GUI-Independent segmentation module from EpiTools

this repository contains the segmentation module from EpiTools-Matlab (/src/src_analysis/module_segmentation) with all the GUI dependencies removed.

The main segmentation function can be found in SegmentIm.m which calls the c routines findcellsfromregiongrowing.cc and growcellsfromseeds3.cc for which all the compiled MEX files (win/lin/mac) are included as well.

To know more about the segmentation routine check out our wiki page: epitools.github.io/wiki/Analysis_Modules/03_segmentation/ or the epitools article http://dx.doi.org/10.1016/j.devcel.2015.12.012

example execution

%% load example image (Projected Drosophila Wing Disc - Ecad:GFP)
load('ProjIm.mat')

%% crop image for testing (right click -> "Crop Image")
[crop, rect] = imcrop(ProjIm,[]);
close();

%% compute segmentation and output segmentation feedback
s1=0.5;     % first smoothing (seeding)
minA=2;     % minimum cell area
minI=20;    % minimum membrane intensity
mergeT=0.8; % minimum border intensity ratio for merging cells
s2=0.5;     % second smoothing (segmentation)
maxA=3000;  % maximum cell area
boundT=0.1; % mimimal seed/boundary ratio
verbose=1;  % segmentation feedback plot

[segmentation, seeds, labels] = SegmentIm(crop,s1,minA,minI,mergeT,s2,maxA,boundT,verbose);

Segmentation feedback

with verbose=1 you can obtain a feedback visualization like this