Getting Started

When you first launch Visual Anatomy, the app will ask you to enter the license key from your purchase. You can copy the license key from your order, and paste (Ctrl + V on Windows/Linux, Cmd + V on Mac) the key on the entry provided, and click Activate. This action will create an instant association between the license and your PC. You can manage your licenses on the License Key page. This activation process only happens on the app’s first launch. Subsequent launches will skip this step.

The app will then check for any updates. If there is one, it will ask if you want to install the update now. If yes, the app will handle the update automatically. If no, you can always initiate an update process manually from the Tools menu.

Once all checks are complete, the Visual Anatomy homepage with all available options will start. From this window, you can create highly detailed 3D Anatomical models in 4 simple steps:

  • Load Directory containing the CT Scan Images
  • Select Tissue Type of Interest, e.g. Bone
  • Create a 2D Mask overlay on the CT Images, highlighting the selected tissue type
  • Generate a 3D Model

1. Load CT Scan Images

Select New -> New Project, from the top bar menu. From the pop up window, select the folder containing your CT Images.

The 2D Images will load onto the black canvas on the left. The slider provided just above (on mac), or to its right (on windows/linux), can be used to scroll through the images. The 2D images will provide either an Axial, Sagittal or Coronal view, depending on how the scan was carried out.

2. Choose Tissue Type

In many ways, this is the most important step in the process. In this step, you choose what type of tissue you want to view in 3D. A drop down menu is provided on the top left, from which you can select what body tissue you are interested in.

Generation of 3D models is based on Hounsfield Units (HU) values. These values are explained in detail in the Hounsfield Units Page. In short, there are predetermined values that in general correspond to certain types of body tissue. The values come in pairs: Low and High HU values. These provide a threshold within which a particular body tissue can be found in CT Scan Images.

For example, Bone Tissue can generally be found within 226 and 2297 HUs. These numbers are not exact, and will not always produce identical results with different sets of CT Images, however, they may start as a baseline. The values can be adjusted from the two entries found in the top left (highlighted in red). You are free to adjust these values, and use Step 3 below to verify if you have properly isolated the body tissue that you want to view.

3. Create 2D Mask

Use the Create Mask Button to generate a 2D overlay on the CT Images, highlighting the tissue type selected in Step 2. In the screenshot below, the mask indicates bone tissue on each CT Image. Use the slider to scroll through the scans, and verify if the Hounsfield Units selected accurately pick out the tissue you are interested in.

Adjust the HU values, to optimize the area picked out by the threshold, and select the Create Mask Button to recreate the overlay. Repeat this cycle, until you are satisfied with the mask.

The yellow button beneath the Generate 3D Button, may be used to change the colour of the 2D Mask and final 3D model. The default colour is yellow, as exhibited in the screenshots. You may change this colour to any that you wish.

Once the Mask is created, use the toggle button highlighted in red, to turn the overlay on/off as you scroll through the CT Images.

4. Generate 3D Model

Once you are satisfied with the 2D Mask, select the Generate 3D Button to create a 3D Model. This 3D model is derived directly from the mask created in Step 3. The canvas on the right provides a window within which the 3D Model can be manipulated. The 3D window is controlled either by mouse, or by touchpad. These controls are explained in detail in the 3D Controls Page.

The blue bar above all buttons in the top left is a Progress Bar, giving feedback on the computations running in the background. It indicates how far a process is from completion. While it is less than 100%, give the application a few moments to finish all ongoing processes.

Finishing Tools

Visual Anatomy provides 3D finishing tools, ideal if you wish to export 3D Models for further analysis or to create physical models, via methods such as 3D Printing.

  • Fill Holes: This option is selected by default as it is recommended for any finishing process. This function, ensures that the surface of the 3D model is watertight. As the name suggests, it ensures there are no holes/gaps on the surface.
  • Smooth: This option is fairly straightforward. Depending on the density of the slices in the CT Scan Images, the 3D Model may contain more detail than is necessary. When selected, the finishing process will smooth the surface of the 3D Model. This step can be repeated several times, until the surface is to your liking. However, too many smoothing repetitions may eventually reduce the accuracy of the model as small details are lost.
  • Reduce: This option is slightly similar to the Smooth function as it reduces the complexity of the 3D model. This function reduces the number of points used to generate the 3D surface. The greater the number of points, the greater the detail of the 3D Model, and vice versa. This option is useful with models that have more detail than is necessary. The greater the complexity, the greater the file size of exported models. Exported model size can range from 10 MB to 1GB depending on the complexity of the 3D model.

Once you have selected the finishing options that you want, click the Finish Button to initiate the process. The finishing process can be repeated, until you are satisfied with the your final Anatomical Model.

Clear Options

As you follow the steps above, you may wish to restart a process from time to time. Use the clear tools to delete Loaded CT Images, 2D Masks Created and/or Generated 3D Models. This will delete generated data, allowing you to restart any step.

Tip: If you are using a computer with low RAM (8GB or less), you can use these tools to speed up other processes. Once you are done with a step, for example; once you have created a 3D Model that you are satisfied with, you can use the Clear 2D Dicom option to clear all data related with the loaded CT Images. This data uses up the most RAM in the whole application (>50%). Therefore, once you clear up this data, you would free up RAM to carry out other process, and may notice a welcome boost to the speed of subsequent processes.

Useful Tools




As the hints suggest, these buttons perform the following functions:

  1. Toggles the background colour of the 3D window, alternating between black (default) and white. This gives you an option to work with a background that you are comfortable with.
  2. Takes a screenshot of the 3D window, and raises a prompt asking you for a location and name with which to save the screenshot in PNG format. This allows you to easily share images of your analysis, to whoever you like.
  3. Opens up a prompt, from which you may select any colour that you wish to convert the generated 3D model to.