Segmentation (TPTBox.segmentation)

Integration with external segmentation pipelines. Provides a consistent NII-based interface over SPINEPS, VibeSeg/TotalVibeSeg, and nnU-Net.

Public API

from TPTBox.segmentation import (
    run_spineps,
    run_vibeseg,
    run_totalvibeseg,
    run_nnunet,
    run_inference_on_file,
    extract_vertebra_bodies_from_VibeSeg,
)

Key functions

Function	Module	Description
run_spineps(img_nii, model, ...)	spineps.py	Run SPINEPS spine segmentation on a NIfTI; returns vertebra + subregion masks
run_vibeseg(img_nii, ...)	VibeSeg/vibeseg.py	Run VibeSeg body composition segmentation
run_totalvibeseg(img_nii, ...)	VibeSeg/vibeseg.py	Run TotalVibeSeg — extended label set
run_nnunet(img_nii, model_dir, ...)	VibeSeg/vibeseg.py	Generic nnU-Net inference on a single NIfTI
run_inference_on_file(path, ...)	nnUnet_utils/inference_api.py	Low-level nnU-Net inference on a file path
extract_vertebra_bodies_from_VibeSeg(seg)	VibeSeg/vibeseg.py	Post-process VibeSeg output to isolate vertebra bodies

Dependencies

Pipeline	Requirement
SPINEPS	pip install spineps + model weights
VibeSeg / TotalVibeSeg	pip install nnunetv2 + model weights (auto-downloaded on first run)
Generic nnU-Net	pip install nnunetv2 + custom model directory

All external tools are imported lazily — the core TPTBox package installs and imports cleanly without them.

Example

from TPTBox import NII
from TPTBox.segmentation import run_spineps

ct = NII.load("ct.nii.gz", seg=False)
vert_seg, subreg_seg = run_spineps(ct, model="small")
vert_seg.save("vertebrae.nii.gz")