Image segmentation along grain boundaries and correlation of potential map (obtained with an AFM technique) with chemical content (SIMS map)

Sample image and/or code


Dear all,

I hope you are well.

I have two images displaying different properties of the same area in a specimen, one chemical map and one potential map of the same region of interest. I also have a structural micrograph or secondary electron micrograph for reference.

What I would like to do is to have the same grain boundary segmentation in both the chemical and potential map, so that I can say e.g. that grain x contains this many chemical counts and has an average potential of some value. I want to be able to extract quantitative information from the same region of interest in each map so that one property (chemical content) can be correlated with the other property (potential value).

Analysis goals

  • The same grain segmentation for two maps displaying different properties in the same region of interest for the correlation of the same properties.


  • I asked a data scientist for assistance which is how the current workflow came about. However, I am struggling to have both maps segmented the same way even if the SE image is registered on each map to serve as a reference. When “analyzing particles” which in my case represents the number of grains, I get a different total number of grains for each map.

  • Imagej does not allow me to copy paste the segmentation or grain selection obtained for one property map to another (e.g. the grain selection of the potential map onto the chemical map). When this is done I still get a different number of total grains.

  • I have been using imagej and inbuilt image denoising plugins (see .pdf). I am also trying to see if Python may be easier (youtube channel: python for microscopists)

Any suggestions or advice is very much welcome and thanks in advance!

Kind regards