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Getting Started

Vesalius3D is an easy to use, intuitive, medical imaging application.

Vesalius3D is easy to use and comes with a wide range of functionalities. New users will be up and running fast.

Within minutes users can:

  • Use presets (starting visualizations)
  • Fly around the data and zoom into areas of interest
  • Optimize and toggle between visualizations
  • Create movies, screenshots and measurements in both 2D and 3D windows
  • Work with the Vesalius3D library
  • Export Dicom or STL file (for 3D printing)

Vesalius3D Overview

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

Most 3D analysis software packages evolved from 2D analysis software and are built upon a 2D foundation. Vesalius3D is different; it was built around a unique 3D rendering engine, combining traditional 2D views with an easy to use 3D view. Vesalius3D renders live. Actions of users are immediately seen in the 2D or 3D views.
Vesalius3D was created to give the user the right tools for the task at hand. Access to both 2D and 3D interaction tools is therefore an integrated part of working with Vesalius3D.

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.


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

A protocol contains predefined starting visualizations that allow users to quickly get to the desired point of view and visualization. Using a protocol opens the dataset in a standard visualization and point of view. Within a protocol, multiple visualizations can be stored that allow the user to toggle through a list of preset visualizations.

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, render objects and settings, cropping planes, transfer functions, quantification objects, etc..


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

Extraction and 3D Printing

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.
Depending the size of the data more resources of your computer are allocated.
You can use a free trial license to test your configuration.

For optimal performance we recommend these system specifications:

OS Windows 10
Video Card NVIDIA GTX 950 or AMD R7 370
Processor Intel Core i5