Remove side particles on Ilastik

Hi, sorry to post a lot but I’m getting really excited with Ilastik.

On the pictures I have to analyze, some particles are touching the border of the image so I don’t want to count them because they are not entirely in the image.

Is there any way to remove the particles that touch the border of the picture in Ilastik ? :slight_smile:

Hi @Antoine_Cure,

really cool that your analysis if moving forward so swiftly :slight_smile:

This sounds like a cool feature to have in ilastik. Unfortunately it isn’t implemented :confused:

However there are a couple of workarounds I can imagine that don’t require coding:

  • use the center of the object as a reference and exclude objects based on proximity of the center to the image edges
  • use the coordinates of the bounding box (an axis aligned rectangle that is drawn around your object. if any of those values are either 0, or at the maximum of the dimensions.

I skimmed through the forum a bit and was surprised that I didn’t find anything for Fiji. Maybe I am not using the right keywords…

@Christian_Tischer: do you know of a Fiji operation or plugin to remove labeled objects that are touching the boundary?

Hello Dominik,

Yes indeed I also considered doing that and that should work perfectly ! But yes it would be a very nice feature :wink:

I previously used FIJI for the analysis and I know it’s possible. In fact FIJI doesn’t remove the particles on the side but simply don’t consider them as particles.

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