Airway segmentation of mouse lung

Support
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1

Hello,

I am working with 3D slicer in hopes to segment the airway of this mouse lung, acquired from lightsheet microscopy. I would like to segment the main airways, but not the alveoli (at least not yet - I am hoping to do this in the future though) to measure the diameter of the airways and how they change in diameter as they get further away from the main bronchial tree. I have tried to use the threshold tool since it is dark in the airways, but I am still picking up the alveoli. I have also tried the grow from seeds module but it seems like it would require a lot of manual effort to get my segments how I would like them. That is fine and I can do the manual painting to fix it, but I was just wondering if there would be a more effective way to do this? I have not been able to use any of the lung/airway modules/extensions since my data is of a single (left) lung of a mouse from lightsheet microscopy and the ones I have seen are for both human lungs from CT. Thank you very much in advance for any advice you have!

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Some extensions that could be helpful are NNInteractive and SegmentWithSAM, both available in the extension manager.

You could try both and see if it at least gives you an easier starting point to work with

For SegmentWithSAM make sure to normalize image values to a 0-255 range. The work would then be layer by layer, but then it gives you a way to propagate your segmentation across slices. I had success solving a similar problem to yours with it. It still takes some fiddling to get the right workflow.

The alveoli are connected and are not isolated islands, right? If they were isolated islands you could use the islands tool in the segment editor and filter out connected components smaller than a certain size. If you have an easy way to make them become disconnected then this also becomes an option