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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.