diff --git a/functions/trialAlignmentScript_Belen.m b/functions/trialAlignmentScript_Belen.m
index 1bf96fe..86e9443 100644
--- a/functions/trialAlignmentScript_Belen.m
+++ b/functions/trialAlignmentScript_Belen.m
@@ -88,59 +88,59 @@
 %%shift correct trials to each other
 %do shift correction
 for shiftCorrectionCounter = 1:numberShiftCorrections
-disp('Performing Shift Correction On All Trials..');
-reference = median(data_r{1},3);
-for i = 1:numberGreen
-    disp(['Working on Trial ' num2str(i)]);
-    medianProj = median(data_r{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');
+    disp('Performing Shift Correction On All Trials..');
+    reference = median(data_r{1},3);
+    for i = 1:numberGreen
+        disp(['Working on Trial ' num2str(i)]);
+        medianProj = median(data_r{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
-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)]);
+    %%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
-    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',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');
+    %%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',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
-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',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');
+    %%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',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
 end
-end
 %%visualize data
 numFrames = 0;
 numFrameList = zeros(1,numberGreen);
diff --git a/functions/trialAlignmentScript_newMicroscope.m b/functions/trialAlignmentScript_newMicroscope.m
new file mode 100644
index 0000000..62a7566
--- /dev/null
+++ b/functions/trialAlignmentScript_newMicroscope.m
@@ -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!!!');
+
+
diff --git a/functions/trialAlignmentScript_test.m b/functions/trialAlignmentScript_test.m
new file mode 100644
index 0000000..5930bfb
--- /dev/null
+++ b/functions/trialAlignmentScript_test.m
@@ -0,0 +1,106 @@
+% trialAlignmentScript_test
+clc;
+close all;
+%
+clear variables;
+
+%% user input
+%pathInput = '/Users/tushevg/Desktop/new_2P_test/TSeries-06072017-1138-048';
+%pathInput = '/Users/tushevg/Desktop/002';
+pathInput = '/Users/tushevg/Desktop/new_2P_test';
+pathOutput = '/Users/tushevg/Desktop/testout';
+
+numberOfShiftCorrections = 4;
+binningFactor = [1, 1, 2];
+nSubIm = 2;
+
+labelTrial = 'Cycle';
+labelChannel = 'Ch';
+
+indexRed = 1;
+indexGreen = 2;
+
+
+%% explore parent directory
+dirInfo = dir(pathInput);
+subDirs = {dirInfo.name}';
+subDirs(strncmp('.',subDirs,1) | ~[dirInfo.isdir]') = [];
+subDirsCount = length(subDirs);
+
+%% explore child direcotries
+d = 1;
+%for d = 1 : subDirsCount
+    
+    %%% extract files from sub directory
+    subDirInfo = dir([pathInput, filesep, subDirs{d}, filesep, '*.tif']);
+    fileNames = {subDirInfo.name}';
+    
+    %%% extract lists of trial/channel names
+    trialNames = regexp(fileNames, [labelTrial,'[0-9]+'], 'once', 'match');
+    [trialUnqNames,~,idxunq_trials] = unique(trialNames);
+    trialCount = max(idxunq_trials);
+    
+    channelNames = regexp(fileNames, [labelChannel,'([12]|[AB])'], 'once', 'match');
+    [~, ~, idxunq_channels] = unique(channelNames);
+    
+    %%% allocate images
+    imgInfo = imfinfo([pathInput, filesep, subDirs{d}, filesep, fileNames{1}]);
+    imgStack = sum((idxunq_trials == 1) & (idxunq_channels == indexRed));
+    imgRed = zeros(imgInfo.Height,...
+                   imgInfo.Width,...
+                   imgStack,...
+                   trialCount,...
+                   sprintf('uint%d',imgInfo.BitDepth));
+    imgGreen = zeros(imgInfo.Height,...
+                   imgInfo.Width,...
+                   imgStack,...
+                   trialCount,...
+                   sprintf('uint%d',imgInfo.BitDepth));
+    
+    
+    %% process trials
+    t = 1;
+    %for t = 1 : trialCount
+        
+        %%% processing trial
+        fprintf('### processing trial %s\n', trialUnqNames{t});
+
+        %%% current trial and channels per trial
+        idx_trial = (idxunq_trials == t);
+        idx_red = idx_trial & (idxunq_channels == indexRed);
+        idx_green = idx_trial & (idxunq_channels == indexGreen);
+        
+        %%% full file lists
+        list_red = strcat(pathInput, filesep, subDirs{d}, filesep, fileNames(idx_red));
+        list_green = strcat(pathInput, filesep, subDirs{d}, filesep, fileNames(idx_green));
+        
+        %%% read images
+        fprintf('# read image stacks %d ... ', imgStack);
+        tic
+        for s = 1 : imgStack
+            imgRed(:, :, s, t) = imread(list_red{s});
+            imgGreen(:, :, s, t) = imread(list_green{s});
+        end
+        fprintf('done. %.4f sec\n', toc);
+        
+        %%% do shift correction on Red channel
+        fprintf('# shift correction on Red channel ... ');
+        tic
+        [rs, cs] = medAlign(imgRed(:,:,:,t), nSubIm, 50, -inf);
+        fprintf('done. %.4f sec\n', toc);
+        
+        %%% re-align channels to shift
+        fprintf('# re-align channels ... ');
+        tic
+        for s = 1 : imgStack
+            imgRed(:, :, s, t) = circshift(imgRed(:, :, s, t), [rs(s), cs(s)]);
+            imgGreen(:, :, s, t) = circshift(imgGreen(:, :, s, t), [rs(s), cs(s)]);
+        end
+        fprintf('done. %.4f sec\n', toc);
+        
+    %end
+    
+    %% translate to old version
+    
+    
+    
\ No newline at end of file