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miura/3D rendering of the results of Tumor Blood Vessels: 3D Tubular Network Analysis

Last active October 21, 2020 01:07
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3D rendering of the results of Tumor Blood Vessels: 3D Tubular Network Analysis
// ImageJ macro
//*** change the window title here, depending on your input image.
OriginalTitle = "BloodVessels_small.tif";
// following window titles are always same.
LabelMask = "FastFiltered_Tubeness_LabelMask.tif";
tagged = "FastFiltered_Tubeness_LabelMask_Skeleton_tagged_skeleton.tif";
VisualisationDilation = 2;
Nthreads = 4;
selectWindow( tagged );
run("Macro...", "code=v=(v==127)*127+(v==30)*192+(v==70)*255 stack");
run("3D Fast Filters","filter=Maximum radius_x_pix="+d2s(VisualisationDilation,0)+" radius_y_pix="+d2s(VisualisationDilation,0)+" radius_z_pix="+d2s(VisualisationDilation,0)+" Nb_cpus="+d2s(Nthreads,0));
run("Fire");
rename("ThickSkeleton.tif");
run("3D Viewer");
call("ij3d.ImageJ3DViewer.setCoordinateSystem", "false");
call("ij3d.ImageJ3DViewer.add", OriginalTitle, "None", OriginalTitle, "0", "true", "true", "true", "2", "0");
call("ij3d.ImageJ3DViewer.add", LabelMask, "None", LabelMask, "0", "true", "true", "true", "2", "0");
call("ij3d.ImageJ3DViewer.add", "ThickSkeleton.tif", "None", "ThickSkeleton.tif", "0", "true", "true", "true", "2", "0");
call("ij3d.ImageJ3DViewer.startAnimate");
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