Segment Module

This module performs organoid segmentation

These include the following subcommands:

• downsample : reduce image size for segmentaion

• stack : stack a folder of images into a single image

• ventricle : segment ventricles from downsampled nuclei image

• foreground : segment organoid foreground

• smooth : smooth a segmentation

scout.segment.downsample(arr, factors)

Downsample image arr by factors in each dimension

Parameters

• arr (Zarr Array) –

• factors (tuple) –

Returns

output

Return type

ndarray