implemented b scope support

alignmentScript.m

@@ -10,6 +10,8 @@
 numImages = 50; %number of images that will be meaned for global shift correction
 referenceChannel = 1; %0: green, 1: red; reference channel for shift corrections
 numShiftCorrections = 1; %number of shift corrections
+bScope = 0; %set 1 if b scope, 0 if not
+
 %% Load Files
 tic;
 currentFolder = pwd;
@@ -36,8 +38,13 @@
     %go into folder
     cd(inFolder);
     cd(folders(f).name);
-    greenFiles = dir('*Ch2_*.tif');
-    redFiles = dir('*Ch1_*.tif');
+    if bscope
+        greenFiles = dir('ChanA_*_*.tif');
+        redFiles = dir('ChanB_*_*.tif');
+    else
+        greenFiles = dir('*Ch2_*.tif');
+        redFiles = dir('*Ch1_*.tif');
+    end
     %check if fileNumber is the same
     if size(greenFiles, 1) ~= size(redFiles, 1)
         error(['Unequal number of files in trial folder "', folders(f).name, '"!!']);