cellcoloc.OptionalRegionSegmentationConfig

class cellcoloc.OptionalRegionSegmentationConfig(enabled=False, method='otsu', percentile=98.0, gaussian_sigma=1.0, background_sigma=None, min_object_voxels=10, min_hole_voxels=10, apply_closing=True)[source]

Settings for the optional threshold-based third-channel analysis.

The default pipeline is a two-channel colocalization problem. When enabled is set to True and a third channel is configured, the pipeline additionally segments a thresholded region mask and reports its area and volume fraction inside each ROI.

__init__(enabled=False, method='otsu', percentile=98.0, gaussian_sigma=1.0, background_sigma=None, min_object_voxels=10, min_hole_voxels=10, apply_closing=True)

Methods

__init__([enabled, method, percentile, ...])

Attributes

`enabled`
`method`
`percentile`
`gaussian_sigma`
`background_sigma`
`min_object_voxels`
`min_hole_voxels`
`apply_closing`