totalsegmentator

VoxPlane — Cross-platform DICOM viewer for CT, MRI & PET/CT with MPR, 3D, fusion, editable segmentation and local AI auto-segmentation via TotalSegmentator.

TotalSegmentator 2D: A Tool for Rapid Anatomical Structure Analysis

Computes CT contrast phase and GI tract contrast using TotalSegmentator and ML

Automatic 3D model of the left atrium, pulmonary veins and appendage from cardiac CT, fully offline. Built on TotalSegmentator. Research use only.

Swift Horos/OsiriX plugin that exports active CT/MR series, provisions an isolated Python TotalSegmentator environment, runs segmentation, and imports RT-Struct overlays back into the host viewer.

Open, modular MCP server for medical image analysis agents: containerized models (MedSAM2, SAM 2.1, TotalSegmentator, lungmask, HD-BET, SynthStrip, nnU-Net, MONAI, TorchXRayVision), preset/custom guidelines, and a code-customizable viewer.

Desktop CT imaging workstation (PySide6/Qt6) with first-principles CT reconstruction, AI organ segmentation, and quantitative validation. Teaching/research only; not a medical device.

Bone Mineral Density estimation from CT scans using PyTorch

Python CLI that turns heterogeneous DICOM archives into analysis-ready CT/MR cohorts: NIfTI conversion, TotalSegmentator segmentation, contrast-phase curation, registration, PyRadiomics, QC viewer

Peer-reviewed pipeline for automated CT-based pelvimetry and mid-pelvic workspace quantification in rectal cancer.

How much can organ shape alone reveal? Using 1,228 whole-body CTs (16 organs, intensity discarded), we predict sex (AUC 0.87), age (MAE 9.3 yr), and show shape is near-unique per person. Hip bones carry the strongest signal. Shape outperforms intensity for sex — the signal is geometric. Code + reproducible pipeline.

Thoracic lymph node stationing tool for chest CT using TotalSegmentator anatomy, bronchial branch parsing, and IASLC-style rule-based station segmentation.

Self-hosted Radiology Visualization Web app with AI assisted segmentation tools

Research desktop app for DICOM CT visualization, vertebral segmentation, and interactive pedicle screw planning.

Organ-wise analysis of pediatric fine-tuning gains in an adult-trained 7-organ CT segmentation model using TotalSegmentator V3 data.

Batch medical-imaging pipeline that ingests 3D CT/MRI volumes to Backblaze B2, runs TotalSegmentator locally to produce multi-label masks over 100+ anatomical structures plus per-structure volumetrics, and writes masks and stats back to B2. Next.js 16 + FastAPI sample app over the B2 S3-compatible API.

Uncertainty estimation and calibration for nnU-Net ensembles in 3D CT segmentation: deep and checkpoint ensembles, temperature scaling, uncertainty maps, external validation, autoencoder, Streamlit viewers

Research tool for continuous NCC-to-LV-myocardium membranous-septum candidate segmentation on cardiac CTA

Automated analysis of lumbar discs, integrating TotalSegmentator for anatomical localization, PyRadiomics for quantitative feature extraction, and machine learning models for clinical classification (Pfirrmann grading).

Open-source automated aortic segmenter + EVAR planner from contrast-enhanced CTA (MATLAB). Research use only.