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MPIBR-vollrathf committed Oct 7, 2016
1 parent 4bdc37f commit 3785948
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Showing 2 changed files with 6 additions and 8 deletions.
8 changes: 3 additions & 5 deletions functions/CellSortLoadTrialsShiftCorrOnTrials.m
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Expand Up @@ -18,18 +18,17 @@
data_r{i} = readTiff(redFiles(i).name);
data_g{i} = readTiff(greenFiles(i).name);
end
disp('Finished Loading Trial Files..');

%do shift correction
disp('Finished Performing Shift Correction On All Trials..');
disp('Performing Shift Correction On All Trials..');
reference = median(data_r{1},3);
for i = 1:numberGreen
medianProj = median(data_r{i},3);
shiftVector = findshift(reference, medianProj, 'iter');
%shift frames
for f = 1:size(data_r{i},3)
data_r{i}(:,:,r) = shift(data_r{i}(:,:,r),shiftVector);
data_g{i}(:,:,r) = shift(data_g{i}(:,:,r),shiftVector);
data_r{i}(:,:,i) = shift(data_r{i}(:,:,i),shiftVector);
data_g{i}(:,:,i) = shift(data_g{i}(:,:,i),shiftVector);
end
end
%put them in single arrays
Expand All @@ -50,7 +49,6 @@
data_g_array(:,:,(numFrameList(i)+1):numFrameList(i+1)) = data_g{i};
data_g{i} = [];
end
disp('Finished Creating Big Data Set');

disp('Finished Loading Trial Files!');
end
6 changes: 3 additions & 3 deletions main.m
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Expand Up @@ -4,14 +4,14 @@
%also choose a binning factor [x, y, t]. nSubIm ist the number of
%iterations the shift correction will do. The more the better, but of
%course it is more time consuming. The standard value here is 10.
inFolder = 'D:\data\rawDataICAPCA';
outFolder = 'D:\data\corr';
inFolder = 'F:\Arbeit\testData\PCAICA';
outFolder = 'F:\Arbeit\testData\PCAICA\corr';
binningFactor = [1, 1, 2];
nSubIm = 10;
CellSortXCorr(inFolder, outFolder, nSubIm, binningFactor);
%% load files
%go to corr folder
outFolder = 'X:\Projects\ICA_PCA\data_dendrites\51EA\day_1';
outFolder = 'F:\Arbeit\testData\PCAICA';
%[data_g, data_r, frames, fn_green, fn_red, fileNamesGreen, fileNamesRed] = CellSortLoadTrials(outFolder);
[data_g, data_r, frames, fn_green, fn_red, fileNamesGreen, fileNamesRed] = CellSortLoadTrialsShiftCorrOnTrials(outFolder);
%If you want to load single files, use the functions below.
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