Added modification to remove the quantileNorm and just do sum in the …

…normalization step, increasing speed.

loadParameters.m.template

@@ -30,6 +30,13 @@ params.NUM_ROUNDS = 5;
 params.BEAD_ZSTART = 1; %goes to :end
 params.COLOR_OFFSETS3D = [20,20,20];
 
+%If the channel data come from very different distributions, applying a quantile Norm 
+%can be useful when combining channel information for the registration. However, 
+%it is highly memory and time intensive, using any other paramter but 'quantile' will
+%simply sum the channels in the normalization step, and this can reduce comptuation time
+%by 20-50%!
+params.NORMALIZE_METHOD = 'quantile';
+
 
 params.PUNCTA_SIZE_THRESHOLD = 30;
 params.PUNCTA_SIZE_MAX = 2000;

stage_normalization/normalizeImage.m

@@ -35,7 +35,15 @@ function normalizeImage(src_folder_name,dst_folder_name,fileroot_name,channels,r
     end
 
     % Normalize the data
-    data_cols_norm = quantilenorm(data_cols);
+    % NEW: Added the flexiblity to skip the quantile normalization. Providing the channels
+    % are from a similar distribution, it can greatly increase speed and reliability to simply
+    % sum the non-normalized channels
+    if strcmp(params.NORMALIZE_METHOD,'quantile')
+        data_cols_norm = quantilenorm(data_cols);
+    else
+        data_cols_norm = data_cols;
+    end
+
     clearvars data_cols;
 
     % reshape the normed results back into 3d images