-
Notifications
You must be signed in to change notification settings - Fork 9
/
maxProj.m
81 lines (71 loc) · 3.96 KB
/
maxProj.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
function maxProj
%Point to a folder to do maximum intensity projections of the images.
% Copyright (C) 2013-2014 University of Dundee & Open Microscopy Environment.
% All rights reserved.
%
% This program 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 2 of the License, or
% (at your option) any later version.
%
% This program 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 this program; if not, write to the Free Software Foundation, Inc.,
% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
tic;
datadir = uigetdir;
cd(datadir);
mkdir projections
%filelist = dir;
platerow = ['A'; 'B'; 'C'; 'D'; 'E'; 'F'; 'G'; 'H'; 'I'; 'J'; 'K'; 'L'; 'M'; 'N'; 'O'; 'P'];
platerow = cellstr(platerow);
platecol = strvcat('1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', '24');
platecol = cellstr(platecol);
field = ['fld 01 '; 'fld 02 '; 'fld 03 '; 'fld 04 '; 'fld 05 '; 'fld 06 '; 'fld 07 '; 'fld 08 '; 'fld 09 '; 'fld 10 '; 'fld 11 '; 'fld 12 '; 'fld 13 '; 'fld 14 '; 'fld 15 '; 'fld 16 '; 'fld 17 '; 'fld 18 '; 'fld 19 '; 'fld 20 '];
field = cellstr(field);
wave = strvcat('wv D360_40x - HQ460_40M ', 'wv HQ480_40x - HQ535_50M ', 'wv HQ565_30x - HQ620_60M ', 'wv HQ620_60x - HQ700_75M ');
wave = cellstr(wave);
zSection = ['z 1).tif'; 'z 2).tif'; 'z 3).tif'; 'z 4).tif'];
zSection = cellstr(zSection);
for currRow = 1:16
for currCol = 1:24
for currField = 1:10
for currWave = 1:4
imgProjection = zeros(520,696);
filename1 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' wave{currWave} ' ' zSection{1}];
filename2 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' wave{currWave} ' ' zSection{2}];
filename3 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' wave{currWave} ' ' zSection{3}];
filename4 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' wave{currWave} ' ' zSection{4}];
% filename1 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' zSection{1}];
% filename2 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' zSection{2}];
% filename3 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' zSection{3}];
% filename4 = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' zSection{4}];
%
try
pixfile1 = uint16(imread(filename1));
pixfile2 = uint16(imread(filename2));
pixfile3 = uint16(imread(filename3));
pixfile4 = uint16(imread(filename4));
catch
continue;
end
for i = 1:520
for j = 1:696
comparevector = [pixfile1(i,j) pixfile2(i,j) pixfile3(i,j) pixfile4(i,j)];
imgProjection(i,j) = max(max(comparevector));
end
end
filenameout = ['projections/' platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' ' wave{currWave} ' Proj).tif'];
%filenameout = [platerow{currRow} ' - ' platecol{currCol} '(' field{currField} ' Proj).tif']
imgProjection = uint16(imgProjection);
imwrite(imgProjection, filenameout, 'tif');
end
end
end
currRow
end
toc;