SlicerSeqSeg Extension

numisveinsson
Fri, 10 Apr 2026 17:29:06 +0000
Development

Hi everyone,

I’m sharing SeqSeg, a new 3D Slicer extension for seed-based segmentation of tubular/vascular structures from CT or MR. You place two fiducial seeds and a radius estimate; the module runs the SeqSeg pipeline (with nnUNet) and loads the segmentation (and optional surface mesh) back into Slicer. Pretrained weights can be pulled from Zenodo via a button in the module UI.

Source / documentation: https://github.com/numisveinsson/SlicerSeqSeg

Underlying method (Python package): https://github.com/numisveinsson/SeqSeg

Publication

Sveinsson Cepero, N., Shadden, S.C. SeqSeg: Learning Local Segments for Automatic Vascular Model Construction. Ann Biomed Eng 53, 158–179 (2025). https://doi.org/10.1007/s10439-024-03611-z

I’m planning to submit the extension to the Slicer Extensions Index so it can be installed from the Extension Manager; until then it can be used by adding the module path or building from source as usual.

Feedback, bug reports, and collaboration ideas are welcome—either here or on GitHub issues.

Thanks,
Numi

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