README.md

CellDIVE pipeline

Prepares data and does 2D segmentation of CellDIVE images slice by slice using deepcell method.

Usage example

cwltool pipeline.cwl subm.yaml

Requires meta.yaml with names of channels that will be used for segmentation of cell and nucleus compartments.

The expected input directory structure:

HuBMAP_OME/
├── region_001
│     ├── S20030077_region_001.ome.tif
│     ├── S20030078_region_001.ome.tif
│     │              ...
│     └── S20030105_region_001.ome.tif
└── region_00N
      ├── S20030077_region_00N.ome.tif
      ├── S20030078_region_00N.ome.tif
      │             ...
      └── S20030105_region_00N.ome.tif

The output structure:

pipeline_output/
├── expr
│   ├── reg001_S20030077_region_001_expr.ome.tiff
│   ├── reg002_S20030078_region_002_expr.ome.tiff
│   │                  ...
│   └── reg00N_S20030105_region_00N_expr.ome.tiff       
└── mask                                                                                  
    ├── reg001_S20030077_region_001_mask.ome.tiff
    ├── reg002_S20030078_region_002_mask.ome.tiff               
    │                  ...                   
    └── reg00N_S20030105_region_00N_mask.ome.tiff