Watershed segmentation of particles

This example shows how to make a watershed segmentation where seeds come from local maxima of distance map. The maxima may be filtered to avoid over-segmentation.

The image data is generated similarly to what was done in particle analysis example.

def particle_segmentation():
        """
        Demonstrates segmentation of particles using watershed seeded
        by (filtered) local maxima of distance map.
        """

        # Generate particle image
        generate_particles(1000, 0)


        # Read generated data file
        img = pi.read(output_file('particles'))

        # Convert to wider data type so that we can label each particle
        pi.convert(img, ImageDataType.UINT16)

        # Calculate distance map
        dmap = pi.newimage(ImageDataType.FLOAT32)
        pi.dmap(img, dmap)

        # Find maxima
        # Note that in some cases the system is able to automatically
        # change the data type of output images, so we don't have to
        # specify any data type in the pi.newimage() command.
        # This does not work always, though, as there might be many
        # possible output data types.
        maxima = pi.newimage()
        pi.localmaxima(dmap, maxima)

        # Remove unnecessary maxima to avoid over-segmentation
        pi.cleanmaxima(dmap, maxima)

        # Create image with labeled maxima only.
        # First set all pixels to zero, then label maxima.
        pi.set(img, 0)
        pi.labelmaxima(img, maxima)

        # Grow labels back to original geometry, using distance map value
        # as filling priority.
        pi.grow(img, dmap)

        # Save result
        pi.writeraw(img, output_file('particles_watershed'))

One slice of the input image.

Result of watershed segmentation without using cleanmaxima. Random colors have been assigned to the segmented regions. Notice extraneous regions between some of the spheres.

Result of watershed segmentation after using cleanmaxima. Random colors have been assigned to the segmented regions. There are no extraneous regions between the spheres as in the previous figure.