Macro for active contours


I have a blob image and I want to measure Intensity of some blobs by hand, to do that I want to use active contours, which would then iterate over the shape of the blob and then calculate total intensity in that region. Any ideas if such a macro exists already or any pointers on how I could write such a thing?

Attached is an image on which I want to use the macro to get the intensity by manually making ellipses and storing the intensity in a file. Any help is appreciated.

Hi, not what you asked, but are you aware that most of the blobs are ‘saturated’? You will be erroneously measuring 255 in too many places.
Do a histogram of your image to see if the image carries the information you want to measure (i.e. for all the pixels with 255 intensity, you cannot really know how bright they are, other that “too bright for the acquisition sensor”).

Hey, Yeah this image is just for testing, the original image will have blobs of variable intensity and I need some kind of a simple extension of active contour plugin, where I draw an ellipse and it iterates to find the boundaries and gives me the intensity at the end of the iteration. Sounds possible to write as a macro? or should I think in terms of a short java program? just wanted to know if any tool is out there to get intensity in a roi of choice.



There is a snakes plugin by Thomas Boudier. Perhaps you should try that. I doubt that a plugin for segmentation would give you the intensity of the detected blobs, but once you have the binary regions segmented, you can use the Particle Analyzer (built-in IJ) or Particles8 plugin to get the integrated density or the mean value, etc. by “Redirecting” the binary image to the original image (where the intensity should be measured). Have a look at the documentation of the Particle Analyzer in the IJ site.

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Hi, I have integrated these segmentation tools into a Fiji plugin which you can build from my Github repo at:

would also need:

Tracking part is not done yet.