The Story of TotalSegmentator

Jakob Wasserthal
University Hospital Basel
The task

I need a segmentation of the left ventricle in my CT image.

Manually

15 years ago

Manually

15 years ago
Manual contour of the left ventricle

Draw the contour
by hand.

Slice by slice.

Deep Learning

10 years ago
PyTorch
Framework
PyTorch
+
U-Net
Architecture
U-Net
+
Programmer
Expertise
PhD
+
GPU
Compute
Lots of GPU
+
Manual annotation
Training data
Manual labels
Time to your segmentation→ 1 year

Deep Learning

10 years ago

You also need the
left atrium?

Start again from zero!

Left ventricle and left atrium contours

nnU-Net

5 years ago
PyTorch
Framework
Built in
+
U-Net
Architecture
Self-configuring
+
Programmer
Expertise
PhD Coding
+
GPU
Compute
Lots A bit of GPU
+
Manual annotation
Training data
Manual labels
Time to your segmentation→ 1 year 1 month

TotalSegmentator

3 years ago
PyTorch
Framework
Not needed
+
U-Net
Architecture
Not needed
+
Programmer
Expertise
No coding
any doctor can do it
+
GPU
Compute
No GPU
+
Manual annotation
Training data
Pretrained
Time to your segmentation→ 1 year 1 day

TotalSegmentator

3 years ago
TotalSegmentator heart segmentation, axial
TotalSegmentator heart segmentation, oblique
TotalSegmentator: what is it?

A pretrained nnU-Net that automatically segments over 300 anatomical structures in CT scans, right out of the box.

Robustness

Random data from PACS (n = 1559)

Dataset distributions
Pathology distribution
Tube current and kVp distribution
Wasserthal et al. TotalSegmentator: Robust Segmentation of 104 Anatomic Structures in CT Images. Radiology: AI (2023)

Automatically segments >340 structures

Overview of segmented classes
Body trunk, hip implant, skin, intracerebral hemorrhage
Coronary arteries, lung vessels, effusions
Wasserthal et al. TotalSegmentator: Robust Segmentation of 104 Anatomic Structures in CT Images. Radiology: AI (2023)
How to use

Three ways to run it

1
Python
Command line or Python API
$ pip install TotalSegmentator
OR
2
3D Slicer
Extension, with a graphical interface
TotalSegmentator
OR
3
Web
Upload in the browser
www.totalsegmentator.com
Usage worldwide
>100,000
users
>250,000
images processed per day

How do we use this in our clinical routine?

Clinical integration

Lung Report

Automatic quantification of

Emphysema
Pleural effusion
Pericardial effusion
Lung CT with emphysema overlay
Lung Report
Lung report
Next

Future

~2027

Preview:
cine MRI heart segmentation

Thank you

to the entire USB radiology research team

github.com/wasserth/TotalSegmentator

QR code to TotalSegmentator on GitHub

Backup

Clinical integration

Abdomen Volume Report

Organ volume in reference to the overall population

Organ volume report: abdomen
Spleen volume vs. population
Lumbar vertebrae vs. population
← → navigate · F fullscreen · O overview · N notes