/
MainCC.m
63 lines (57 loc) · 2.49 KB
/
MainCC.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
clear all
[Path] = uigetdir();
%
Dummy = dir([Path,'/*.lsm']); Files = {Dummy.name};
Dummy2 = dir([Path,'/*.oib']); Files2 = {Dummy2.name};
FolderName = strsplit(Path,'/'); FolderName = FolderName{end};
Files = [Files,Files2]
%%
try
ParametersT = readtable([Path,'/',FolderName,'_parameters.txt'],'Delimiter','\t');
ValuesT = readtable([Path,'/',FolderName,'_values.txt'], 'Delimiter','\t')
catch
ValuesT = table(); ParametersT = table();
end
for i = 1:length(Files)
reader = bfGetReader([Path,'/',Files{i}]);
[~,Width,Height, Channels, Slices, Frames, ~, XRes, YRes, ZRes,Zoom,~,~] = readMetadataBFOME(reader);
VoxelSize = XRes*YRes*ZRes; %size in um^3
Stack = bfopen([Path,'/',Files{i}]);
Ch1 = Stack{1}(1:Channels:Channels*Slices); Ch1 = double(cat(3,Ch1{:}));
Ch2 = Stack{1}(2:Channels:Channels*Slices); Ch2 = double(cat(3,Ch2{:}));
try
Ch3 = Stack{1}(3:Channels:Channels*Slices); Ch3 = double(cat(3,Ch3{:}));
Im = cat(4,Ch1,Ch2,Ch3);
% Dimension order is XYZC !!
catch
Ch3 = zeros(size(Ch2));
Im = cat(4,Ch1,Ch2,Ch3);
end
try
Parameters = ParametersT(i,:);
catch
%Parameters = table('VariableNames',{'minZ','maxZ','ThresLevel','WatershedParameter','Remove','ST','FT'});
Parameters = table();
end
% default parameters to override
%Parameters.minZ = 1;
%Parameters.maxZ = Slices;
%Parameters.ThresLevel = 0.2;
%Parameters.WatershedParameter = 0.5;
%Parameters.Remove = 50;
%Parameters.ST = 4.5;
%Parameters.FT = 1000;
[RProps, Parameters] = CellCounterCC(Im, Channels, Slices,VoxelSize,Parameters);
writetable(RProps,[Path,'/',Files{i},'_RProps.txt'], 'Delimiter','\t')
Values = table();
Values.File = {Files{i}};
Values.SmallHigh = length(find(log(RProps.Area) < Parameters.ST & RProps.MeanIntensity > Parameters.FT)) ;
Values.SmallLow = length(find(log(RProps.Area) < Parameters.ST & RProps.MeanIntensity < Parameters.FT)) ;
Values.BigHigh = length(find(log(RProps.Area) > Parameters.ST & RProps.MeanIntensity > Parameters.FT)) ;
Values.BigLow = length(find(log(RProps.Area) > Parameters.ST & RProps.MeanIntensity < Parameters.FT)) ;
Parameters.File = {Files{i}};
ValuesT(i,:) = Values;
ParametersT(i,:) = Parameters;
end
writetable(ValuesT,[Path,'/',FolderName,'_values.txt'], 'Delimiter','\t')
writetable(ParametersT,[Path,'/',FolderName,'_parameters.txt'],'Delimiter','\t')