This project contains the functions used for cell segmentation. In general, functions are quite general (smoothing, morphological transformations, analysis of binary masks and local thresholds). Some of them are optimized for specific ways in which the data was gathered or was going to be analyzed. They normally need bfmatlab on path to work.
Because this method relies heavily on thresholding and binary image operations, a good SNR is vital.
This folder also contains useful functions:
- Match sets of XY coordinate points. Check the
hungarianlinker.mfunction andalign_manual_automatic_counts.mfor a practical example. - Median filter with plotting options (
my_medfilt2.m) - A very rudimentary function to split RGB channels (
split_RGB.m)
The function channel_segment.m implements a general pipeline for segmentation of an image in one channel.
These functions are tunned for DAPI in blue channel (discards everything else).