scaffold-icon Scaffold Viewer


Some datasets in the SPARC knowledgebase search results are registered to an anatomical scaffold: a 3D model of the anatomy of interest. This is indicated by the 3D box icon shown at the top of this page. To click on the icon in the search results opens a Scaffold Viewer tab in which the scaffold and embedded data can be viewed and interacted with in 3D. The following image of the Scaffold Viewer tab shows a fitted rat stomach scaffold with neurite data from Powley et al.

Scaffold viewer tab

Interaction and Viewing

Moving the mouse pointer over the scaffold or embedded data highlights and overlays a label for what is under it. With an entity highlighted, to click the left button performs a search for the label terms in the SPARC knowledgebase. The search can bring up related datasets for the study, allowing further viewer tabs to be opened.

Interactively rotating, zooming and panning the view gives a greater understanding of the 3D structure. Hold down one of the mouse buttons and drag to change the view. The following table lists the controls.

Mouse action Result
left-click Search knowledgebase for highlighted entity
Left-drag Rotate
Middle-drag, wheel Zoom
right-click Pan

On some systems, e.g. macOS, modifier keys Ctrl, Alt, etc. may be used in place of different buttons.

Some Scaffold views may contain time-varying or multi-state data. In these cases, a slider control is shown to change the time or state, and a play button enables animation between states. These controls are shown in the above rat stomach Scaffold viewer.

Viewer Configuration

The open-control icon at the top-left corner of the window brings up a menu of additional viewing controls:

  • Reset View - Restore the initial view of the scaffold to the default state.
  • View All - Zoom in/out to see all of the scaffold in its current orientation.
  • Visibilty Controls - Checkboxes controlling the visibility of each entity.

To click on the open-control icon closes this menu.