use denoised image for LoG

matlab/+Segment/getImages.m

@@ -31,12 +31,12 @@ if is3D(im)
     end
     if  USE_CUDA
         logRadius=min_radius_pixels.*(1/sqrt(3));
-        imLog=HIP.LoG(imRaw,logRadius,[]);
+        imLog=HIP.LoG(im,logRadius,[]);
     else
         % use difference of gaussian approximation
         logRadius=min_radius_pixels;
-        imd1=imgaussfilt3(imRaw,sqrt(2).*logRadius);
-        imd2=imgaussfilt3(imRaw,logRadius./sqrt(2));
+        imd1=imgaussfilt3(im,sqrt(2).*logRadius);
+        imd2=imgaussfilt3(im,logRadius./sqrt(2));
         imLog=imd1-imd2;
     end
 else
@@ -45,16 +45,16 @@ else
         logRadius=(1/sqrt(2)).*min_radius_pixels;
         logRadius(2)=logRadius(1);
         logRadius(3)=0;
-        imLog=HIP.LoG(imRaw,logRadius,[]); 
+        imLog=HIP.LoG(im,logRadius,[]); 
     else
         if length(min_radius_pixels)>1
             logRadius=0.5*min(min_radius_pixels(1:2));
         else
             logRadius=0.5*min_radius_pixels ;
         end
-        szFilter=round(size(imRaw)/3);
+        szFilter=round(size(im)/3);
         h=fspecial('log',szFilter,logRadius);
-        imLog=imfilter(imRaw,h,'replicate');
+        imLog=imfilter(im,h,'replicate');
     end    
 end
 
@@ -93,6 +93,9 @@ if is3D(im)
         end
     else
         imx = medfilt3(im);
+        for i=1:30
+            imx=medfilt3(imx);
+        end
     end
 else
     % 2D

matlab/+Segment/thresholdImages.m

@@ -12,10 +12,10 @@ else
 end
 
 if sensitivity>1 && round(sensitivity)==sensitivity
-    lm=multithresh(imLog,sensitivity)
+    lm=multithresh(imLog,sensitivity);
     bwLog=logical(imLog>lm(end));
     bwLog=bwareaopen(bwLog,4*min_area_pixels);
-    lm=multithresh(im,sensitivity)
+    lm=multithresh(im,sensitivity);
     bw=logical(im>lm(end));
     bw=bwareaopen(bw,min_area_pixels);
     return;