makeColonyDist : returns the distance mask for the colony It dilates, the image, fills the holes, and then returns for each pixel the distance from the nearest non zero pixel. INPUT : mask : image of mask of cells OUTPUT : dist_mask : distance between that pixel and nearest non zero pixel. Copyright (C) 2016 Wiggins Lab Written by Paul Wiggins. University of Washington, 2016 This file is part of SuperSegger. SuperSegger 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. SuperSegger 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 SuperSegger. If not, see <http://www.gnu.org/licenses/>.
0001 function dist_mask = makeColonyDist(mask) 0002 % makeColonyDist : returns the distance mask for the colony 0003 % It dilates, the image, fills the holes, and then returns for each pixel 0004 % the distance from the nearest non zero pixel. 0005 % 0006 % INPUT : 0007 % mask : image of mask of cells 0008 % OUTPUT : 0009 % dist_mask : distance between that pixel and nearest non zero pixel. 0010 % 0011 % Copyright (C) 2016 Wiggins Lab 0012 % Written by Paul Wiggins. 0013 % University of Washington, 2016 0014 % This file is part of SuperSegger. 0015 % 0016 % SuperSegger is free software: you can redistribute it and/or modify 0017 % it under the terms of the GNU General Public License as published by 0018 % the Free Software Foundation, either version 3 of the License, or 0019 % (at your option) any later version. 0020 % 0021 % SuperSegger is distributed in the hope that it will be useful, 0022 % but WITHOUT ANY WARRANTY; without even the implied warranty of 0023 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 0024 % GNU General Public License for more details. 0025 % 0026 % You should have received a copy of the GNU General Public License 0027 % along with SuperSegger. If not, see <http://www.gnu.org/licenses/>. 0028 0029 0030 dist_mask = imdilate(mask, strel('disk',5)); % dilates image 0031 dist_mask = imfill( dist_mask, 'holes' ); % fills holes 0032 dist_mask = ~imerode(dist_mask, strel('disk',5)); % opposite of erode 0033 dist_mask = bwdist(dist_mask); % distance to nearest non-zero pixel 0034 0035 %imshow( dist_mask, [] ); 0036 0037 0038 end 0039