How to annotate Bronchopulmonary segments in CT on 3D Slicer ?

Support
1

Hello to all the community here,

Me and my research team are currently hitting a wall in trying to identify a process in 3D slicer to annotate Bronchopulmonary segments in CT with 3D Slicer.
Which brings me on this forum to ask for help!

Thanks in advance,
Joris

2

Hello Joris,

You may want to try the Lung CT Segmenter module of the Lung CT Analyzer extension which includes an option for airway segmentation.

image

I manually annotated one of the segmentations like this:

image
image724×695 65.1 KB

There is no computerized bronchopulmonary segment annotation available in Slicer yet - it would probably be interesting to train AI on a set of segmentations to do this automatically or use the VMTK for centerline calculations.

3

Hi,
I am an Interventional Pulmonologist and for us all navigating to a PPL (Peripheral Pulmonary Nodule) is the most important aspect to reach and do some diagnostic work… I wish to know if Slicer has a fly-through option endoscopically and if any code can be written for the same? I am a doctor and can’t write code I would appreciate if someone from the Slicer team can help as this it is the most important function with which we can be supported. This would be useful for all Interventional Pulmonologists

Another application is when patients have airway abnormalities and we could be helped with 3D models for stents (moulds) making,…

Can someone please connect and help

Warm Regards
Dr Kedar Hibare
Interventional Pulmonologist
Narayana Health City Bangalore India
kedarhibare@gmail.com

4

The built-in endoscopy module provides some of that functionality. You can add more tools with the VMTK extension and the Chest Imaging Platform.

https://slicer.readthedocs.io/en/latest/user_guide/modules/endoscopy.html

5

Hi Rudolf,
Thanks for the suggestion, I’ll take a look at this module!
But I have a strong intuition that bronchopulmonary segments can be annotated using a wise combination of the existing segmentation tools in Slicer. A more experienced user could come up with it. To me the difficulty lies in drawing huge cuts, in dividing the wider lung region into the smaller segments, I ignore what tool can perform this operation from a set of points placed on the segments border for example.
image