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Integrated Maps Viewer

The integrated maps viewer can be used to access and interact with flatmaps / 3D maps, anatomical scaffolds, data, and simulations.

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The integrated maps viewer can be used to access and interact with:

  • Flatmaps / 3D maps;
  • Anatomical scaffolds;
  • Data; and
  • Simulations.

Access the integrated maps viewer

There are two ways to access the integrated maps viewer.

  1. From the SPARC homepage
  2. From the SPARC Apps page

From the SPARC homepage:

  1. Click on the View the Maps button (this will open the Maps page directly).
    1. By default, the integrated maps viewer shows a human male Flatmap. This is done using the flatmap viewer, from which anatomical scaffolds, data, and simulations can be accessed.
  2. Click on the SPARC Apps from the navigation (this will go to the SPARC Apps page).

From the SPARC Apps page:

  1. Click View AC Map to open the default Anatomical Connectivity flatmap (human male) or click the available species.
  2. Click View 3D Body to open the 3D whole-body scaffold.
  3. Click View FC Map to open the Functional Connectivity flatmap.

Flatmap viewer

The flatmap viewer consists of a zoomable map that includes various anatomical features associated with a particular species (human male, by default). From the flatmap viewer, you can:

  1. Change the species of interest (Human Female, Human Male, Rat, Mouse, Pig, and Cat; note that all flatmaps are currently showing beta connectivity features);
  2. Search for a particular anatomical feature;
  3. Either:
    • Split / rearrange the different views;
    • Open help mode to see tooltips with information about each feature on the map;
    • Toggle the fullscreen mode; and
    • Get a permalink for the current view(s).
  4. Show information of the Map;
  5. Use the minimap to navigate the (zoomed-in) flatmap;
  6. Interact with the flatmap itself;
  7. Show / hide the sidebar (where you can search for specific datasets);
  8. Decide which neural pathways to show / hide;
  9. Open new map; it can be AC Map, FC Map, 3D Human Map, or Sync Map;
    (Open Sync Map will open a 3D map viewer in split screen as shown here)
  10. Change the background color, viewing mode, flight path display (2D/3D), the way organs are rendered; and
  11. Zoom in / out and reset the zoom level (you can also do so using your mouse).
  1. Switch to 3D on the flight path display and use mouse right-click to rotate the 3D map.

Flatmaps

From a flatmap, you can:

  1. Click on a given marker or a feature dataset marker (e.g., the Pancreas marker) to open the sidebar and show all the datasets related to it (e.g., 3 datasets are related to the pancreas; note that this hides all the other markers which can be shown back by removing the filtering in the sidebar);
  2. Select a specific anatomical feature (e.g., the brainstem); and
  3. Select a particular neuron or group of neurons (e.g., the Neuron type aacar 13) to show neuron and connectivity information in the sidebar.

3D maps

3D maps can be opened from the Open new map tooltip.

  1. Click the Open 3D Human Map to open the 3D Human Map in the full map area.
  2. Click on the Open Sync Map to open the 3D map viewer in split screen;
  3. The corresponding 3D version is linked with the flatmap by default, or it can be unlinked independently from one another.

Sidebar

The sidebar can be used to:

  1. See all the datasets that are currently available;
  2. Search all the datasets that match one or several keywords (e.g., all the datasets that match stomach);
  3. Filter the results using one constraint (e.g., filter all the datasets that match Dog);
  4. Filter the results using several constraints (e.g., filter all the datasets that match both Dog and Colon); and
  5. Click the search history values to show the recent search.

Sidebar dataset cards:

  1. Mouse over the sidebar dataset card will highlight the feature on the flatmap.
  2. Clicking the View Dataset button (e.g., View Dataset 99) will open the dataset page.
  3. Clicking the data type buttons (e.g., Scaffolds (1)) will switch the thumbnails to scaffold thumbnails, and it will show the View Scaffoldbutton; clicking that will open the scaffold.
  4. Clicking the copy to clipboard button will copy the information of the dataset card to clipboard.

When the Connectivity tab is opened in the sidebar by clicking a neuron on flatmap (e.g., clicking "Neuron type bolew unbranched 10"), the information in the connectivity tab is connected with the sidebar's Search tab and also with the flatmap.

  1. Clicking Explore origin data, Explore destination data, or Search for data on components will switch to the Search tab by applying the connectivity data in filters.
  2. Clicking Show connectivity on map will move the map to show the highlighted area.
  3. Clicking Copy to clipboard button will copy the connectivity information to clipboard.

Anatomical scaffolds

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

Data

Access to data is done through the sidebar where you can search for datasets that contain data that can be rendered using the Data viewer. For instance, open the sidebar and:

  1. Search for RAGP (i.e. right atrial ganglionic plexus);
  2. Click on the Plots (4) button;
  3. Click on the View Plot button;
  4. Click on the right arrow button and go back to step 3 until you have opened all four plots;
  5. This is how one plot is initially rendered; and
  6. This is how all four plots are eventually rendered using the 4-page view.

Simulations

Access to simulations is done through the sidebar, as illustrated here.

Updated about 1 month ago