8. Find the electrode insertion angle to target brain regions of interest
Choose some points in the brain that you would like to target with an electrode, and then press 'w' to see the corresponding entry point and angle of the probe
Run the allenAtlasBrowser (recommended) or AtlasTransformBrowser function. Navigate through the atlas to find the brain regions you would like to target in your experiment, modifying the dorsoventral angle of the reference atlas to find a slice that contains all of your regions of interest (see Navigating in the reference atlas). As always, press 'o' to highlight the brain region the mouse is hovering on.
Now, press 'p' to activate probe point mode and click on the desired points in the reference atlas. (see Selecting regions of interest).
Finally, press 'w' to activate probe view mode. Move the mouse around to explore both brain regions (as reported in the figure title) and the coordinate (displayed in the top left corner of the figure). The example below was an attempt to position an electrode that passes through CA1, the superior colliculus, and the periaqueductal gray.
The insertion point at the zero dorso-ventral coordinate of bregma, as well as the probe's angle and insertion distance, are reported in the console.
---estimated probe insertion---
entry position at DV = 0: AP = -2.18 mm, ML = -5.31 mm
insertion distance from the above position: 6.062 mm
18.4 degrees in the posterior direction
56.1 degrees in the medial direction
If you save these clicked points by pressing 's' and analyze them using displayProbeTrack.m you can also view a 3D representation of the brain and the probe (as below), and a plot of the brain regions it passes through (see Visualize & analyze brain regions traversed by an electrode).
Note that this repository contains another function, allen_atlas_probe.m that is also designed to find desired electrode trajectories.