Prepares data and does 2D segmentation of CellDIVE images slice by slice using deepcell method.
cwltool pipeline.cwl subm.yaml
Requires meta.yaml with names of channels
that will be used for segmentation of cell and nucleus compartments.
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
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