intRemoveFalseMicroCol

 intRemoveFalseMicroCol : used to remove regions that are not cells.
 It removes anything with outline intensity below the background
 intensity.

 INPUT :
   mask_bg : background mask of cells
   phase : phase image
   CONST : segmentation parameters
 OUTPUT :
   mask_bg_mod : modified mask with removed regions

 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 [ mask_bg_mod ] = intRemoveFalseMicroCol( mask_bg, phase, CONST )
0002 % intRemoveFalseMicroCol : used to remove regions that are not cells.
0003 % It removes anything with outline intensity below the background
0004 % intensity.
0005 %
0006 % INPUT :
0007 %   mask_bg : background mask of cells
0008 %   phase : phase image
0009 %   CONST : segmentation parameters
0010 % OUTPUT :
0011 %   mask_bg_mod : modified mask with removed regions
0012 %
0013 % Copyright (C) 2016 Wiggins Lab
0014 % Written by Paul Wiggins.
0015 % University of Washington, 2016
0016 % This file is part of SuperSegger.
0017 %
0018 % SuperSegger is free software: you can redistribute it and/or modify
0019 % it under the terms of the GNU General Public License as published by
0020 % the Free Software Foundation, either version 3 of the License, or
0021 % (at your option) any later version.
0022 %
0023 % SuperSegger is distributed in the hope that it will be useful,
0024 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0025 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0026 % GNU General Public License for more details.
0027 %
0028 % You should have received a copy of the GNU General Public License
0029 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0030 
0031 % inner outline of the mask
0032 mask_bg = logical(mask_bg);
0033 mask_er = bwmorph(mask_bg, 'erode',1 ) - bwmorph(mask_bg, 'erode',2);
0034 
0035 label_bg = bwlabel(mask_bg);
0036 mask_er = logical(mask_er);
0037 label_er = label_bg;
0038 label_er(~mask_er) = 0;
0039 
0040 % remove labels outline that are not in background mask
0041 ind_bg = unique(label_bg(:));
0042 ind_er = unique(label_er(:));
0043 kill_l = ind_bg(~ismember(ind_bg, ind_er));
0044 
0045 % mean intensity of outlines
0046 props = regionprops(label_er, double(phase), 'MeanIntensity');
0047 vals = [props.MeanIntensity];
0048 
0049 % mean intesnity of cell and non cell regions
0050 mean_noncell = mean(phase(~mask_bg));
0051 mean_cell    = mean(phase(mask_bg));
0052 dI = mean_noncell-mean_cell;
0053 
0054 % indices of regions to be removed
0055 ind = find(vals > mean_noncell-dI*CONST.superSeggerOpti.dIcellNonCell);
0056 kill_list = [kill_l',ind];
0057 
0058 mask_kill = ismember(label_bg, kill_list);
0059 mask_bg_mod = mask_bg;
0060 mask_bg_mod(mask_kill) = 0;
0061 
0062 
0063 
0064 end
0065