Bone to material contact

Hello everybody,

I kinda need some your help.

In this image is represented an histologic cut of bone and biomaterial. The new bone formation is characterized by the color rose/violet and the biomaterial is the brown particles. So I need to stablish my ROI, and I need a tool to help me to color the bone in green and the biomaterial in blue (for example) and i need to calculate the % of contact between the two colors, so the bone to biomaterial contact.

Can u guys help me ?

Can I do that with ImageJ? Do i need a specific

Hello there,
I would first try to see if you can do a segmentation on these regions.I think the Trainable Weka segmentation would be useful here. You can tell the plugin to first segment the violet+brown regions (as a single region) and save as output file 1. The next step would be to just segment the brown regions to give output file 2. Then threshold both the output files and use the ‘Analyse particles’ to get the areas of your thresholded regions. Divide the total area from output file 2 / total area of output file 1. It will then give you a ‘percentage’ of occupancy of your brown region. Here is an example:

File 1

File 2

(Total Area of the regions from Output file 2/ Total area of regions from output file 1)*100 = percentage of occupancy.

Feel free to ask if you have any questions.

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Thank you Praveen for your quick answer.
I tried to download the plugin Trainable Weka segmentation for ImageJ, but i’m having problems installing it. When i finish installing and i select the plugin on Image the following message appeared.

I think you should try downloading Fiji and running the plugin. You can find it here -
Or maybe @iarganda can help?

Yes, please, go ahead and use Fiji. Otherwise the multiple dependences of the plugin can make the installation very difficult.

Ok i just installed Fiji and it works just fine.
But i can’t get your images :frowning:

Here what i got…

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Great thats a good start. I would ask the plugin to segment the violet and the brown regions as a single ‘class’. Once you have done that, you click on ‘Create result’. Then you do the threshold on this new image to get what i posted before here in my post.

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Dear Praveen,

I can’t get your pics… I did find a way to separate the 3 parts (bone, biomaterial and softtissue) in 3 different colors. So by this picture can u tell me a way of measure the contact surface between the green and the red ?