new functions for zeiss lsm files

lsm_tif_2_mytif.m

@@ -0,0 +1,56 @@
+
+% convert Zeiss Tifs labels to my Tifs
+
+clear all;
+
+folder = 'D:\Data\2012-08-20_ML124\' ; % 'D:\Data\2012-08-15_MLslides\';%   %  'D:\Data\2012-08-26_mp07\'; % 
+subfolder =  'm124\'; % 'm106a\';  % 'mp07b\'; %   
+froot ='ml124B'; % 'm106a'; %  'mp07b'; % 
+
+% dir(folder); 
+
+Zs =65;
+Ims = 10;
+r = 2; % channel to make red
+g = 3; % channel to make green; 
+b = 1; % channel to make blue
+
+
+
+for i=10:Ims
+    Imax = zeros(2048,2048,3,'uint16'); % so much for flexible image size
+    for z=1:Zs
+        fname = [froot,'_z',sprintf('%02d',z-1),'_p',sprintf('%02d',i-1),'.tif'];
+        try
+            Iin = imreadfast([folder,subfolder,fname]);
+        catch er
+            disp(er.message)
+            continue
+        end
+        [h,w,chns] = size(Iin);
+        intype = class(Iin); 
+        Iout = zeros(h,w,3,intype);
+        if r<= chns
+            Iout(:,:,1) = Iin(:,:,r); 
+            Imax(:,:,1) = max( cat(3,Imax(:,:,1),Iin(:,:,r)),[],3);   
+        end
+        if g<= chns
+            Iout(:,:,2) = Iin(:,:,g); 
+            Imax(:,:,2) = max( cat(3,Imax(:,:,2),Iin(:,:,g)),[],3);   
+        end
+        if b <= chns
+            Iout(:,:,3) = Iin(:,:,b); 
+            Imax(:,:,3) = max( cat(3,Imax(:,:,3),Iin(:,:,b)),[],3);   
+        end
+        figure(1); clf; 
+        subplot(1,2,1); imagesc(Iout);
+        subplot(1,2,2); imagesc(Imax); 
+        pause(.1);
+
+        fout = [froot,'_',sprintf('%02d',i),'_z',num2str(z),'.tif'];
+        imwrite(Iout,[folder,fout]); 
+        disp([num2str(i),': ',num2str(z/Zs*100,2),'% finished']);
+    end
+        imax_name = ['max_',froot,'_',sprintf('%02d',i),'.tif'];
+    imwrite(Imax,[folder,imax_name]); 
+end