3D Whole Body Map

Opening 3D Maps

3D maps can be opened from the Open new map tooltip from the Integrated Maps Viewer and AC Flatmap

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.

1. The corresponding 3D version is linked with the flatmap by default, or it can be unlinked independently from one another.

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

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 the figure below, 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 below. 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.

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.

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.