Vesalius3D Overview

  1. Menu bar – Basic operations
  2. Controls bar – Access to frequently used functionality
  3. 3D view
  4. Right click – Context menu
  5. 2D views
  6. 3 pages of grouped functionality
    • Visualisations
    • Measurements
    • 3D printing

Vesalius3D combines high quality volumetric visualization with easy navigation. This combination allows for fast and efficient visualization and understanding of complex volumetric data.


  • Instant patient specific anatomy
  • Reveal details and structures missed using only standard 2D slices
  • Fly around inside the patient
  • Easy to use and filled with functionality

Easy to use and filled with functionality

Vesalius3D presents 2D and 3D window simultaneously, allowing to work in 2D and 3D, exploiting the benefits of both views.

Vesalius3D is an easy to use application, with a short learning curve. Just upload the data and Vesalius3D provides instant access to most used visualizations. Presets are offered to quickly go to a specific Visualization and allow a user to save the work done on a dataset.

Most 3D formats such as DICOM, STL and stacked JPG are supported. Simultaneous rendering of multiple datasets from different modalities is offered.


Presets define how data is presented to the user. They are efficiency tools used to present the user a visualization fast (Visualizations) or to save the work done on a dataset (States).

Starting Visualizations
Starting visualizations are a set of most used visualizations to quickly present the user a visualization of the desired tissues. Vesalius3D comes with standard visualizations for CT MR and Ultrasound. Users can add, modify and change visualizations and so customize Vesalius3D for their specific workflow.

States are a powerful tool to store your work and be able to get back to the exact view and layout later. The state saving functionality stores all settings related to a specific data set: view layout, visualizations, cropping planes, measurements and extractions.

Data Viewing

Vesalius3D offers both 2D and 3D windows side by side and customizable to the user’s requirements. All views have full screen support, are detachable, and can be arranged on multiple monitors and screens.

2D windows
Traditional 2D views are offered in conventional axial, coronal, sagittal directions. Oblique planes are available to offer a 2D view of any cross section of the data. Mouse/keyboard interaction is used for moving and zooming in/out, window level and center manipulation, and resetting the view settings.

3D windows
The 3D windows have been designed with ease of use and understanding of 3D structures in mind. The 3D overview windows give the treating physician a clear view and instant insight into the patient specific anatomy.
Point picking allows the user to correlate a specific point in 3D with its corresponding 2D planes.


Vesalius3D provides various tools for measurement. There are 2D and 3D quantification tools.

  • 2D quantification tools include distances, angles, and contour areas
  • 3D quantification tools include distances, contours, angles, and volume segmentations

Extractions and 3D printing

Vesalius3D offers the optimal balance between Visualization, Navigation and Extraction. Extractions enable better understanding of the patient’s anatomy, enhance preoperative planning and are used for education.

The Extraction module of Vesalius3D contains the tools for extraction of anatomical structures from any medical imaging modality. The structures are extracted in a few minutes.

Example of an extraction as highlight in a visualization

Example of a 3D print made from an extraction

Step by step process

Vesalius3D features a step by step process to guide users through the extraction process.
The process is easy and users can see the effect of their actions immediately.

  1. Crop: Mask using cropping planes
  2. Threshold: Mask using bandwidth of data
  3. Erase: Mask to isolate the desired parts
  4. Grow Region: Mask to select the part(s) of interest
  5. Create surface: Use Mask to create 3D structure

The extraction process

How does it work – Masking
Vesalius3D uses masks for extraction.
Masks are filters applied to the data that result in an extraction of the data. Vesalius3D uses a range of masks.
The combination of a set of masks is the extraction.
Typical masks are cropping boxes, threshold values, erasers, previous masks and the possibility to select single or multiple components.


  • Automatic and semiautomatic features to speed up the extraction process
  • Step by step guidance
  • Continuous feedback of actions in 2D and 3D window
  • Export 3D printable files
  • Multiple extractions in one dataset
  • Start from scratch or use a previous extraction
  • Combine or substract extractions

Some examples of how extractions in Vesalius3D are made

Extraction of an aortic arch
Watch this video on Vimeo

Extraction of a baby in the womb
Watch this video on Vimeo

Extraction of a carotis
Watch this video on Vimeo

Data Library

The Vesalius3D Data Library is used to manage and store 3D image data and its corresponding meta data.

The Vesalius3D library supports data of multiple modalities and formats including 2D image stacks in most common formats, various RAW formats, and DICOM images (“.dcm” extension). Vesalius3D is compliant with the DICOM standard for image communication and image file formats. The PACS module allows for query and retrieve of image files from PACS.

Features include:

  • Multiple data types support (including: Philips DICOM in Cartesian format (US), GE VolDICOM (US), DICOM sliced 3D data (MR, CT, etc.), Sliced 3D data in all major image formats, including png, jpg, bmp, tiff, gif, etc, ICS format, MRC format, Tomtec DAT format)
  • PACS support to integrate within hospital workflow
  • Imported data is kept in the original state (no conversion), so no information is lost

System Requirements

Vesalius3D will work on many Windows-based PC’s and laptops (Windows 7 and 10).
Depending the size of the data more resources of your computer are allocated.
The most important feature is your Graphical Processing. The better the Graphical card the better the performance.

A gaming laptop or a pc with a decent video card will normally be sufficient.

Furthermore Vesalius3D has settings to optimize Vesalius3D for a users computer.
See the tutorial video – Optimizing for your PC.

You can use a free trial license to test your configuration.

The Ultimate Human Anatomy VR Experience

Vesalius3D can be used from standard PC’s to Virtual Reality environments with stereo visualization and 3D controllers by using Vesalius3D VR

The ultimate way to experience 3D data is in stereo.
The C-Station is a VR workstation specifically designed for Vesalius3D users.

Vesalius3D VR is used live during conference presentations, group discussions, team meetings, training sessions and in classrooms. Fast understanding and ability to explain patient specific anatomy gives faster learning, better planning, more efficient meetings and less surprises in the operating room.

Release Information

NEW in Vesalius3D 2.7.0

  • Optimized workflow
  • A new start screen
  • MRI visualization improved
  • Importing of data simplified
  • Higher image quality for MRI CT and Ultrasound
  • Settings to optimize Vesalius3D performance on your PC

And more

Previous releases

NEW in Vesalius3D 2.6.3

  • Dark user interface better focus
  • Extended help functionality with manuals, instruction videos, FAQ’s and Keyboard controls
  • Pre-defined visualizations for all datasets
  • Extended functionality in less clicks

And more

NEW in Vesalius3D 2.5.0

  • The Improved library contains states. States are a powerful tool to store your work and be able to get back to the exact view and layout later
  • Improved quantification module. Added functionality and navigation to a specific measurement in a one click action
  • Movies and screenshots can now be made from anywhere
  • Exporting measurements is now possible

And more