aicsimageprocessing.segmentation package¶

Submodules¶

aicsimageprocessing.segmentation.nucleusSegmentation.fill_nucleus_segmentation(cell_index_img, nuc_original_img)[source]¶

This function is built to fill in the holes of the nucleus segmentation channel

Parameters

cell_index_img – A ZYX ndarray - represents the segmented image of all cell bodies
nuc_original_img – A ZYX ndarray - represents the original image of the nuclei channel

Returns

Return type

A ZYX ndarray - represents a corrected segmented image of the nuclei

aicsimageprocessing.segmentation.nucleusSegmentation.keep_connected_components(image, low_threshold, high_threshold=None)[source]¶

This will keep components that have a larger volume than low_threshold and a smaller volume than high_threshold

Parameters

image – An n-dimensional array of booleans
low_threshold – If any component is smaller than this value, it will be removed
high_threshold – If any component is bigger than this value, it will be removed

Returns

Return type

n-dimensional boolean array with same size as image