How to implement lobe and vessel segmentation in Lung CT Segmenter?

@Eserval and @rbumm, both thoracic surgeons, have been in a video call recently to address the above question.

@Eserval demonstrated his excellent segmentation recipe (100% 3D Slicer) which consists of:

  • Lung mask and airway segmentation with Lung CT Segmenter
  • Creating a vessel mask
  • Creation of empty a PV and PA segment
  • Manual placement of seeds in the pulmonary vein and pulmonary artery (complicated stuff)
  • Grow from seeds vessel segmentation “inside vessel mask”
  • Creation of upper, middle and lower lobe segments (left) and upper and lower lobe (right)
  • Slice painting inside right or left lung mask in the lobe segments
  • Fill between slices to complete the lobes
  • Duplicate the lobes into lung segments
  • Use the “Scissor” function to isolate each individual lung segment
  • Use “Level tracing” to segment the tumor

The procedure usually takes @Eserval about 1-2 hours. @Eserval if possible please add some cooking stage images and a final result - or a link to a youtube video …

@Eserval and @rbumm agreed on closer cooperation, moving parts of this recipe into the lung CT segmenter, and establishing this thread to collect additional ideas from the community. The final goal will be a semiautomatic planning tool for lung surgery, maybe an additional module in the Chest Imaging Platform.


Great. I’m eager to see some pictures

Hello everyone,

Thanks Rudolf for the post. I`ll post the materila ASAP.


Great, it would probably best to get details included in 3D Slicer recipes:

and post one result image here in this thread.

Here is the final product of the segmentation. We use it in our institution to plan lung resections.
That case was an S6 segmentectomy where the 3D reconstruction helped manage an anomalous vein for the S2 segment.

We have an almost done video publication that includes an explanation of the steps. I’ll post on the Segmentation Recipes ASAP.



1-2 hours sounds great! I usually need 4-8hrs but with loads of manual structure coloring with a digitizer pen. were you able to post your workflow to Recipes? could you point us to a link? thanks a lot!