rpe_morph.m

%--------------------------------------------------------------------------
% im_thin_clean_br
% pre-processing helper function
% (c) 2015-2016 Andrew R. Cohen and Rohini Joshi
%
%   license - for review evaluation only
%       THIS IS UNRELEASED CODE - VIEWING AND DOWNLOAD ONLY BY MANUSCRIPT REVIEWERS
%   the software will be released under the GPL concurrent with publication
%
%       This is the source code for the paper:

%  R. Joshi, M. Winter, J. S. Saini, T. A. Blenkinsop, J. H. Stern, S. Temple and 
%       A. R. Cohen, "Automated measurement of cobblestone morphology for 
%       characterizing Stem cell-Derived Retinal Pigment Epithelial cell cultures".

% EXCEPTION: as described in the paper, the source code for the steerable 
%   wavelet filters must be downloaded separately from http://bigwww.epfl.ch/demo/circular-wavelets. 
%   All use of that component is governed by the license agreement described there.
% 
% Andrew Cohen
% acohen@coe.drexel.edu
% http://bioimage.coe.drexel.ed
%
%--------------------------------------------------------------------------
% img = imread('..\images\ZOI\Category 5\Category 5 ZO-1 20X B.JPG');
function im_thin_clean_br = rpe_morph(img)
level = graythresh(img);
img_bw = im2bw(img, level);
im_skel = bwmorph(img_bw, 'skel', Inf);

im_thin = bwmorph(img_bw, 'thin', Inf);

im_thin_clean = bwmorph(im_thin, 'clean');

im_thin_clean_br = bwmorph(im_thin_clean,'branchpoints');
imr = bwmorph(im_thin_clean,'endpoints');
im_thin_clean_br = im_thin_clean_br | imr;

loc = (bwmorph(im_thin_clean_br, 'thicken',  3));
img_marked(:,:,1) = 127*im_thin_clean + 127*loc;
img_marked(:,:,2) = 127*im_thin_clean + 127*loc;
img_marked(:,:,3) = 127*im_thin_clean;

figure,imshow(img_marked);
imwrite(img_marked, 'PossibleJunctionPoints.tif', 'tif');