Need a example macros to segment a thrombus and caclulate it`s area

Need an example macros code to segment a thrombus on a .tiff image and caclulate it`s relative area. Does anybody have a similar experience?
Thank you.

Hello @mat29,

Can you post an example of the image you want to segment? It would help to understand the difficulty of the task and what methods is more suitable for your problem.


Brown-red-colored in the center is a thrombus, need a macros for a 100 of such images, want to do color segmentation and area computation, could cope with a single image on my own with manual segmentation, thank you

In this case, you might not need a macro. I tried using the SIOX plugin to segment the thrombus and the result looks reasonable:

You can play with it until you obtain a segmentation you like and then save the “segmentator” into a file so you can apply it later to all your images as explained here. After that, you just need to call the particle analyzer to obtain the areas of the segmented regions.

Let me know if it works for you.


thank you…

If the segmentation takes too much time, you can always downsample your image first. SIOX should use the color information so the size is not a big deal later.

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how to install your plugin?

I coped on my own, changed source code to .jar now, I can segment, thx

What to select as a foreground and background, should i select a part of a thrombus and a white backround respectively?

Where is that button to save the Segmentator, please tell

It’s included in Fiji, you don’t need to build it from source.

If you don’t see the Save segmentator button, you might not have the latest version of the plugin. Run Help > Update… to make sure your ImageJ/Fiji installation is up to date.


what is the update site and where to find the latest .jar, update did not help, thank you

problem is fixed, i have removed the old .jar thanks

How to compute the area of the background and foreground objects on a stack of processed black and white images and how to save it in one .xls file? Thank you

@mat29 Instead of replying to your own posts, you can edit and update a previous post by clicking the pencil icon below your post.

Please carefully read the documentation about setting measurements, measuring, and the results table.
If you have further questions, we are ready to help you on this forum.


thank you, I have coped, amazing plugins

How to segment out and compute a vessel lumen free of thrombus? Thank you

Can’t you use the same strategy? Selecting the vessel lumen as foreground and the rest as background in SIOX?