REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat anti-Choline-acetyltransferase	EMD Millipore	RRID: AB_2079751
Cy3 donkey anti-goat IgG	Jackson ImmunoResearch	RRID: AB_2307351
Bacterial and virus strains
AAV-EF1a-FLEX-TVA-mCherry	UNC vector core
AAV-CA-FLEX-RG	UNC vector core
EnvA G-deleted rabies e-GFP	Salk Institute GT3	32635
Chemicals, peptides, and recombinant proteins
Ketamine	Covetrus	11695-0703-1
Phosphate buffer	Fisher Scientific	S369–500, S375-500
Paraformaldehyde	Alfa Aesar	A11313.OE
Fluoro-Gold	Fluorochrome, LLC	Fluorochrome, LLC
Fast Blue	Polysciences, Inc	Polysciences, Inc
Deposited data
Visualization of experimental 3D data	http://zaborszkylab.org/3DCholinergicSpace/
Experimental models: Organisms/strains
Rat: Sprague-Dawley	Charles River Laboratories	001
Rat: ChAT::Cre	Gift from Dr. K. Deisseroth, Stanford University	Were backcrossed with wild-type Long-Evans (Harlan)
Software and algorithms
NeurolucidaR	MBF Bioscience	v.7.50.4
PostGIS	Open Geospatial Consortium	https://postgis.net/
PostgreSQL	PostgreSQL Global Development Group	https://www.postgresql.org/
ImageJplugin (Java)	NIH	https://imagej.nih.gov/ij/
QGIS mapping client	Open Source Geospatial Foundation (OSGeo)	https://www.qgis.org/
R statistical framework	The R Foundation	https://www.r-project.org/
Silhouette method	Rousseeuw59
Pvclust	Suzuki and Shimodaira41	https://github.com/shimo-lab/pvclust
Images, vectorial cell data and related software code	Data: https://doi.org/10.5281/zenodo.14502163 Code:https://doi.org/10.5281/zenodo.14588790