- First you need a thresholded version of the image to start processing
- Next clean up the image a bit, for the bone image a 2x Opening was sufficient but some images require more. Then select the largest single component (you cannot have disconnected structures)
run("Erode (3D)", "iso=255");
run("Erode (3D)", "iso=255");
run("Dilate (3D)", "iso=255");
run("Dilate (3D)", "iso=255");
run("Find Connected Regions", "allow_diagonal display_image_for_each display_one_image display_results regions_for_values_over=100 minimum_number_of_points=5000 stop_after=-1");
- Select the largest window
selectWindow("Region of value 255 containing 6340372 points");
run("Gaussian Blur...", "sigma=2.50 stack");
run("3D Viewer");
- Select
Display as:
Surface
- Select downsampling of 1 (2 makes some of the surfaces disappear)
- Select a threshold of around 100 (large makes it thinner, smaller makes it thicker)
- Export Surfaces -> STL (binary)