added a specific script for leona and fixed the "shift" problems

functions/CellSortLoadTrialsShiftCorrOnTrials.m

@@ -28,8 +28,8 @@
     shiftVector = findshift(reference, medianProj, 'iter');
     %shift frames
     for f = 1:size(data_r{i},3)
-        data_r{i}(:,:,f)  = shift(data_r{i}(:,:,f),shiftVector);
-        data_g{i}(:,:,f)  = shift(data_g{i}(:,:,f),shiftVector);
+        data_r{i}(:,:,f)  = imtranslate(data_r{i}(:,:,f),shiftVector', 'linear');
+        data_g{i}(:,:,f)  = imtranslate(data_g{i}(:,:,f),shiftVector', 'linear');
     end
 end
 %put them in single arrays

functions/CellSortShiftCorrection.m

@@ -7,8 +7,8 @@
 parfor r = 1:size(data_g, 3)
 %     waitbar(r/size(data_g, 3), wb,[num2str(r) ' of ' num2str(size(data_g, 3))]);
     shiftVector = findshift(referenceFrame, data_r(:,:,r), mode);
-    data_r(:,:,r)  = shift(data_r(:,:,r),shiftVector);
-    data_g(:,:,r)  = shift(data_g(:,:,r),shiftVector);
+    data_r(:,:,r)  = imtranslate(data_r(:,:,r),shiftVector', 'linear');
+    data_g(:,:,r)  = imtranslate(data_g(:,:,r),shiftVector', 'linear');
 end
 disp('Finished Shift Correction!');
 % close(wb);

functions/trialAlignmentScript_Leona.m

@@ -2,7 +2,7 @@
 close all
 clc
 %% Load Trial Files
-inFolder = 'D:\data\session_1';
+inFolder = 'D:\data\Leona';
 outFolder = 'D:\data\out';
 binningFactor = [1, 1, 2];
 nSubIm = 10;
@@ -67,11 +67,7 @@
         data_r(:,:,i) = circshift(data_r(:,:,i),[rs(i),cs(i)]);
         data_g(:,:,i) = circshift(data_g(:,:,i),[rs(i),cs(i)]);
     end
-
-    %binning
-    data_r = uint16(binning(data_r, binningFactor, 'mean'));
-    data_g = uint16(binning(data_g, binningFactor, 'mean'));
-
+
     %save stacks in memory
     cd(outFolder);
     disp(['Write Files Of Folder ', folders(f).name ' in ' outFolder ' to RAM']);
@@ -98,17 +94,59 @@
     shiftVector = findshift(reference, medianProj, 'iter');
     %shift frames
     for f = 1:size(data_r{i},3)
-        data_r{i}(:,:,f)  = shift(data_r{i}(:,:,f),shiftVector);
-        data_g{i}(:,:,f)  = shift(data_g{i}(:,:,f),shiftVector);
+        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_r{j}, nSubIm, 50, -inf);
+    temp_r = data_r{j};
+    temp_g = data_g{j};
+    %shift red and green channel
+    parfor f = 1:size(data_r{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_r{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_r{j}(:,:,f), 'iter');
+    %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_r{1},3);
+numberGreen = size(data_g,2);
+for i = 1:numberGreen
+    disp(['Working on Trial ' num2str(i)]);
+    medianProj = median(data_r{i},3);
+    shiftVector = findshift(reference, medianProj, 'iter');
+    %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
+parfor i=1:numberGreen    
+    %binning
+    data_r{i} = uint16(binning(data_r{i}, binningFactor, 'mean'));
+    data_g{i} = uint16(binning(data_g{i}, binningFactor, 'mean'));
 
-%save tiff files
-for i=1:numberGreen
     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;
@@ -143,5 +181,11 @@
 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 all
 disp('Finished Complete Script!!!');

main.m

@@ -30,6 +30,10 @@
 
 data_g = data_g(xInterval,yInterval,:);
 data_r = data_r(xInterval,yInterval,:);
+%% bin data again
+secondBinningFactor = [1,1,1];
+data_g = binning(data_g, secondBinningFactor, 'mean');
+data_r = binning(data_r, secondBinningFactor, 'mean');
 %% 1. PCA
 %calculate PCAs
 nPCs = 100;