cellcoloc.ColocalizationConfig

class cellcoloc.ColocalizationConfig(min_cell_voxels=200, overlap_fraction_threshold=0.02, min_overlap_voxels=20, evaluate_optional_region_cell_positivity=False)[source]

Thresholds controlling how cell-to-marker overlap is interpreted.

min_cell_voxels

Minimum size required for cell labels after segmentation cleanup.

overlap_fraction_threshold

Minimum fraction of the cell mask that must overlap a marker object for the cell to be counted as positive.

min_overlap_voxels

Minimum absolute overlap size required for positivity.

evaluate_optional_region_cell_positivity

When True and an optional third channel has been segmented, the pipeline additionally evaluates which cells overlap that third-channel segmentation. This yields separate optional-region positivity columns as well as a combined marker-and-optional-region double-positive flag.

__init__(min_cell_voxels=200, overlap_fraction_threshold=0.02, min_overlap_voxels=20, evaluate_optional_region_cell_positivity=False)

Methods

__init__([min_cell_voxels,Β ...])

Attributes

min_cell_voxels

overlap_fraction_threshold

min_overlap_voxels

evaluate_optional_region_cell_positivity