Maps

Maps on the SPARC Portal

The SPARC Portal displays detailed maps of the peripheral nervous system (PNS) based on SPARC data and information available in literature. These include the Anatomical Connectivity (AC) flatmaps, the Functional Connectivity (FC) flatmaps, and the Whole Body 3D map.

Explore the different maps in SPARC Apps (Figure 1).

Flatmaps

Flatmaps published on the SPARC Portal provide 2D graphical representations of the anatomy, functionality, and topology of the connectivity of the PNS, in a Google Maps-like web-interface.

There are two types of flatmaps: an Anatomical Connectivity (AC) flatmap and a Functional Connectivity (FC) flatmap.

The AC and FC flatmaps allow knowledge captured in the SPARC Connectivity Knowledge base of the Autonomic Nervous system to be visualized and interactively explored on the SPARC Portal, including presenting relevant SPARC-published data as a user navigates through the interface.

The FC flatmap is a tool that provides the semantic description of all anatomical locations in the mammalian body along with the connectivity of networks that transfer information (neural connectivity) or mass flow (blood vessels and lymphatics) between these locations.

Learn more about Anatomical Connectivity (AC) and Functional Connectivity (FC) flatmaps.

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Creating and displaying your own flatmap

Detailed instructions on creating and displaying your own flatmaps are available on the Anatomical Flatmap Resources page.

Anatomical Models

3D Whole Body

The 3D whole-body map shows physical connectivity in an anatomically realistic context. Current developments are working toward enabling portal users to interactively explore connectivity seamlessly between the neuron population representation on the flatmaps and the nerve representation in the whole-body map.

Organ Scaffold Maps

Beyond the two-dimensional flatmaps, we also look to register data to three-dimensional organ scaffolds to provide maps in a common coordinate framework enabling disparate data to be integrated in order to improve our understanding of the collective SPARC knowledge. Learn more about Anatomical Models as datasets, how to explore them in the Scaffold Viewer, and how to map your data to existing scaffolds.

What can I do with Maps?

View anatomical features

Hovering over anatomical features will highlight it and prompt a tooltip with the feature ID. Clicking on these features will highlight it in green and outline it in red. Clicking the teardrop map marker will prompt the flatmap sidebar and provide all datasets and/or scaffolds relating to the selected feature. As seen in Figure 8, the liver has been selected and highlighted. Clicking the teardrop map marker prompts the flatmap sidebar with datasets relating to the liver. For more information, refer to the How to use the sidebar in Maps documentation.

View neuron pathways

In a similar manner, information on the neural pathways and other anatomical features can be observed. As seen in Figure 9, selecting the ‘Neruon type sdcol g’ pathway prompts a tooltip that provides more information. Scrolling down in the tooltip reveals a Search for data on components button, shown in Figure 10. This prompts related datasets in the flatmap sidebar.

Similarly, in the FC map, information on the neural pathways can be observed by clicking on the desired pathway. Scrolling down reveals more information.

View scaffolds

In the AC flatmap, scaffolds can be viewed by clicking on the relevant anatomical features, like the urinary bladder. This will change the map interface to the ‘Bladder Scaffold 3D’ view.

Scaffolds can also be viewed by utilising the sidebar. Clicking on the chevron icon on the right, the sidebar can be opened. Scaffolds can be filtered by using the Data type category and choosing Scaffolds. Under any desired dataset, clicking on the Scaffolds tab allows a View Scaffold button. The View Scaffold button will prompt the corresponding scaffold in the display.

Accessing Maps

There are two ways to access Maps on the SPARC Portal (Figure 2). From the SPARC Portal homepage

1. Click on the View the Maps button (1) to open Maps directly. 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. Learn how to interact with the Integrated Maps Viewer.
2. Click on the SPARC Apps tab (2) from the top navigation bar

From the SPARC Apps page (Figure 3):

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.