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Overview of Integrated Maps Viewer

How to interpret information on the flatmaps, anatomical scaffolds, and data viewers?
Updated at: 07/21/2021

Introduction

The Integrated Maps Viewer of the SPARC Portal provides interactive access to a growing collection of data, maps, and computational studies that focus on the autonomic nervous system's role in controlling organ function.

Integrated Maps Viewers

Let’s learn about the maps visualization interface where you analyze the interactive maps which reveal the anatomy and functional relationships of the autonomic nerves and the organs that they innervate.

Flatmap Viewer

The flatmap is a zoomable map representing anatomical features to search for knowledge about those features on the map. The flatmap viewer is the first interface you would discover while exploring the maps visualization interface.

Flatmap window

The Help icon icon provides quick help to understand how to get started with this maps visualization interface.

Help window

On the left-hand side of the flatmap window, there is a menu that allows you to select a species of interest and to the right side of this window are some self-explanatory icons.

Species Menu List

By default, all the neural pathways are displayed. You may control the visibility of each pathway by selecting the respective neural pathway checkbox.

Pathways Window

On the species-specific flatmap, you would come across several inverted-drop-shaped icons called the markers.

Maker Image

These markers provide options to view the 3D scaffold, data, and the simulation, etc., associated with the anatomy of interest.

Marker Options

Explore data

Every markerMarker Icon provides an option to search for a dataset related to different organs and nerves.

  1. On the species flatmap, hover over the marker of the region of interest.
  2. Click Explore data on the pop-up window that appears on hover.
  3. On the new tab, the webpage displays all the datasets related to the area under study.

Explore simulations

The markersMarker Icon allow us to view the simulation of different organs and nerves.

  1. On the species flatmap, hover over the marker of the region of interest.
  2. Click View simulations on the pop-up window that appears on hover.
  3. On the new tab, the page displays all the simulations of the mathematical model related to the area under study.

View 3D scaffold

The markersMarker Icon allow us to view the 3D scaffold of an anatomical organ.

  1. On the species flatmap, hover over the marker of the region of interest.
  2. Click View 3D scaffold on the pop-up window that appears on hover.
  3. A new pop-up window displays the 3D scaffold of the organ of the study.

3D Heart Scaffold Viewer

Some of the SPARC datasets are registered to an anatomical scaffold: a 3D model of the anatomy of interest. 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. The left-click 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

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

Left-clicking over the embedded data opens 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

Data Viewer

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