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brl_MIP_segmentation.m
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function [im3, im2, im1] = brl_MIP_segmentation(imagestack, threshold)
% © 2015 Allen Institute.
% This file is part of smartACT.
% smartACT is free software: you can redistribute it and/or modify it under
% the terms of the GNU General Public License as published by the Free
% Software Foundation, either version 3 of the License, or (at your option)
% any later version. smartACT is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
% You should have received a copy of the GNU General Public License along with smartACT.
% If not, see <http://www.gnu.org/licenses/>.
%
% This package is currently not maintained and no support is implied.
% Questions may be directed to Brian Long
% <[email protected]> with 'smartACT' in the subject line.
%
imagestack = smooth3(double(imagestack),'box', [3 3 1]);
t3 = squeeze(max(imagestack ,[],3));
t2 = squeeze(max(imagestack ,[],2));
t1 = squeeze(max(imagestack ,[],1));
% now segment using the threshold
athresh = threshold*max(imagestack(:));
im3 = bwlabel(t3>athresh);
im2 = bwlabel(t2>athresh);
im1 = bwlabel(t1>athresh);