker containers:

• hubmap/ims-mxif-pipeline:latest
• hubmap/cytokit:latest

If not present locally will be downloaded by cwltool.