modules.md

CellBin allows software flexibility to support individual single-step module operations. The corresponding execution is placed in directory scripts.

Image quality control

python qc.py
--tiles_path /data/SS200000135TL_D1
--chip_no SS200000135TL_D1

• --tiles_path The path of all tiles.
• --chip_no The chip number of the Stereo-seq data.

Stitching

python stitching.py
--tiles_path /data/SS200000135TL_D1
--output_file /result/stitched_image.tif

• --tiles_path The path of all tiles.
• --output_file The output path of the stitched image file.

Registration

python registration.py
--image_file /result/stitched_image.tif
--output_file /result/registered_image.tif
--gene_exp_data /data/SS200000135TL_D1.gem.gz
--chip_no SS200000135TL_D1

• --image_file The stitched image.
• --output_file The registered image.
• --gene_exp_data The compressed file of spatial gene expression data.
• --chip_no The chip number of the Stereo-seq data.

Tissue segmentation

python segmentation.py
--type tissue
--image_file /result/registered_image.tif
--output_file /result/tissue_mask.tif

• --type Can be tissue or nuclei.
• --image_file The registered image.
• --output_file The tissue mask image.

Nuclei segmentation

python segmentation.py
--type nuclei
--image_file /result/registered_image.tif
--output_file /result/nuclei_mask.tif

• --type Can be tissue or nuclei.
• --image_file The registered image.
• --output_file The nuclei mask image.

Nuclei mask filtering

python filtering.py
--tissue_mask /result/tissue_mask.tif
--nuclei_mask /result/nuclei_mask.tif
--output_file /result/nuclei_mask.tif

• --tissue_mask The tissue mask image.
• --nuclei_mask The nuclei mask image.
• --output_file The filtered nuclei mask image.

Molecule labeling

python labeling.py
--image_file /result/nuclei_mask.tif
--gene_exp_data /data/SS200000135TL_D1.gem.gz
--output_path /result

• --image_file The nuclei mask image.
• --gene_exp_data The compressed file of spatial gene expression data.
• --output_path The output path.