2d/3d thresholdImages same, logScale=[.25,.25,1.25]

matlab/+Segment/getImages.m

@@ -117,7 +117,7 @@ end
 
 
 function imLog=msLog(im,min_radius_pixels)
-logScale=[0.25:0.25:2];
+logScale=[0.25:0.25:1.25];
 imLogCombined=[];
 if length(min_radius_pixels)==3 && min_radius_pixels(3)>0
     % 3d    

matlab/+Segment/segReduce.m

@@ -13,7 +13,7 @@ else
 end
 %
 bwOut=bw;
-nIter=100; %10*max(min_radius_pixels);
+nIter=pi*max(min_radius_pixels)/2;
 for nDilate=1:nIter
     bwKernels=bwOut&~bwLog;
     bwKernels=Segment.aiAreaOpen(bwKernels,0.5*min_radius_pixels);  

matlab/+Segment/thresholdImages.m

@@ -21,34 +21,20 @@ if sensitivity>1 && round(sensitivity)==sensitivity
     return;
 end
 
-if is3D(im)
-    nsz=2*floor(size(im)/16)+1;
-    T=adaptthresh(imLog,0.5,'NeighborhoodSize',nsz,'statistic','gaussian');
-    bwLog=imbinarize(imLog,T);
-    bwLog=Segment.aiAreaOpen(bwLog,min_radius_pixels);
-
-    nsz=4*floor(size(im)/16)+1;
-    T=adaptthresh(im,sensitivity,'NeighborhoodSize',nsz,'statistic','gaussian');
-    bw=imbinarize(im,T);
-    bw=Segment.aiAreaOpen(bw,min_radius_pixels);
-    return;
-end
-
 if segParams.isPhase
     [bw,bwLog]=phaseThreshold(im,bwLog,min_radius_pixels,segParams,...
         sensitivity,medianMask);
     return;
 end
-% else (not 3d)
+
 nsz=4*floor(size(im)/16)+1;
 T=adaptthresh(imLog,0.5,'NeighborhoodSize',nsz,'statistic','gaussian');
 bwLog=imbinarize(imLog,T);
 bwLog=Segment.aiAreaOpen(bwLog,min_radius_pixels);
 
-% use 2x the default nhood size
-T=adaptthresh(im,sensitivity,'NeighborhoodSize',4*floor(size(im)/16)+1,'statistic','gaussian');
+nsz=4*floor(size(im)/16)+1;
+T=adaptthresh(im,sensitivity,'NeighborhoodSize',nsz,'statistic','gaussian');
 bw=imbinarize(im,T);
-
 bw=Segment.aiAreaOpen(bw,min_radius_pixels);
 4;