The version used for the first submission.

Reduced smoothing, slightly darker filopodia.
Processed the whole sequence, texture coherency preserved with old/naive FF generator.

cmath3d/TriangleMesh.cpp

@@ -775,7 +775,7 @@ int ActiveMesh::ImportVTK_Ftree(const char *filename,const int idx,
 			std::cout << s << ": r=" << r << ", r*r=" << r*r << "\n";
 
 			//float dotsCount=10.f*r*r;
-			float dotsCount=200.f*r;
+			float dotsCount=100.f*r;
 			int qM=(dotsCount > 1300.f)? 1300 : (int)dotsCount;
 
 			for (int q=0; q < qM; ++q)
@@ -1725,7 +1725,8 @@ void ActiveMesh::PhaseII(const i3d::Image3d<i3d::GRAY16>& texture,
 {
 	i3d::GrayToFloat(texture,intermediate);
 
-	i3d::GaussIIR(intermediate,3.f,3.f,2.5f);
+	//i3d::GaussIIR(intermediate,3.f,3.f,2.5f);
+	i3d::GaussIIR(intermediate,2.f,2.f,2.f);
 #ifdef SAVE_INTERMEDIATE_IMAGES
 	intermediate.SaveImage("4_texture_filtered.ics");
 #endif

src/main.cpp

@@ -26,9 +26,11 @@ int main(int argc,char **argv)
 		//I'm called as generator/simulator
 		ParamsSetup();
 
+		//ID53: mesh #14 looks nice
+
 		//ISBI:
 		//for (int i=0; i < 50; ++i)
-		for (int i=5; i < 6; ++i)
+		for (int i=0; i < 25; ++i)
 		{
 			LoadNewMesh(i);
 
@@ -170,10 +172,10 @@ int LoadNewMesh(int fileNo)
 	char VTK_fTreeA[1024];
 	char VTK_fTreeB[1024];
 
-	sprintf(VTK_nucleusSurf,"../sample_sequence/ID25/ID25_t%03d_nucleusSurf.vtk",fileNo*2);
-	sprintf(VTK_nucleus,    "../sample_sequence/ID25/ID25_t%03d_nucleus.vtk",fileNo*2);
-	sprintf(VTK_fTreeA,     "../sample_sequence/ID25/ID25_t%03d_fTree01.vtk",fileNo*2);
-	sprintf(VTK_fTreeB,     "../sample_sequence/ID25/ID25_t%03d_fTree02.vtk",fileNo*2);
+	sprintf(VTK_nucleusSurf,"../sample_sequence/ID64/ID64_t%03d_nucleusSurf.vtk",fileNo*2);
+	sprintf(VTK_nucleus,    "../sample_sequence/ID64/ID64_t%03d_nucleus.vtk",fileNo*2);
+	sprintf(VTK_fTreeA,     "../sample_sequence/ID64/ID64_t%03d_fTree01.vtk",fileNo*2);
+	sprintf(VTK_fTreeB,     "../sample_sequence/ID64/ID64_t%03d_fTree02.vtk",fileNo*2);
 
 	//first, obtain a fresh volumetric mesh of the cell body
 	//(before it gets overwritten in the following code)
@@ -269,6 +271,7 @@ int RenderMesh(int fileNo)
 
 		//create a FF by "diffusing displacement seeds/vertices"
 		mesh.ConstructFF(FF);
+/*
 		char n[1024];
 		sprintf(n,"old_vx_%03d.ics",fileNo);
 		FF.x->SaveImage(n);
@@ -276,7 +279,7 @@ int RenderMesh(int fileNo)
 		FF.y->SaveImage(n);
 		sprintf(n,"old_vz_%03d.ics",fileNo);
 		FF.z->SaveImage(n);
-/*
+
 		//create a FF by "rendering displacement triangles"
 		mesh.ConstructFF_T(FF);
 		sprintf(n,"new_vx_%03d.ics",fileNo);
@@ -298,12 +301,12 @@ int RenderMesh(int fileNo)
 	mesh.RenderDots(mask,texture);
 	//
 	//or always one shot:
-/*
-	i3d::Image3d<i3d::GRAY16> texture;
-	mesh.RenderOneTimeTexture(mask,texture);
-*/
+	//i3d::Image3d<i3d::GRAY16> texture;
+	//mesh.RenderOneTimeTexture(mask,texture);
 
-	texture.SaveImage("phantom.tif");
+	char fileName[1024];
+	sprintf(fileName,"phantom_t%03d.tif",fileNo);
+	texture.SaveImage(fileName);
 
 #ifdef DO_PHASE_II_AND_III
 	std::cout << "rendering texture II  #" << fileNo << "\n";
@@ -322,8 +325,7 @@ int RenderMesh(int fileNo)
 #endif
 
 	std::cout << "exporting texture #" << fileNo << "\n";
-	char fileName[1024];
-	sprintf(fileName,"text_t%03d.tif",fileNo);
+	sprintf(fileName,"texture_t%03d.tif",fileNo);
 	texture.SaveImage(fileName);
 
 	std::cout << "exporting mask #" << fileNo << "\n\n";