Scripts

Fishtank provides a number command line scripts to help with common tasks. These scripts are installed when you install fishtank. You can see the list of available scripts by running fishtank --help.

scripts.align_experiments(ref, moving, ...)	Align experiments using optical flow.
scripts.aggregate_polygons(input[, output, ...])	Aggregate polygons from multiple FOVs.
scripts.assign_proseg(transcripts, ...[, ...])	Assign additional transcripts to cells using ProSeg.
scripts.assign_spots(input[, polygons, ...])	Assign spots to the nearest polygon.
scripts.cellpose(input, fov, channels[, ...])	Segment cells using Cellpose.
scripts.decode_spots(input[, strategy, ...])	Decode spots using specified strategy.
scripts.detect_spots(input, fov, ref_series, ...)	Detect spots in an image and quantify their intensity.
scripts.fovs(input[, file_pattern])	List fields of view in an input directory.