This repository has been archived by the owner. It is now read-only.
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Browse files
Browse the repository at this point in the history
add loading data from new microscope directory structure
- Loading branch information
1 parent
f16fcdd
commit 5ef8eca
Showing
3 changed files
with
344 additions
and
48 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,190 @@ | ||
| % trialAlignmentScript_newMicroscope | ||
| clc; | ||
| close all; | ||
| clear variables; | ||
| warning('off','all'); | ||
|
|
||
| %% user input | ||
| pathInput = '/Users/tushevg/Desktop/new_2P_test/TSeries-06072017-1138-048'; | ||
|
|
||
| numberOfShiftCorrections = 4; | ||
| binningFactor = [1, 1, 2]; | ||
| nSubIm = 2; | ||
|
|
||
| labelTrial = 'Cycle'; | ||
| labelChannel = 'Ch'; | ||
|
|
||
| indexRed = 1; | ||
| indexGreen = 2; | ||
|
|
||
| %% explore parent directory | ||
| dirInfo = dir([pathInput, filesep, '*.tif']); | ||
| fileNames = {dirInfo.name}'; | ||
|
|
||
| %% extract lists of trial/channel names | ||
| trialNames = regexp(fileNames, [labelTrial,'[0-9]+'], 'once', 'match'); | ||
| [trialUnqNames,~,indexTrial] = unique(trialNames); | ||
| trialCount = max(indexTrial); | ||
|
|
||
| channelNames = regexp(fileNames, [labelChannel,'([12]|[AB])'], 'once', 'match'); | ||
| [~, ~, indexChannel] = unique(channelNames); | ||
|
|
||
| %% allocate containers | ||
| data_r = repmat({}, trialCount, 1); | ||
| data_g = repmat({}, trialCount, 1); | ||
|
|
||
| %% read all frames and trials | ||
| for t = 1 : trialCount | ||
|
|
||
| %%% processing trial | ||
| fprintf('### processing trial %s\n', trialUnqNames{t}); | ||
|
|
||
| %%% current trial and channels per trial | ||
| idx_trial = (indexTrial == t); | ||
| idx_red = idx_trial & (indexChannel == indexRed); | ||
| idx_green = idx_trial & (indexChannel == indexGreen); | ||
|
|
||
| %%% full file lists | ||
| list_red = strcat(pathInput, filesep, fileNames(idx_red)); | ||
| list_green = strcat(pathInput, filesep, fileNames(idx_green)); | ||
|
|
||
| %%% allocate image stack | ||
| imgInfo = imfinfo(list_red{1}); | ||
| imgStack = min([length(list_red),length(list_green)]); | ||
| imgRed = zeros(imgInfo.Height,... | ||
| imgInfo.Width,... | ||
| imgStack,... | ||
| sprintf('uint%d',imgInfo.BitDepth)); | ||
| imgGreen = zeros(imgInfo.Height,... | ||
| imgInfo.Width,... | ||
| imgStack,... | ||
| sprintf('uint%d',imgInfo.BitDepth)); | ||
|
|
||
| %%% read images | ||
| fprintf('# read image stacks %d ... ', imgStack); | ||
| tic | ||
| for s = 1 : imgStack | ||
| imgRed(:, :, s) = readTiffNoStack(list_red{s}); | ||
| imgGreen(:, :, s) = readTiffNoStack(list_green{s}); | ||
| end | ||
| fprintf('done. %.4f sec\n', toc); | ||
|
|
||
| %%% fill containers | ||
| data_r(t) = {imgRed}; | ||
| data_g(t) = {imgGreen}; | ||
|
|
||
| end | ||
|
|
||
| %% ------------------------- %% | ||
| %% --- SHIFT CORRECTIONS --- %% | ||
| %% ------------------------- %% | ||
|
|
||
| %% shift correct trials to each other | ||
| %do shift correction | ||
| disp('Performing Shift Correction On All Trials..'); | ||
| reference = median(data_g{1},3); | ||
| numberGreen = size(data_g,2); | ||
| for i = 1:numberGreen | ||
| disp(['Working on Trial ' num2str(i)]); | ||
| medianProj = median(data_g{i},3); | ||
| shiftVector = findshift(reference, medianProj, 'iter', 0, 0.25*size(reference,1)); | ||
| %shift frames | ||
| for f = 1:size(data_r{i},3) | ||
| data_r{i}(:,:,f) = imtranslate(data_r{i}(:,:,f),shiftVector', 'linear'); | ||
| data_g{i}(:,:,f) = imtranslate(data_g{i}(:,:,f),shiftVector', 'linear'); | ||
| end | ||
| end | ||
| %% do another med align | ||
| for j =1:numberGreen | ||
| disp(['Working on Trial ' num2str(j)]); | ||
| [rs, cs] = medAlign(data_g{j}, nSubIm, 50, -inf); | ||
| temp_r = data_r{j}; | ||
| temp_g = data_g{j}; | ||
| %shift red and green channel | ||
| parfor f = 1:size(data_g{j},3) | ||
| temp_r(:,:,f) = circshift(temp_r(:,:,f),[rs(f),cs(f)]); | ||
| temp_g(:,:,f) = circshift(temp_g(:,:,f),[rs(f),cs(f)]); | ||
| end | ||
| data_r{j} = temp_r; | ||
| data_g{j} = temp_g; | ||
| end | ||
| %% do another shift correction for every frame, takes some time | ||
| reference = median(data_g{1},3); | ||
| numberGreen = size(data_g,2); | ||
| for i = 1:numberGreen | ||
| disp(['Working on Trial ' num2str(i)]); | ||
| for f = 1:size(data_r{i},3) | ||
| shiftVector = findshift(reference, data_g{j}(:,:,f), 'iter',0, 0.25*size(reference,1)); | ||
| %shift frames | ||
|
|
||
| data_r{i}(:,:,f) = imtranslate(data_r{i}(:,:,f),shiftVector', 'linear'); | ||
| data_g{i}(:,:,f) = imtranslate(data_g{i}(:,:,f),shiftVector', 'linear'); | ||
| end | ||
| end | ||
| %% do another shift correctionto align trials to each other | ||
| reference = median(data_g{1},3); | ||
| numberGreen = size(data_g,2); | ||
| for i = 1:numberGreen | ||
| disp(['Working on Trial ' num2str(i)]); | ||
| medianProj = median(data_g{i},3); | ||
| shiftVector = findshift(reference, medianProj, 'iter',0, 0.25*size(reference,1)); | ||
| %shift frames | ||
| for f = 1:size(data_r{i},3) | ||
| data_r{i}(:,:,f) = imtranslate(data_r{i}(:,:,f),shiftVector', 'linear'); | ||
| data_g{i}(:,:,f) = imtranslate(data_g{i}(:,:,f),shiftVector', 'linear'); | ||
| end | ||
| end | ||
| %% save tiff files | ||
| for i=1:numberGreen | ||
| %binning | ||
| data_r{i} = uint16(binning(data_r{i}, binningFactor, 'mean')); | ||
| data_g{i} = uint16(binning(data_g{i}, binningFactor, 'mean')); | ||
|
|
||
| saveastiff(data_r{i}, [outFolder filesep folders(i).name '_r.tif']); | ||
| saveastiff(data_g{i}, [outFolder filesep folders(i).name '_g.tif']); | ||
| end | ||
| %% generate quality plot | ||
| %put them in single arrays | ||
| numFrames = 0; | ||
| numFrameList = zeros(1,numberGreen); | ||
| for i = 1:numberGreen | ||
| numFrames = numFrames + size(data_g{i},3); | ||
| numFrameList(i+1) = numFrames; | ||
| end | ||
|
|
||
| %preallocate data | ||
| data_r_array = zeros(size(data_g{i},1),size(data_g{i},2),numFrames, class(data_r{1})); | ||
| data_g_array = zeros(size(data_g{i},1),size(data_g{i},2),numFrames, class(data_g{1})); | ||
| disp('Creating Big Data Set..'); | ||
| for i = 1:numberGreen | ||
| data_r_array(:,:,(numFrameList(i)+1):numFrameList(i+1)) = data_r{i}; | ||
| data_r{i} = []; | ||
| data_g_array(:,:,(numFrameList(i)+1):numFrameList(i+1)) = data_g{i}; | ||
| data_g{i} = []; | ||
| end | ||
|
|
||
| %calculate quality plot | ||
| reference = mean(data_r_array, 3); | ||
| qualityPlot = zeros(1,size(data_r_array, 3)); | ||
| for i = 1:size(data_r_array,3) | ||
| qualityPlot(i) = sqrt(squeeze(mean(mean((cast(data_r_array(:,:,i),'like', reference) - reference).^2,1),2))); | ||
| end | ||
| figure('Name','Quality Plot'); | ||
| plot(qualityPlot); | ||
| for i=1:numberGreen | ||
| vline(numFrameList(i), 'black', greenFiles(i).name); | ||
| end | ||
| title('Quality Of Shift Correction'); | ||
| xlabel('frame'); | ||
| ylabel('std of frame'); | ||
| %% export complete files | ||
| disp('Saving Big Data Set..'); | ||
| options.big = true; | ||
| saveastiff(data_r_array, [outFolder filesep folders(i).name '_complete_r.tif'], options); | ||
| saveastiff(data_g_array, [outFolder filesep folders(i).name '_complete_g.tif'], options); | ||
|
|
||
| %% Finished | ||
| clear variables | ||
| disp('Finished Complete Script!!!'); | ||
|
|
||
|
|
Oops, something went wrong.