Scaffold Viewer

Some datasets are registered to an anatomical scaffold, i.e. a 3D model of some anatomy of interest. Such datasets can be viewed using the scaffold viewer, either via the Data & Models tab or via the SPARC Apps tab.

ScaffoldVuer: Scaffold visualization on the SPARC Portal

ScaffoldVuer is the javascript front end application written using Vue.JS framework to visualize scaffolds. It currently accepts an in house json format, OBJ, STL and GLTF format. It has the capability to export currently visualized objects with the GLTF format.

• Scaffoldvuer demo
• Example of an accepted generic brainstem scaffold on Portal
• Repository and documentation

Anatomical scaffolds

Access to anatomical scaffolds can be done either through the flatmap itself or through the sidebar, as illustrated here.

Access the scaffold viewer via the Data & Models tab

From the SPARC homepage

1. Click on the Data & Models tab (this will open the page below);
2. Click on the Anatomical Models button; and
3. Click on the Generic pig heart scaffold dataset.

Clicking on the Generic pig heart scaffold dataset will open a new page (see below):

1. Click on the View Scaffold button (this will show the Gallery tab) or simply on the Gallery tab; and
2. Click on the (second) View Scaffold button.

Clicking on the (second) View Scaffold button will open a final page with the integrated maps viewer on it and with the scaffold viewer within it (see below). After collapsing the sidebar, you can:

1. Interact with the scaffold itself;
2. Decide which regions to show / hide;
3. Change the background color; and
4. Open a new map (AC Map, FC Map or 3D Map)
5. Zoom in / out and reset the zoom level (you can also do so using your mouse).

Access the scaffold viewer via the SPARC Apps tab

From the SPARC homepage

1. Click on the SPARC Apps tab (this will open the Apps page);
2. Click on the View AC Map to open the Anatomical Connectivity (AC) flatmap;

From the Maps page

1. Click on the button to expand the sidebar;
2. Search for a dataset using the Search field (here, we use stomach as a search term) and click on the Search button (this will list all the datasets that match your search term(s));
3. Filter the results using Scaffold as a data type;
4. Click on the right arrow button until you see the scaffold data type or ask for only scaffold data types to be shown; and
5. Click on the View Scaffold button.

Clicking on the View Scaffold button will open the scaffold viewer and offer the same interface as above: