Integrated Maps Viewer

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

From the SPARC homepage

1. Click on the Maps tab (this will open the page below).

By default, the integrated maps viewer shows a rat flatmap. This is done using the flatmap viewer, from which anatomical scaffolds, data, and simulations can be accessed.

Flatmap viewer

The flatmap viewer consists of a zoomable map that includes various anatomical features associated with a particular species (rat, 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, except the Rat flatmap, are currently beta features);

2. Search for a particular anatomical feature;

3. Open the corresponding 3D version of the flatmap (available for Human Female, Human Male, and Rat; note that all 3D maps are beta features);

4. Either:

   • Split / rearrange the different views;
   • Show / hide some tooltips;
   • Toggle the fullscreen mode; and
   • Get a permalink for the current view(s).

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. Change the background color, as well as the way organs are rendered; and

10. Zoom in / out and reset the zoom level (you can also do so using your mouse).

Flatmaps

From a flatmap, you can:

1. Click on a given marker (e.g., the heart marker) to open the sidebar and show all the datasets related to it (e.g., 40 datasets are related to the heart; 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 spinal cord); and
3. Select a particular neuron or group of neurons (e.g., the Neuron type aacar 13) to get some information about them.

3D maps

Clicking on the Open 3D Map button in the flatmap viewer will open the 3D map viewer (see below) which has some of the features found in the flatmap viewer, as well as the ability to:

1. link the flatmap and its corresponding 3D version, or keep them independent 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); and
4. Filter the results using several constraints (e.g., filter all the datasets that match both Dog and Colon).

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.