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Overview of Scaffold Viewer

Information about the scaffold viewer.
Updated at: 08/04/2021

Some of the SPARC datasets are registered to an anatomical scaffold: a 3D model of the anatomy of interest. Below are the two ways to navigate to the scaffold viewer on the SPARC Portal:

  1. Exploring Scaffold Viewer through the Flatmap

    Go to Maps tab -> On the Flatmap, hover over the marker (inverted-drop-shaped icons) -> Click View 3D scaffold.

    Flatmap Scaffold

  2. Exploring Scaffold Viewer through Datasets

    Go to Find Data tab -> Choose a dataset -> Select the Gallery tab -> Click on the image thumbnail with the yellow-colored box to the top-right.

    Dataset Scaffold

Exploring Scaffold Viewer through the Flatmap

Hover over the marker on the species flatmap and click View 3D scaffold on the pop-up window to open a scaffold of the organ of study where embedded data can be viewed and interacted with in 3D.

Moving the mouse pointer over the scaffold or embedded data highlights the region under study. Left-clicking at a particular location displays the region name along with highlighting the region checkbox providing the flexibility to select/unselect a specific region.

Note: You may alter the transparency of a highlighted region through the opacity option accessible at the right of the scaffold window.

Heart Scaffold Left-click over the embedded data to open a new window that provides a brief description of the RNA-Seq data along with options to explore datasets and view the ICN plot.

ICN plot image

The RNA-Seq results are visualized using the heatmaps. By default, the heatmap enables you to see the expression of all genes in all the cells/samples from the different groups in the experiment.

You can also create a heatmap for a custom set of genes. To visualize these genes:

  1. Select gene - Choose genes from the list.
  2. Select cell/sample - Choose cells/samples from the list.
  3. Click View Heatmap.

Data viewer 1

Clicking on the dataset available at the top center allows you to download the dataset. Click Get Dataset.

Data viewer 2

On the new page, you will get the complete information of the dataset along with the option to download by clicking the Get Dataset button.

Get Dataset Image

Interactive Graphics Controls

Interactively rotating, zooming and panning the view gives a greater understanding of the 3D structure. To do this, left-drag to rotate, scroll wheel to zoom and right-drag to pan the 3D scaffold. On some systems, e.g., macOS, modifier keys Ctrl, Alt, etc. may be used in place of different buttons. The interactive graphics controls are explained below:

  • Zoom in/Mouse wheel upward movement (Pushing it away from yourself) - Helps to examine the object of interest in greater detail.
  • Zoom out/Mouse wheel downward movement (Pulling it towards yourself) - Helps to examine the object of interest in a wider view.
  • Reset view - Restore the initial view of the object of interest to the default state.
  • Change background color - Modifies the color of the background.
  • Toggle fullscreen - To switch between fullscreen and default window mode.
  • Help - A guide to assist you to explore SPARC's mapped data.
  • Resize
    • Use 1 - Enlarge and dock the window on the Maps toolbar.
    • Use 2 - Undock window from the Maps toolbar and reduce the window size to default.
  • Dock
    • Use 1 - Fixed in position on the Maps toolbar.
    • Use 2 - Move to the Flatmap tab.
  • Close - To exit an application window.

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.

Stomach Window

Exploring Scaffold Viewer through Datasets

Exploring the scaffold viewer thorough the second way (Find Data -> Choosing a Dataset -> Gallery tab) launches a webpage providing the file details in addition to the Scaffold Viewer. The left-click at a particular marker (inverted-drop-shaped icons) highlights the region checkbox providing the flexibility to select/unselect a specific region. Refer to the Interactive Graphics Controls to learn how to interact with the scaffold viewer.

ScaffoldViewer FindData