Qualify bone remodelling by assessing the amount of colored signal within a ROI

WTAA2 (2’)_5.0x.tif (8.5 MB)


This image is a coronal view of a mouse skull. We want to assess the activity of bone remodelling by quantifying the amount of pink signal (TRAP staining) within the bone include in a certain ROI

Could you please provide me a protocol that includes :

  • the creation of a ROI
  • the calculation of the amount of pink signal in the bone within the ROI .
  • repeat this procedure on several images (batch)

Thank you very much


To help get you started…

Take a look at the ImageJ User Guide - the section on ROI Manager…… For how to select/save/measure ROIs… take a look at these helpful links as well:

The Segmentation workshop will help you the most here…

In this case - you’ll want to use the Color Threshold to select those pink regions… or you could even use:

That would use machine learning to find those pink regions… either tool could be used.

Then you’ll need to script. So to get started scripting in ImageJ - here are some other helpful links:

There are also some great tutorials by @haesleinhuepf here: https://www.youtube.com/playlist?list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U

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Thanks a lot
I am working on it !!!

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If you have more questions… just ask us here. We can help. :slight_smile: