Summary¶

Baysor can be used in several ways.

Cell segmentation¶

A minimal command for cell segmentation:

baysor run -m MIN_MOLECULES [-s SCALE -x X_COL -y Y_COL -z Z_COL -g GENE_COL -c config.toml -o OUTPUT_DIR] MOLECULES_FILE [PRIOR_SEGMENTATION]

A full run takes some time, so a quick preview helps to understand the data and to choose the parameters of the full run:

baysor preview -m MIN_MOLECULES [-x X_COL -y Y_COL -g GENE_COL -c config.toml -o OUTPUT_FILE] MOLECULES_FILE

Many analyses don't need a segmentation and can use local neighborhoods instead, the Neighborhood Composition Vectors (NCVs):

baysor segfree -m MIN_MOLECULES [-k K_NEIGHBORS -x X_COL -y Y_COL -g GENE_COL -c config.toml -o OUTPUT_FILE] MOLECULES_FILE

See Segmentation-free analysis and baysor segfree --help.