An extension for virtual endoscopy

Dear All,

We already have an Endoscopy module in Slicer. However that requires the lumen being already segmented. I have been working on a module which performs the centerline extraction followed by lumen segmentation, for pancreatic duct (it can be used for other lumens too). This may be a useful module for lumen analysis.

I have not made a demonstration webpage yet, just have the repository at:

I’m hoping to add this through the extension management system and would like to hear about your suggestions/opinions.



You have all kinds of cool projects, thanks Yi!

If you haven’t already seen it should have a look at Delphine Naine’s master’s thesis, one of the original driving use cases for Slicer. It would be great to see some of that functionality come back.

I am very interested in your work. Thank you for sharing

May I ask / suggest this would be very useful for us for the lung to map the airways … especially if there is a nodule to which we have to reach endoscopically. Often these nodules are peripheral (outer one third of the lung) as since the airways get narrow and branch it’s difficult to reach them with confidence. There is a ton of new equipment being pumped by many companies into this technology (Lung point, Electromagnetic navigation, Robotic bronchoscopy, Cone Beam CT etc etc ) but for a low cost setting / open source we have very little… it would be ideal if you could help design something which will help navigate the airways to a lesion of interest with your background work on Pancreas

Happy to hear from you

Warm Regards
Dr Kedar Hibare

Hi Steve,

Of course I remember Delphine’s great work. I still remember using that module in the Tcl/Tk based Slicer 1.6 version. :smiley:


Hi Dr. Hibare,

Sure! I believe it should be straightforward to extend such a module to the airway endoscopy. I’ll work on that.

Thanks for your suggestion!


Dear Professor Gao:

   Can you share some pictures about the result  of the virtual endoscopy project?

Thanks a lot for submitting these extensions!

There is some overlap with the VMTK extension, which offers an opportunity in reducing maintenance workload. For example, VMTK can compute vesselness, segment lumen automatically using a few simple methods, and create a centerline tree. The tree is compatible with curves module so that you can automatically find the shortest path between two points (maybe the tree that your modules extract could be used, too):

The resulting tree in the Slicer core Endoscopy module (if your modules create a curve node as output then that can be used there, too).

We should review what is common between existing and new modules and how to consolidate them, so that they combine all the good properties and features.

What is in the gth818n folder?
What does SegmentLumenFromAxis module do?
How the VIrtualEndoscopy module differs from the Endoscopy module in Slicer core? Could they be merged into a single module?
Could we make some segmentation features available in the Segment Editor as effects?

These could be all great projects for the upcoming project week.

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And this paper for short: Nain D. An interactive virtual endoscopy tool with automotive path generation[D]. Massachusetts Institute of Technology, 2002.
Shows the centerline idea.
This does not affect the innovation of the project。