dark tubes with bright plate

src/MATLAB/+RSF/darkTubes.m

-function imfm = darkTubes(im,CONSTANTS,thickness)
+function imOut = darkTubes(im,CONSTANTS,thicknessIn)
 
+thickness = abs(thicknessIn);
 voxelSize = CONSTANTS.imageData.PixelPhysicalSize;
 voxelSize([1,2]) = voxelSize([2,1]); % swap (x,y,z) to matlab column major (y,x,z)    
 vx = max(voxelSize)./voxelSize;
@@ -8,13 +9,26 @@ sigma = 1/sqrt(3) * (thickness ./ 2) * vx;
 
 cudaTarget = getCudaTarget;
 imf = HIP.LoG(im,sigma,cudaTarget);
+
+if thicknessIn < 0
+    % bright plate
     imn = imf;
     imn(imn>0)=0;
     imn=abs(imn);
+    sigmaPlate = [5,1,1].*sigma;
+    imfPlate = HIP.LoG(imn,sigmaPlate,cudaTarget);
+    imnPlate = imfPlate;
+    imnPlate(imnPlate>0) = 0;
+    imnPlate = abs(imnPlate);
+    imnPlate = imnPlate .* imregionalmax(imnPlate);
+    imOut = imnPlate;
+else        
+    % dark blob
     imp=imf;imp(imp<0)=0;
     imfm = fibermetric(imp);
     imfm = imfm .* imregionalmax(imfm);
-% imfm = RSF.clipRSF(imfm);
+    imOut = imfm;
+end
 
 4;
 

src/MATLAB/clusterExamples/goVideoDarkTubes.m

@@ -37,8 +37,17 @@ imfmX = imfm.*imregionalmax(imfm);
 % imp = imp .* imregionalmax(imp,6);
 % imn = imn .* imregionalmax(imn,6);
 
-sliceThickness = 100;
-for Z = sliceThickness: 1   :size(im,1)-sliceThickness
+% bright plate
+sigmaPlate = [5,1,1].*sigma;
+imfPlate = HIP.LoG(imn,sigmaPlate,cudaTarget);
+imnPlate = imfPlate;
+imnPlate(imnPlate>0) = 0;
+imnPlate = abs(imnPlate);
+imnPlateX = imnPlate.*imregionalmax(imnPlate,6);
+
+sliceThickness = 10;
+bClear = true;
+for Z = 100: 1   :size(im,1)-100
     
     clipLimits=[];
     clipLimits.dim = 1;
@@ -50,13 +59,15 @@ for Z = sliceThickness: 1   :size(im,1)-sliceThickness
     im2 = getClipFrame(imn,clipLimits);
     im3 = getClipFrame(imp,clipLimits);
     im4 = getClipFrame(imfm,clipLimits);    
-    im5 = getClipFrame(imfmn,clipLimits);
     im6 = getClipFrame(imraw,clipLimits,gray());
     im7 = getClipFrame(imfmX,clipLimits);
-
-    imOut = [ im1,im2, im7 ; im6, im3, im4   ];
-    if sliceThickness == Z
+    im8 = getClipFrame(mat2gray(imnPlate),clipLimits);
+    imOut = [ im6,im2, im8 ; im3, im4, im7   ];
+    clf;imagesc(imOut);drawnow
+    title(num2str(Z))
+    if bClear
         imwrite(imOut,outfile);
+        bClear = false;
     else
         imwrite(imOut,outfile,'writemode','append');
     end