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Superblobber

This is a multi-threshold blobber for automatic segmentation of diffraction spots, particles and the like. It repeatedly runs the blobber at ever increasing LOWER thresholds (the upper threshold is usually the maximum pixel value in the image), keeping track of how the blobs split as they get smaller.


Example

  1. Load an image.
    1. MLx -> Image Files -> Tiff -> Read
    2. Select MLx / Widgets / Blob/ Sample Images / RAE_ion.tiff
      1.  
      2.  This image has some bright blobs that are close together - so that the threshold there needs to be high to separate them (yellow arrow), and it also has some dim blobs, where the threshold has to be low in order not to miss them (green arrows).  
      3. Here a few thresholds showing that multiple thresholds are needed to segment the image.
             
             
             
  2. Load the blobber widget if necessary, and make the blob button window
    1. MLx -> Load Widget ... Blob
    2. More Buttons -> Blob
  3. Set the super-blobber minimum area if desired, using the Super Blob...-> Set Min Area menu. The minimum area defaults to 10 pixels. This example uses that default.
  4. Superblob the image: Super Blob... -> Doit.
    1. If the image has been superblobbed before, there will be a *.sblobs file in the same folder as the image.
      1. Optionally, the .sblobs file may be saved elsewhere.
        1. View the blob parameters using the Info...->parameters command.
        2. Double click on the sblob_save_in_image_folder parameter and set the parameter to :no.
        3. The superblobber routine will ask where to put the .sblobs file
      2. The outlines of the blobs will be shown in a second or two.
    2. If the image has NOT been superblobbed before, or if MacLispix doesn't find the .sblobs file, then the image will be superblobbed. This can take several minutes. During the superblobbing, a pink progress bar appears near the top of the screen:

The superblobbed image will look like this :

where the image here has been zoomed x2 with the Zoom...->2 button.

The superblobber is still under development: the Info and Stats windows (buttons to the right) do not yet work for the superblobber. A way to access the blobs is via a mask image:

  1. Make the mask image: Super Blob..-> Show Masks
  2. Set the threshold slider upper limit to 1 (note - the slider includes or excludes one blob per intensity level because the blob pixel values are the index number for that blob.
  3. Leave the blob minimum area unchanged, unless you wish to exclude smaller blobs.
  4. Blob the image. See green outlines.
  5. The various information and statistics work for this window (the title has a "-B" suffex rather than "-SB").


References

Bright, D.S., "An Object Finder Based on Multiple Thresholds,Connectivity and Internal Structure", Microbeam Analysis (1987), pp. 290-292

Bright, D.S., "An Object Finder for Digital Images Based On Multiple Thresholds, Connectivity and Internal Structure", Journal of Computer-Assisted Microscopy 1(4): 307-329 (1989).