Roughness calculation

I have a problem regarding ‘‘roughness calculation’’ plugin. I am new to this. I open my image which is from confocal imaging z stacks. It gives me between 20-120 different sets of data. different for different images. I dont know what is it for and how it divides the images into small parts and gives me sets of data. Unfortunately I cannot upload my LSM file here. but this is the result of imagej for one of the images. Please let me know what are these 106 belong to.

Hi @sababiba

this plugin is very old and maybe no longer state of the art.

Apparently, it calculates statistical values for describing the shape of a surface (roughness of the surface).

Counter questions:

  • What do you want to measure (physically)?
  • What is the purpose of the analysis?
  • What do your images show? Could you maybe upload a sceenshot of one?
  • What kind of values / value ranges do you expect?


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I want to measure biofilm surface roughness.
I want to compare the roughness of two different biofilms I have.
My images show the cells which are producing my biofilm layers. They are zstacks taken by confocal microscopy.
What I read in articles, the Ra should be around 0.1-0.5.

Thanks Robert


If you point me to some papers where scientists actually measure roughness and wrote how roughness is mathematically defined, I may guide you how to do this in ImageJ :wink:


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