Electrophysiology/histology alignment tool fix

[petersaj]

Brain regions recorded by electrophysiology cannot usually be determined by histology alone: the tip of the probe is difficult to pinpoint, so while the trajectory is clear, the exact depth of the probe is not.

I used to have the function AP_align_probe_histology to adjust where the probe lies along the trajectory based on firing rate, unit depth, and multiunit correlation. Changes to the GUI means this no longer works, and I hope to add a new alignment tool in the future.

In the meantime:

• Electrophysiological landmarks are most reliable, if available. For example, if the top of the probe is outside of the brain, the surface of the cortex can be identified through LFP or the first units.
• alignatlasdata is an alignment tool from Enny van Beest and might work as-is: https://github.com/EnnyvanBeest/GeneralNeuropixelAnalysisFunctions/blob/main/Histology/alignatlasdata.m
• atlaselectrophysiology is an alignment tool from Mayo Faulkner at the IBL (in python, requires IBL data/naming conventions): https://github.com/int-brain-lab/iblapps/tree/master/atlaselectrophysiology. Using this requires converting file formats from AP_histology, which is apparently possible (done here AP_align_probe_histology #17), though I don't have code to do that at the moment.

[petersaj]

I've now done this - but this process is so lab-specific (file names and locations, variable names, etc.) that it's doesn't seem immediately feasible to make this generalized without sacrificing utility for my own lab.

If you're interested in how I implement it, the code is here: https://github.com/PetersNeuroLab/PetersLab_analysis/tree/main/%2Bplab/%2Bhistology

There are 2 steps:

1. Map annotated histology probes to their associated recording data: plab.histology.map_probe_ephys
2. Manually adjust by depth and scale: plab.histology.adjust_probe_ephys