Table 2.
Workflow of segmentation and 3D post-processing
| Segmentation (ImageJ, version 1.53) | Description |
|---|---|
| 1. File → Import Image Sequence | Import the DICOM images as a 2D image stack. |
| 2. Image → Adjust → Window/Level (W&L) | Adjust the window and level to be focused on the vascular structures. |
| 3. Analyze → Tools → ROI Manager | Define the ROI for the whole stack using the “Polygon Selection” tool in combination with ROI interpolation (ROI Manager → More → Interpolate ROIs). |
| 4. Plugins → Macros → Clear Outside Macro | Using the macro defined in Table 1, bones and other high-density structures outside the ROI can be removed from the stack. |
| 5. Image → Adjust → Brightness/Contrast | (Optional) Contrast can be improved to remove residual non-vascular structures (i.e., early contrast-enhanced parenchyma). |
| 6. Paintbrush Tool | (Optional) Remove non-vascular structures slice-by-slice with a black paintbrush. |
| 7. Image → Transform → Flip Horizontally | The image stack has to be flipped horizontally before using the 3D Viewer plugin, caused by the triangulation algorithm. |
| 8. Plugins → 3D Viewer | Generate an STL file using the following parameters: Display as = Surface, Color = White, Threshold = 50, and Resampling factor = 2. After confirming the 8-bit conversion of the stack, a binary STL file can be exported (File → Export surfaces). |
| 3D post-processing (Blender, version 3.0) | Description |
| 1. File → Import → STL | Import the STL file into Blender. |
| 2. Object → Set Origin → Geometry to Origin | Move the object to the center of the scene. |
| 3. Edit mode: Select → Select Linked → Linked | Use the “Select Linked” tool to remove unconnected (unlinked) non-vascular parts of the object (i.e., residuals of parenchyma). |
| 4. Edit mode: Mesh → Bisect | Use the “Bisect” tool to cut the vasculature open (usually, at least the aorta and procedure relevant arteries). Without this step, a closed vascular model will be generated. |
| 5. Add modifier: Subdivision surface | Use the “Subdivision Surface Modifier” to smooth the object and prevent the formation of steps from triangulation. |
| 6. Add modifier: Solidify | Generate vessel walls using the “Solidify Modifier” with a wall thickness of 1 mm. |
The open-source software ImageJ was used for segmentation, while the open-source 3D software Blender was used for post-processing the vascular models.