| name | total-segmentator |
| description | Tool for robust segmentation of 104+ anatomical structures in CT images. Uses nnUNet-based models for whole-body, organ, and bone segmentation. One-line CLI for comprehensive body-part segmentation. |
| tags | ["medical-image-segmentation","ct-anatomy-segmentation","whole-body-ct","nnunet-inference","total-segmentator"] |
Overview
TotalSegmentator segments 104+ anatomical structures in CT images using nnUNet-based models. Run full-body, organ, or bone segmentation with a single CLI command.
Installation
uv pip install TotalSegmentator
CLI Usage
TotalSegmentator -i input_ct.nii.gz -o output_seg.nii.gz
TotalSegmentator -i input_ct.nii.gz -o organ_seg.nii.gz -ta organ
TotalSegmentator -i input_ct.nii.gz -o bone_seg.nii.gz -ta appendicular_bones
Python API
from totalsegmentator.python_api import totalsegmentator
segmentation = totalsegmentator("input_ct.nii.gz", "output_seg.nii.gz")
Workflow
- Obtain CT scan in NIfTI format
- Run
TotalSegmentator -i input.nii.gz -o output.nii.gz
- Task types:
total (104 structures), organ, vertebra, ribs, appendicular_bones
- Output is a multi-label segmentation mask
- Extract volumes per label for quantitative analysis