Importing a 3D model

This is relevant for SPARC researchers.

Context

Generic organ scaffolds are available to SPARC researchers to facilitate registration of their segmented data to 3D organ maps (models) produced by the SPARC MAP-Core.

The Import 3D model tool in the 3D environment window will open and display the generic 3D organ scaffold (legacy VTK format) that you specify. It creates left and right viewports in the 3D environment; your segmentation will be on the right and the organ scaffold (3D model) that you import will be on the left.

The Import 3D model tool is designed to make it easier for SPARC researchers to compare key fiducial markers on their segmentation file(s) to the fiducial markers on the generic organ scaffold(s).

Before you start

  1. Download the .vtk file corresponding to the 3D model you want to use from the SPARC Portal. Note that there are several ways to do this, one is described below:

    1. In a web browser, go to the SPARC Portal and type "scaffold" into the Datasets search box at the top right of the web page.

    2. Click the link for the scaffold of interest. From the web page for that data set, click the Files tab, then the derivative folder.

    3. Click the checkbox for the 'mesh' .vtk file and click the Download button.

    4. If the dataset also contains a ‘marker’ .csv file that corresponds to the .vtk file, click its checkbox and download the .csv file as well.

    5. Save the file(s) on your computer in the same directory.

  2. Open your image or image stack. The Welcome dialog is displayed to connect you with the SciCrunch database, an anatomical terminology list (or parcellation list) compliant with FAIR data principles.

    Input Subject information about the image sample and select the Criteria for anatomic terms from the drop-down menus.

  3. Annotate/segment your image data. Place contours and markers using SPARC Terms. Trace trees if desired. Note that you can classify segments of trees with SPARC terms.
  4. Save the data as an XML file (*.xml).

Display a 3D model in the 3D environment next to your experimental model

  1. Click the Import 3D Model button. Then navigate to and select the .vtk mesh scaffold file you downloaded previously.

  2. The scaffold image will be displayed in the left viewport of the 3D environment window, with your data file displayed on the right.

    • You can move each image separately in 3D to compare the scaffold model to your segmentation data.

    • If you have a ‘marker’ .csv file in the same directory as the .vtk file, fiducial markers will appear on the 3D model in the left viewport.

    • If marker names used in your data file match the names of fiducial points on the generic 3D model, the fiducial points on the generic 3D model will change to match the color of the corresponding marker in your data file.