cellcoloc.ChannelConfig

class cellcoloc.ChannelConfig(cell_channel, marker_channel, optional_region_channel=None)[source]

Describe which channels should be used for the analysis.

cell_channel

Zero-based channel index containing the larger cellular compartment that should be segmented with Cellpose, for example cytoskeleton or soma.

marker_channel

Zero-based channel index containing the marker-positive structure that determines the colocalization class, for example nuclei or DAPI.

optional_region_channel

Optional zero-based channel index for a third channel that is thresholded to estimate a region coverage metric, for example tumor infiltration. Set to None to disable the optional third-channel analysis entirely.

__init__(cell_channel, marker_channel, optional_region_channel=None)

Methods

__init__(cell_channel,Β marker_channel[,Β ...])

Attributes

cell_channel

marker_channel

optional_region_channel