REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Ketamine HCl	Covetrus	REF: 11695-6840-1
AnaSed (Xylazine)	Akorn	REF: 59399-110-20
96% PFA	Thermo Scientific	REF: AC416780030
D-PBS, 1X, without calcium or magnesium	Corning	REF: MT21031CV
Sodium azide	Sigma	REF: 2002-25G
Agarose Low EEO	Sigma	REF: A9539-10G
CUBIC-L	TCI America	T3740-100ML
CUBIC-R+(M)	TCI America	T3741-100ML
ddH2O	N/A	N/A
Sucrose	Ward’s Science	REF: 470302-804
Tissue-Plus OCT Compound	Fisher	REF: 23-730-571
Cholera Toxin Subunit B, Alexa Fluor 647 Conjugate	Invitrogen	REF: C34778
Sterile PBS	Thermo Scientific	REF: J61196-AP
0.9% Saline	Hospira	REF: RL-7302
Nair	Fisher	REF: NC0132811
Artificial Tears	Akorn	REF: 59399-162-35
Triple Antibiotic Ointment	Med-Vet International	REF: CUR001231H
Experimental models: Organisms/strains
Mouse: C57BL/6J, female, 10 weeks old	The Jackson Laboratory	000664
Mouse: Ai14, female, 10 weeks old	The Jackson Laboratory	007914
Software and algorithms
Zen Black	ZEISS	Version: 3.1
Imaris	Oxford Instruments	Version: 9.9
Windows 10 Professional for Workstations (Image analysis workstation)	Microsoft	Version: 21H2 (Build 19044.1586)
FIJI/ImageJ (1.8.0_172)	Schindelin et al. (2012) https://doi.org/10.1038/nmeth.2019	https://imagej.net/software/fiji/
Labkit	https://doi.org/10.3389/fcomp.2022.777728	https://imagej.net/plugins/labkit/index
CLIJ	https://doi.org/10.1038/s41592-019-0650-1	https://clij.github.io/clij-docs/
CLIJ2	https://doi.org/10.1038/s41592-019-0650-1	https://clij.github.io/
Other
Zeiss Z7 Light Sheet Fluorescence Microscope	ZEISS	REF: Z7
Illumination lenses (5X, 0.1 NA, n=1.33–1.58)	ZEISS	REF: 400900-9030-000
Detection lens (5X, 0.16 NA, n=1.33–1.58)	ZEISS	REF: 420330-8220-000
Solid state laser 561 nm (50 mW)	ZEISS	REF: 400600-9210-000
Solid state laser 638 nm (75 mW)	ZEISS	REF: 400600-9230-000
Laser blocking Notch filter 405/488/561/638 nm	ZEISS	REF: 404900-9101-000
Emission filters	ZEISS	REF: 404900-9322-000
PCO.Edge 5.5 sCMOS cameras	PCO	PN: 70108070129
Dell Precision Workstation 7920	Dell	SKU: 210-AMRM
Micropipette Beveler	Sutter Instruments	REF: BV-10
Flaming/Brown Micropipette Puller	Sutter Instruments	REF: P-97
Stereoboom Microscope	Laxco	N/A
Ophthalmic Surgical Microscope	ZEISS	REF: OPMI S5
Small Animal Stereotaxic Instrument	KOPF	REF: Model 940