Added many fixes for SuperSeggerViewerGui for multichannel imaging

Internal/intImRead.m

@@ -14,6 +14,11 @@
     end
 end
 
+
+if numel(size(im)) > 2
+    disp('Images are in color - attempting to convert to monochromatic.');
+    im = convertToMonochromatic(im);
+end
 end
 
 

batch/BatchSuperSeggerOpti.m

@@ -209,8 +209,8 @@ function BatchSuperSeggerOpti(dirname_,skip,clean_flag,res,startEnd,showWarnings
         cleanup = onCleanup( @()( delete( h ) ) );
     end
 
-    %parfor(j = 1:num_xy,workers)
-        for j = 1:num_xy
+    parfor(j = 1:num_xy,workers)
+        %for j = 1:num_xy
 
         dirname_xy = dirname_list{j};
         intProcessXY( dirname_xy, skip, nc, num_c, clean_flag, ...

batch/trackOptiAlignPad.m

@@ -110,8 +110,8 @@
 crop_box = cell(1, num_xy);
 
 % parallelized alignment for each xy
-for jj=1:num_xy
-%parfor(jj=1:num_xy, workers)
+%for jj=1:num_xy
+parfor(jj=1:num_xy, workers)
     crop_box{jj} = intFrameAlignXY( SHOW_FLAG, nt, nz, nc, nxy(jj), ...
         dirname_, targetd, nameInfo, precision, CONST);
 end
@@ -182,11 +182,6 @@
             end
             im = intImRead(in_name);
 
-            if numel(size(im)) > 2
-                disp('Images are in color - attempting to convert to monochromatic.');
-                im = convertToMonochromatic(im);
-            end
-
             if (ic == nc(1)) && (iz == nnz2 | iz == -1)
                 % align phase image at half the z axis
                 if ~initFlag % first time through, or high error
@@ -236,11 +231,11 @@
 
                     figure(ic)
                     clf;
-                    if mod(ic,2) == 0
-                        imshow( cat( 3, backer, backer0+fluor, backer0));
-                    else
-                        imshow( cat( 3, backer+fluor, backer0, backer0));
+
+                    if ~isfield (CONST.view,'fluorColor')
+                        CONST.view.fluorColor = {'g','r','b'};
                     end
+                    comp( {backer}, {fluor,CONST.view.fluorColor{ic-1}} );
                 end
                 drawnow;
             end
@@ -322,11 +317,11 @@
 
                     figure(ic)
                     clf;
-                    if mod(ic,2) == 0
-                        imshow( cat( 3, backer, backer0+fluor, backer0));
-                    else
-                        imshow( cat( 3, backer+fluor, backer0, backer0));
+
+                    if ~isfield (CONST.view,'fluorColor')
+                        CONST.view.fluorColor = {'g','r','b'};
                     end
+                    comp( {backer}, {fluor,CONST.view.fluorColor{ic-1}} );
                 end
                 drawnow;
                 hold on;

batch/trackOptiCropMulti.m

@@ -28,7 +28,7 @@
 
 if ~isempty(dirname)
 
-    file_filter = '*.tif';
+    file_filter = '*.tif*';
     dirname = fixDir(dirname);
 
     contents=dir([dirname,file_filter]);
@@ -72,10 +72,10 @@
             % displays the first and last image on top of each other
             nameInfo.npos(:,1) = [nt(1); nc(1); nnxy; nz(1)];
 
-            im1   = imread( [dirname, MakeFileName(nameInfo) ]);
+            im1   = intImRead( [dirname, MakeFileName(nameInfo) ]);
 
             nameInfo.npos(:,1) = [nt(end); nc(1); nnxy; nz(1)];
-            imEnd = imread( [dirname, MakeFileName(nameInfo) ]);
+            imEnd = intImRead( [dirname, MakeFileName(nameInfo) ]);
             figure(1);
             clf;
 
@@ -120,9 +120,9 @@
 
                         disp( in_name );
 
-                        im = imread( in_name );
+                        im = intImRead( in_name );
                         out_name = [targetd, MakeFileName(nameInfo)];
-                        imwrite( im(yy,xx), out_name, 'TIFF' );
+                        intImWrite( im(yy,xx), out_name );
                     end
 
                 end

batch/trackOptiSkipMerge.m

@@ -136,8 +136,9 @@ function intSkipPar(i,dirname_xy,nameInfo,nt,nc,nz,skip,num_c,num_z)
 nameInfo_tmp.npos(4,1) = 1;
 name = MakeFileName(nameInfo_tmp);
 
+
 % do the min merge of z phase
-phase = imread( [dirname_xy,'phase',filesep,name] );
+phase = intImRead( [dirname_xy,'phase',filesep,name] );
 for k = 2:num_z
     nameInfo_tmp.npos(4,1) = nz(k);
     name  = MakeFileName(nameInfo_tmp);
@@ -155,9 +156,15 @@ function intSkipPar(i,dirname_xy,nameInfo,nt,nc,nz,skip,num_c,num_z)
 dataname_ref = [dirname_xy,'seg', filesep,name_ref,'_err.mat'];
 data = load(dataname_ref);
 
+
+
 % loads the data reference for the min merge of z phase, sets tha name and
 % nameInfo, and the fluorescence field from the image to be merged.
 if mod(i-1,skip)
+
+    imRange = nan( [2, num_c ] );
+    imRange(:,1) = intRange( phase(:) );
+
     data.phase = phase;
     data.basename = name;
     nameInfo_tmp = nameInfo;
@@ -169,9 +176,15 @@ function intSkipPar(i,dirname_xy,nameInfo,nt,nc,nz,skip,num_c,num_z)
         name = MakeFileName( nameInfo_tmp );
         fluorImage = imread( [dirname_xy,'fluor',num2str(nc(k)-1),filesep,name]);
         data.(['fluor',num2str(nc(k)-1)]) = fluorImage;
-    end    
+
+        imRange(:,k) = intRange( fluorImage(:) );
+    end  
+
+    data.imRange = imRange;
+
 end
 
+
 save(dataname2,'-STRUCT','data');
 
 end

cell/trackOptiClist.m

@@ -45,6 +45,7 @@
 % Get the track file names...
 contents=dir([dirname '*_err.mat']);
 
+imRangeGlobal = [];
 
 if isempty( contents )
     clist.data = [];
@@ -91,6 +92,20 @@
 
 
         data_c = loaderInternal([dirname,contents(i).name]);
+
+        % get info on max and min values of each channel over all timesteps
+        if isfield( data_c, 'imRange' )
+            if isempty( imRangeGlobal )
+                imRangeGlobal = data_c.imRange;
+            else
+
+                for kk = 1:size( imRangeGlobal, 2 )                    
+                    imRangeGlobal(1,kk) = min( [data_c.imRange(1,kk),imRangeGlobal(1,kk)] );
+                    imRangeGlobal(2,kk) = max( [data_c.imRange(2,kk),imRangeGlobal(2,kk)] );
+                end
+            end
+        end
+
         if ~isempty( data_c.CellA)
             % record the number of cell neighbors
             if CONST.trackOpti.NEIGHBOR_FLAG && ...
@@ -265,6 +280,10 @@
 
     clist = gateTool( clist, 'add3Dt' );
 
+    % add channel max and min
+    clist.imRangeGlobal = imRangeGlobal;
+
+
     %add3dtime stuff
     len_time_ind = grabClistIndex(clist, 'Long axis (L)', 1);
 

segmentation/doSeg.m

@@ -83,6 +83,8 @@
         phase = mean( phaseCat, 3);      
     end
 
+    imRange = nan( [2, num_c ] );
+
     if ~mod(i-1,skip)
 
         if CONST.superSeggerOpti.segmenting_fluorescence
@@ -93,6 +95,8 @@
             phase = max(phase(:)) - phase;           
         end
 
+        imRange(:,1) = intRange( phase(:) );
+
         % do the segmentation here
         [data, ~] = CONST.seg.segFun( phase, CONST, header, dataname, crop_box);
         if ~isempty( crop_box )
@@ -107,8 +111,12 @@
             nameInfo_tmp.npos(4,1) = 1;
             name = MakeFileName( nameInfo_tmp );
             fluor_tmp = intImRead( [dirname_xy,'fluor',num2str(nc(k)-1),filesep,name] );         
-            data.(['fluor',num2str(nc(k)-1)])=fluor_tmp;            
+            data.(['fluor',num2str(nc(k)-1)])=fluor_tmp;        
+
+            imRange(:,k) = intRange( fluor_tmp(:) );
         end
+
+        data.imRange = imRange;
 
         save(dataname,'-STRUCT','data'); % Save data structure into the seg file.
     end

segmentation/superSeggerOpti.m

@@ -196,7 +196,7 @@
 
     % remove bright halos from the mask
     mask_halos = (magicPhase>CUT_INT);
-    mask_bg = logical((mask_colonies_-mask_halos)>0);
+    mask_bg = logical((mask_colonies-mask_halos)>0);
 
     % removes micro-colonies with background level outline intensity - not bright enough