Tuesday, November 23, 2021

Made really good progress on the 3d version of the code.
Have a 3d vis of probes from steinmetz neuropixels.

The blue brain model used https://github.com/AllenInstitute/mouse_connectivity_models - and the allen dorsal flatmap to project from 3d to 2d
Further, they have the recipe here https://portal.bluebrain.epfl.ch/resources/models/mouse-projections/mouse-long-range-connectome-recipe-format/

Made two videos about my PhD - these are good to have in mind!!
One is about the thesis.
One is about the connectivity.
I have put them in google drive, hopefully they will be useful.

DANDI

github/dandisets
00029 can be used for testing.
Check out YODA neuroscience, and keep in mind this talk https://www.youtube.com/watch?v=8OMLmUnc6Cs
Very important = datalad clone dandiset.
This uses symlinks so that I don't need to download it all.
It uses git annex.
So git annex whereis symlink (tells you where to download from)
datalab get FILE would then download it (S3 is where it is stored.)

dandi ls filename gives information
dandi ls online_url also works!
https://gin.g-node.org/G-Node/Info/wiki

Dandihub has an online terminal as well as an NWB widgets notebook.
datalad install . works like the clone
NWBwidgets can fetch individual items.

Considerations

Is the network version the best?
How to get it to work well online?
Conversions to notebook and py file probably needed.