https://www.digikey.ch/en/products/detail/samtec-inc/SS-106-G-2/1105585

Waiting on photos from Anup

For the ccf coordinates, why not do it in "true" CCF, like measure from the 0,0,0 coordinate in the dorsal-anterior-left corner of the volume? Currently it seems like CCF is also measuring AP/ML from some assumed bregma location. I think this would be useful because it would make more clear what parts of the given coordinate correspond to some assumptions we make about skull markers.

• Center tip of in-plane slice vertically
• Jump to 2/4/6/8 mm size instead of scaling based on size of recording region
• Zoom in/out options
• Smooth
• Cycle through shader options on click (all areas transparent, area highlighted, area transparent with other areas even more transparent) + change color on the in-plane slice as well

phi 0 facing left
phi 180 facing right
counterclockwise

theta 0 vertical
theta 90 flat

spin (beta) stays the same

Currently the 4 probe panels are "from the back" switch them to be "from the front"

• Hover over pixels and show area text
• #10
• Highlight individual brain areas for targeting

https://forum.unity.com/threads/remote-addressables-work-fine-in-local-builds-fail-in-unity-cloud-build.1243225/#post-7924300

Currently if you're spinning to 180 it just stops there, and if you want to spin further you have to go all the way back around the other way.

Need to do projected collision checks along the path of a movement to fix this, seems like a pain

Super minor but the probe active area is a peach-like color, and so is probe 2 - it's hard to see where the active area is on that probe, therefore. Maybe white could be a good color for the active area? Or could be something like neon yellow? Or you could just add some kind of glow effect?

https://int-brain-lab.slack.com/archives/CU7EP9A2H/p1644344612319119?thread_ts=1644344552.729999&cid=CU7EP9A2H

DV 0.952
AP 1.087

mouseSkull.zip

The CCF atlas is rotated relative to in vivo, use IBL trajectory data to estimate this offset and then remove it in the stCCF coordinate space

When the manipulator is rotated the AP/ML axis definitions don't work anymore. Add an option to display the axis position relative to bregma in manipulator position.

Probably a good idea to have ability to undo the deletion of a probe.

Part of SC in the image below is dark colored because of a shadow cast by the anterior lateral probe. I think if it's possible to make the probes not cast shadows it would be good, because the image is pretty graphically complex already.

Would be great to have some kind of save/load functionality - I guess it would just save a text file with the coordinates of all probes, perhaps also with some metadata about the graphical display, like which areas are rendered in 3D, and which rig(s) are shown? Then you could just select that file and get back to where you were.

Add an option that lets you lock the probe to rotate around an area

Maybe [X] instead? But kind of close to other keys... maybe add a ctrl+z option for reversing changes and recovering deleted probes?

Add an option to alpha-clip the brain shader when the slice views are enabled

The in-plane slice automatically zooms out when you increase the recording span, but it would be nice to have independent control of this so you can zoom out while keeping a dense recording span.

Drop-down menu that searches through all of the Beryl areas so that you can highlight on/off areas by switching between transparent<->opaque

Would be great to have ability to increase the font size. The contrast is also really low and difficult to read:

Not sure of the best algorithm but it's looking pretty choppy in a lot of places, especially as soon as you rotate out of coronal:

Seems like there should be some way to compute some nice sharp lines to plot here instead.

https://docs.unity3d.com/2021.2/Documentation/Manual/macos-building-notarization.html