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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.
- Load an image.
- MLx -> Image Files -> Tiff -> Read
- Select MLx / Widgets / Blob/ Sample Images / RAE_ion.tiff
| 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).
- Here a few thresholds showing that multiple thresholds are needed to
segment the image.
- Load the blobber widget if necessary, and make the blob button window
- MLx -> Load Widget ... Blob
- More Buttons -> Blob
- 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.
- Superblob the image: Super Blob... -> Doit.
- If the image has been superblobbed before, there will be a *.sblobs
file in the same folder as the image.
- Optionally, the .sblobs file may be saved elsewhere.
- View the blob parameters using the Info...->parameters command.
- Double click on the sblob_save_in_image_folder parameter and
set the parameter to :no.
- The superblobber routine will ask where to put the .sblobs file
- The outlines of the blobs will be shown in a second or two.
- 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 small square is the go-away box for the bar. Use this to get rid
of the bar if the superblobbing is interrupted with an apple-period. (Note
- if the process is interrupted, the blob outlines at that stage will be
shown. There will probably be large blobs that still need subdividing.
- The 24/96 shows that the 24th threshold level out of 96 levels is the
- The 50 seconds is the estimate of the total running time. It is extrapolated
from the running time so far, assuming that each setp or threshold level
takes the same time.
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:
- Make the mask image: Super Blob..-> Show Masks
- 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.
- Leave the blob minimum area unchanged, unless you wish to exclude smaller
- Blob the image. See green outlines.
- The various information and statistics work for this window (the title
has a "-B" suffex rather than "-SB").
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).