Frequently Asked Questions

Table of Contents


Which medical imaging formats are supported by Vesalius3D?

  • Stacks of 2D images stored in most common bitmap formats, including BMP, Dr. Halo CUT, DDS, EXR, Raw Fax G3, GIF, HDR, ICO, IFF, JBIG, JNG, JPEG, JPEG2000, KOALA, Kodak PhotoCD, MNG, PCX, PGM/PPM, PNG, Macintosh PICT, Photoshop PSD, Sun RAS, SGI, TARGA, TIFF, WBMP, XBM and XPM
  • Stacks of 2D DICOM (DCM) files of any modality, including CT, MRI, PET, PET-CT, and SPECT-CT, including JPEG2000 encoded 2D DICOM files
  • 3D DICOM files using Cartesian Export from Philips iE33 ultrasound devices
  • 3D VolDICOM files using GE Vivid Ultrasound devices
  • 3D MRC files, a file format for electron density
  • 3D Image Cytometry Standard files (ICS) for microscopic data

Which imaging modalities are supported by Vesalius3D?

  • Ultrasound (Echo), CT, MRI, PET, PET-CT, SPECT-CT:
    • Stacks of 2D DICOM (DCM) files of any modality, including CT, MRI, PET, PET-CT, and SPECT-CT, including JPEG2000 encoded 2D DICOM files
    • 3D DICOM files using Cartesian Export from Philips iE33 ultrasound devices
    • 3D VolDICOM files using GE Vivid Ultrasound device

Can I load multiple datasets simultaneously in Vesalius3D?

Yes you can. Select multiple datasets in the Library and choose the “open” functionality (CRTL+O) or use the “add”, “add recent” or “add from Library” functionality.

Can I load directly into Vesalius3D or do I need to use the Library?

Yes, data can be loaded directly into Vesalius3D. Browse to the folder storing the data, select the desired data file, and click “Open”. Note that this dialog only supports data formats that store a volumetric dataset in a single data file. When a set consisting of multiple separate images should be opened, the data first has to be imported using the Vesalius3D Data Library.


How can I easily fly through the data in Vesalius3D?

The “near plane” is a special plane for the 3D window. It allows users to traverse (fly through) the dataset. It is a cropping plane between the user and the 3D dataset. The plane is fixed and the user can drag the data through the plane creating a first world perspective. “Window – Add Near Plane” or clicking the “right mouse button” in the 3D view and selecting the “Add Near Plane” functionality.

How do I orientate a dataset using the mouse and keyboard in Vesalius3D?



Dolly (pull dataset closer)

Ctrl + left click

Ctrl + middle click


Left click


Alt + left click

Shift + right click


Shift + left click

Shift + middle click

Middle click

Alt + middle click


Right click

Ctrl + right click

Alt + right click

What is the difference between a orthogonal and an oblique cropping plane?

Ortogonal planes move along the 3 axis of the data. The planes that share an axis have similar colors. The left and right cropping planes are red, the anterior-posterior planes green and the inferior superior planes are blue.

Oblique planes can be positioned and oriented freely in the 3D view. Oblique planes are shown in a brown-ochre color. When additional oblique planes are added, these planes get a different color.

How is the near plane different from an oblique plane?

The near plane is a cropping plane between the user and the 3D dataset. The plane is fixed and the user can drag the data through the plane creating a first world perspective. (Fly through experience). There is only one near plane.

An oblique plane is not fixed and can be oriented freely though the data and the 3D space.  There can be multiple oblique planes.


What does the high resolution visualization functionality in Vesalius3D do?

By default Vesalius3D is optimized for performance. For a higher quality of the visualization(s) the option “High Resolution Lighting” can be selected.

It is activated via “Window – High Resolution Lighting” or clicking the “right mouse button” in the 3D view and selecting the “High Resolution Lighting” functionality.

When the visualization settings are changed the “High Resolution Lighting” functionality switches off.

Can I optimize Vesalius3D for performance and for visualization?

The “Quality” slider (next to each visualization in the datasets panel) allows the user to alter the ratio between the quality of the volume rendering versus the speed of the rendering. The higher the quality is set (slider to the right), the more the rendering speed is impacted. This depends on the quality of the system on which Vesalius3D was installed.

A second optimization is a result of selecting the “render resolution”. This setting allows you to toggle between 8-bit and 16-bit resolution. Enabling 16-bit resolution does impact rendering performance, and degradation in interaction speed may be noticeable. Activating 16 bit rendering is done in the settings menu (“File – Settings – Application”).

Unexpected results

Vesalius3D crashed what should I do?

It is very unfortunate that Vesalius3D crashed and it should of course not happen. Please try again and see if the problem reoccurs. If this is the case, please contact with a description of your workflow before the crash and we will help you the best we can.

After loading a dataset, Vesalius3D tries to open a “Presets” window. This window remains empty and Vesalius3D closes. Why?

There seems to be an issue with your graphics card in combination with rendering the data in the 3D-View. Please contact to help solve this issue.

After loading a dataset, my 3D-View remains black and I do not see my data. My 2D-Views however do show the data. What is happening?

This means that the graphical computing power on your computer is not sufficient. There sadly is no way to use Vesalius3D with this graphics card. In order to use Vesalius3D please upgrade your graphics card, see the System Requirements.


Is there a limit to the Vesalius3D Library?

It is limited to the size of the hardware you installed the Library on.

I uploaded new data into the Library, where is it?

The Vesalius3D Library has many search functionalities to locate your data. An easy way is to type the patient name or the current data into the search field.

Where is the Library on my computer?

Under “File – Settings – Database Settings” , the database location is shown.


When I save my work in Vesalius3D how can I find it?

States can be found in the Library and after opening a dataset (combination of datasets)

From an open dataset  states can be found under “Presets – Open Presets – Presentation States”. Thumbnail(s) of the state(s) of the dataset or combination of datasets are now shown.

In the “Library” datasets with a state or mulitple states have a checkmark in the column State. Thumbnail(s) of the state(s) will be shown in the Presentation States window when the corresponding dataset is selected.

I seem to be missing some presentation states. Where did they go?

Vesalius3D displays presentation states of datasets in the Library. If you feel that all associated datasets are in the Library, then press the “Reload States” button in the “Database Settings” tab of the “Settings” menu.

What is the difference between a state and a protocol?

Protocols are not related to datasets. They apply to all data that matches the set of rules in the protocol. States are related to only a specific dataset or combination of datasets.

System requirements

What hardware do you recommend for Vesalius3D?

For optimal performance we recommend these (or higher) system specifications:

Operating SystemWindows 10
Video CardNVIDIA GTX 950 or AMD R7 370
ProcessorIntel Core i5

Can I use Vesalius3D on systems not meeting the hardware recommendation?

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.

Can I use Vesalius3D on MAC OS or Linux?

Sadly, this is not yet possible. Vesalius3D is optimized to work with Windows and no MAC OS or Linux support has been implemented yet.


Can I still use Vesalius3D when I do not update to the latest version?

Yes you can. You are however missing out on the latest features and developments. It is recommended to keep your version of Vesalius3D up to date to ensure the best working version of Vesalius3D.

How can I verify that my Vesalius3D is 100% up to date?

Under “Help – About Vesalius3D” you can find information about your current version of Vesalius3D. As Vesalius3D has two updates per year you can assume that a version older than 6 months needs to be updated.  Starting in Version 2.6 there is a button to check if there is a new version available.

From version 2.5, under “Help – License Information” the currently installed version and the most recent released versions are listed. If your version is older, than the most recent released version, you can update to newer version.


I would like to purchase Vesalius3D, why do i need a subscription?

Vesalius3D is continuously improved. We want our users to have access to the most up-to-date version therefore you receive a license for one year including all updates.  After the first year, you can optionally renew your license at a discounted price to continue to receive updates.

Are discounts available when I buy multiple licenses of Vesalius3D?


5 – 10 licenses5% discount
10+ licenses10% discount
20+ licensesContact our sales department

Are academic discounts given?

No, we currently do not give academic discounts.

Are site wide licenses available?

Yes, if you want to install Vesalius3D on more than 10 computers you can obtain a site license.  Please contact our sales department

Can I use the same license on multiple computers?

No, a Vesalius3D license is a single computer license. If you want to use Vesalius3D on multiple computers you need multiple licenses.

Can I become a reseller for Vesalius3D?

Yes. Resellers commit to 20+ licenses per year. Please contact our sales department


Where can I find instruction videos for Vesalius3D?

Instruction Videos come preinstalled with Vesalius3D. You can find them under “Help – Instruction Videos”.

Instruction Videos are also available online

Where can I find Manuals for Vesalius3D?

Manuals come preinstalled with Vesalius3D. You can find them under “Help – User Manuals”.

Manuals are also available online

Where can I find the End User License Agreement (EULA) of Vesalius3D?

You can find in the folder where you installed Vesalius3D.