Calculating intensity variance of an image on a per pixel basis?

Sample image and/or code


We have some images of GFP puncta captured with a spinning disk microscope.

Analysis goals

One of the analysis that we’d like to perform on the image is to calculate the variance in intensity on a per pixel basis. We’re wondering what the best way to do this (either in ImageJ, or otherwise) would be.


  • What stops you from proceeding? We’re just not sure where to start. If anyone can offer links or suggestions, or tips, that’d be really appreciated.

Thank you!

Could you kindly explain what you mean by variance “on a per pixel basis”?
Please provide the exact mathematical formulation of what you like to obtain.