README.md

Segmentation wrappers around cellpose and deepcell

Command line argument

--method segmentation method cellpose or deepcell
--dataset_dir path to directory with images
--gpus comma separated ids of gpus to use, e.g. "0,1,2", default "all"

Usage

python main.py --dataset_dir /path/to/dataset/ --method deepcell (or cellpose) --gpus "0,1"

Expected dataset_dir structure:

dataset_dir
|-- data_dir1
|    |-- prefix1_nucleus.tif
|    `-- prefix1_cell.tif
|
|-- data_dir2
|    |-- prefix2_nucleus.tif  
|    `-- prefix2_cell.tif
|
...
| 
`-- data_dirN
     |-- prefixN_nucleus.tif  
     `-- prefixN_cell.tif      

Output structure

dataset_dir
|-- data_dir1
|    `-- prefix1_mask.ome.tiff
|    
|-- data_dir2
|    `-- prefix2_mask.ome.tiff 
|    
...
| 
`-- data_dirN
     `-- prefixN_mask.ome.tiff