Visualizing Probe tracks from AP_histology via Brainrender

[jel0624]

Dear Andy,

Have you tried visualizing the probe tracks from AP_histology (probe_ccf npy files) via brainrender?
I have tried to use branrender code to visualize the brain regions +NPX tracks, but it seems that the results are weird.
My impression is that both are in CCF coordinates(?) but maybe i'm missing something.

the python i'm using for brainder is from here (https://github.com/brainglobe/brainrender/blob/main/examples/probe_tracks.py)

Let me know your thoughts or if you have any ideas about this.
Thanks!

[GeonungYoun]

I also visualized the probe track obtained from AP histology using BioRender.

In my case, the AP histology probe_CCF was in 10 µm resolution, while the brain render CCF was in 1 µm resolution, so multiplying the probe_CCF by a scale_factor of 10 worked well for plotting.

Adjusting the radius or linewidth can also help with visualizing the probe track. Apologies if any of this information is inaccurate.

[petersaj]

I haven't used brainrender or biorender - good idea to check that the atlas resolution is the same, another thing to check is the order of the CCF coordinates: I save them in native CCF order [AP,DV,ML], it might be that these programs are expecting a different one.

I just do plotting in matlab - here's an example from my function ap.ccf_draw, this isn't intended for public use so it's not well-documented, but could be usable by anyone with some path name changes:

I'm curious to see examples of your probe trajectories in brainrender/biorender if you get them to work!

By the way, advertising as I've been responding to other issues: I'm working on an overhaul of this histology code (v2_overhaul branch), hopefully done within a month or so, it'll be much more user-friendly but saves everything in different ways so isn't compatible with old saved files.