Imaris XTension: Spots to Surface distances

Hello @tinevez,

Does someone know if it is possible, using Imaris XTensions (I know how to do this in java or python), to compute the distance of all spots to the closest surface?

And, importantly, add this distance as a measurement to each of the spots objects?

For example, below I would like to measure the distance of each spot to the nucleus surface.


Thank you very much for your help!


Hello @Christian_Tischer

I think I did it a long time ago. It is not on Imaris Open?

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If you create a distance transform from the outside of the nucleus surface, the pixel value of the distance transform channel for each of your spots will be the distance.

*I realize that is just within Imaris and doesn’t require extensions, but is there some reason it needs to be done with an extension?


This is a very good point! This is how you would normally do it. I was not aware (did not consider) that one can do a distance transform in Imaris.
I will try ASAP!

Does it work if the pixel size changes between X & Z?

This is a good suggestion although I would add it is still using an XTension, it’s just one of the in-built ones. People who don’t have the XT license can’t do a distance transform of a surface.

Additionally, at least in this specific example, is that if you happen to have the “Cell” license then this distance between the vesicles and nucleus is automatically calculated.


Thanks so much!

Ah, haven’t really had a chance to dig into Imaris and was going from memory. Thought it was built in, thanks for the clarification.

@tinevez The measurement should be accurate in microns as long as Imaris is able to read the metadata for the images.

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Hi @Christian_Tischer @lmurphy,

The criticism that this measurement required an XTension is true. However, the newest version of Imaris now calculates distance measurements from Spots to Spots, Spots to Surfaces (and vv), and Surfaces to Surfaces natively within the creation wizards. This change enables Imaris to handle large images more easily and quickly, plus the measurements can be calculated when using Batch and also color-coded as in the previous image from Christian.

I hope this helps you all and others!


Very useful, indeed!

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