New Neuroglancer feature: Stereotactic coordinates (Paxinos Mouse Brain Atlas)
In this post, we introduce a new feature to Neuroglancer which is useful when browsing your data after it has been aligned to the Allen Mouse Brain Atlas: stereotactic coordinates. This feature is only available if using the BRAIN CoGS Neuroglancer client: https://nglancer.pni.princeton.edu/ (must be connected to Princeton VPN to access).
It is common for researchers to view their data after it has been registered to a brain atlas. For mouse brains, the Allen Mouse Brain Atlas and Paxinos Mouse Brain Atlas are two examples. Because the Allen Institute provides a 3D annotated volume for their Mouse Brain Atlas, it is readily viewable in Neuroglancer. That being said, the Allen Mouse Brain atlas has its limitations. It is useful for knowing what brain region a particular object of interest is in. However, if you want to know the exact coordinates of this object, the best Allen can provide is a voxel (x,y,z) coordinate. It is often more useful to know the stereotactic coordinate from the Paxinos atlas for this object.
Fortunately, there is a simple transformation between Allen voxel space and Paxinos stereotactic space. We have added some text to the top bar of Neuroglancer showing the three stereotactic coordinates from the Paxinos atlas: anteroposterior (AP), mediolateral (ML) and dorsoventral (DV) that correspond to where your cursor is currently located. If you use the Allen Mouse Brain layer we already provide: Allen Mouse Brain Atlas (must be in the Princeton network or VPN for link to work), then the Paxinos coordinates will automatically be activated. However, if you only want to show the volume and not the atlas, you will need to follow the instructions here in order to activate the Paxinos coordinates for this layer: https://github.com/PrincetonUniversity/lightsheet_helper_scripts/blob/master/neuroglancer/how_to_activate_paxinos_coords.ipynb
In the following video, we illustrate how the stereotactic coordinates appear in Neuroglancer. They are shown in blue at the top of the screen and only appear when the cursor is in one of the viewer panels.
Thanks to Ben Engelhard, Daniel Fürth and Alvaro Luna for helpful discussions in the process of making this feature.