Introduction to Maps
A guide through the basics of the SPARC Portal Maps interface
This guide will run through the basics of the SPARC Portal Maps interface:
What can I do with Maps?
The SPARC Portal displays detailed maps of the peripheral nervous system based on SPARC data and information available in literature. These include the Anatomical Connectivity (AC) flatmap, the Functional Connectivity (FC) flatmap, and the Whole Body 3D map. The Maps tab of the portal provides further information on each of these maps and what they display, as seen in Figure 1. Clicking on the View Map buttons redirects to the corresponding map.
Figure 1: Maps landing page
Map Interface Controls
Anatomical Connectivity (AC) Map
Figure 2: Maps interface controls
A: Search bar. Features in the flatmap, including organs, tissues, nerves and ganglia, can be searched for in the search box.
B: The title of the currently viewed map/scaffold. When multiple maps/scaffolds have been opened, a drop-down menu is displayed that allows the currently displayed flatmap/scaffold to be changed.
C: The species of the currently displayed flatmap. When a flatmap is being viewed, the species can be changed by using this drop-down menu.
D: Beta tag. This will often appear in maps that are currently under development.
E: What’s new information. Hovering over the What’s new? provides information relating to the latest updates to the SPARC Portal maps.
F: Flatmap legend. The legend provides generic information on what the features in the flatmap represent. Hovering over these features will display the specific feature that is represented.
G: Nerves toggle. This toggle allows hand-drawn nerves to be visualised. By default, these nerves are hidden. These nerves are based on information found in SCKAN.
H: Observed species toggle. This toggle allows filtering of features that are found in either Rattus Norvegicus (i.e. the common rat) or generally in mammals.
I: Neural pathways interface. The pathways visualised in the flatmap can be controlled in this area. By interacting with the tick boxes, specific pathways can be hidden. Both the legend and pathways interface can be hidden by using the arrow to the left.
J: Open new map. This icon allows the user to open a new map. Refer to the Working with Multiple Views in Maps documentation for more information.
K: Display settings. The display of the flatmap can be manipulated by clicking the computer icon. This prompts an interface that allows the user to change the viewing mode, organs and outlines display, and the background colour.
Note:
Refer to the SPARC Portal Annotation Tool documentation for more information on the Viewing Mode setting.
Figure 3: The display interface that allows manipulation of the flatmap visualisation
The Viewing Mode selector in the Display settings dialog (which can be seen in Figure 3) has three options:
1. Exploration, clicking on a path presents a pop up showing the components of the path which can be used in a search query.
Figure 3.1: Exploration Mode: after selecting a path
2. Network Discovery, clicking on a path will highlight the targeted path and paths connected to it.
Figure 3.2: Network Discovery Mode: Highlighting nearby pats to the one selected
3. Annotation (Login only), annotations can be added to a selected path. Annotations created in this way will only be viewable by others once the annotation is approved
Figure 3.3: Annotation Mode: Viewing the annotations of a path (non-user generated)
L: Flatmap controls and help.
- Split Screen - Clicking this button allows the user to view multiple maps/scaffolds at once. The multi-flatmap view can also be configured here. For more information refer to the Working with Multiple Views in Maps documentation.
- Help - Clicking this button prompts support boxes throughout the map/scaffold display to provide further information on the features.
- Fullscreen - Clicking this button allows a fullscreen display of the map/scaffold.
- Permalink - Clicking this button generates a permalink to the current version and orientation of the map/scaffold display.
Figure 4: The generated permalink to the current version and orientation of the map/scaffold display.
M: Display information. Clicking Show information or on the icon will visualise information on the currently displayed map or scaffold.
N: The overview panel. The current location of the user with respect to the full view of the flatmap can be seen here. As the map is manipulated, a blue box indicates what region of the flatmap is being viewed.
O: The map sidebar. The chevron on the right-hand side of the map interface opens the sidebar. Here datasets, maps, and scaffolds can be accessed. For more information, refer to the How to use the sidebar in maps documentation.
Figure 5: The map sidebar. Datasets, scaffolds and more can be accessed here. Clicking on features in the flatmap prompts the sidebar with related information.
P: Zoom controls of the interface. The zoom level of the map/scaffold being currently viewed can be manipulated with these controls. The right-most button allows a fit-to-window display. Note that zooming in/out can also be achieved by scrolling.
Functional Connectivity (FC) Map
Note:
The majority of the controls in the FC flatmap interface are the same as those in the AC flatmap. See the Anatomical Connectivity map section for further details.
Figure 6: The Functional Connectivity (FC) map interface. By default, all systems are hidden.
A: Systems interface. The systems displayed in the FC can be identified and filtered using this interface. Clicking the dropdown options allows the selection of FTUs on the map.
Note:
By default, all systems are hidden on the FC map. All systems can be visualised by checking the All option of the Systems interface.
B: Neural pathways interface. Similar to the AC map, the pathways visualised in the flatmap can be controlled in this area. Please take note that the FC map visualises the arterial and venous blood vessels.
3D Whole Body Map
Figure 7: The 3D whole-body map interface.
A: Map regions interface. The regions of the 3D whole-body map can be identified and filtered in this area. Clicking the whole-body dropdown reveals all systems available for visualisation.
Interacting with the display
The map/scaffold interface can be manipulated in various ways.
- When viewing the 2D flatmaps, left-clicking allows movement around the display.
- When viewing the 3D maps/scaffolds, left-clicking rotates the map/scaffold being viewed. Movement around the display can be achieved by right-clicking.
- Zooming in and out of the display can be achieved by scrolling, pitching in/out on a mousepad, or by the controls in the bottom left corner (as mentioned in part L of the Controls section).
Viewing anatomical features
Figure 8: Selecting an anatomical structure (e.g. the Liver) on the rat flatmap.
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.
Viewing 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.
Figure 9: Selecting the pelvic ganglion highlights the feature and connected paths. Selecting the path ‘Neuron type sdcol g’ prompts a tooltip with further information.
Figure 10: Scrolling down the tooltip that appears when selecting neuron pathways, a ‘Search for data on components’ button appears.
Similarly, in the FC map, information on the neural pathways can be observed by clicking on the desired pathway. Scrolling down reveals more information.
Figure 11: Selecting the neuron ‘aacar 13’ prompts the tooltip with information.
Viewing 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.
Figure 12: Clicking on anatomical features like the urinary bladder opens the scaffold of the organ.
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.
Figure 13: Accessing scaffolds via the sidebar by filtering datasets that involve scaffolds.
Updated 7 months ago