Exporting Imaris Filament Traces as Skeletons?


I’ve been using the Imaris Filament Tracer to annotate some 3D images, and it looks great, but now I need to extract the traces for downstream processing. Is there a way to binarize these traces and export them as skeletons? I have the Imaris/Fiji bridge but haven’t figured out a way to extract the traces, just the image itself.

I didn’t find any other related topics on the forum but if I missed an extant thread let me know!


You might be best off contacting your Imaris rep, but maybe @Meredith_Price will have a response.

I thought Imaris used to have an “Open” forum, but it seems like that no longer exists?

You may be able to find an XTension that will do something similar if your copy of Imaris supports XTensions. For example https://bidc.ucsf.edu/export-surface-vertices-text

1 Like

In general, I agree with @Research_Associate that it would make sense to ask Imaris technical support.

However, I do happen to know one of the built in XTensions (if you have the license) is called something like “Create Channel from Filament” which will create a channel of a binary form (if you don’t select the option about extrapolating intensity that it offers).

That other channel will be available in FIJI if you use the bridge or if you resave the .ims file and open it in FIJI.


Thank you! This did the trick.


Does anyone have a way to do similar but to save the coordinates and diameters of each point in all the filaments? Not as an image mask but as a list of points and diameters?

I know this has been flagged as solved for exporting the tracing/filaments as a mask.

Hi @cudmore

I’m not what you mean by each point in all the filaments? The spines? Either way, it’s probably best you ask the Imaris technical support staff.

I have been intensively writing Imaris-oriented codes for 5 years.

Have a look at one post from my Imaris programming blog(Imaris_新浪博客).
This might help you understand how Filament data is arranged in Imaris.


If you need any ImarisXT, contact me and I can write one for you in one day.

My github site:

1 Like