REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Fluorescein isothiocyanate (FITC) conjugated albumin	Sigma-Aldrich	A9771-1G; MDL: MFCD00282182
Porcine skin gelatin	Sigma-Aldrich	G1890-500G; CAS: 9000-70-8
Ketamine (KetaVed)	Vedco	NDC: 50989-996-06
Xylazine (AnaSed)	Akorn	NDC: 59399-110-20
Paraformaldehyde, granular	Electron Microscopy Sciences	Cat#19210
Sodium hydroxide, pellets, ≥ 97.0%	Sigma-Aldrich	221465-500G; CAS: 1310-73-2
Hydrochloric acid solution, 1.0N, bioreagent, suitable for cell culture	Sigma-Aldrich	H9892-100ML; CAS: 7647-01-0
Agarose	Sigma-Aldrich	BP1356-100; CAS: 56-40-6
Sodium azide, ≥ 99.5%	Sigma-Aldrich	S2002-100G; CAS: 26628-22-8
Sodium periodate, 99% for analysis	Thermo Fisher Scientific	198381000; CAS: 7790-28-5
Sodium phosphate, monobasic	DOT Scientific	DSS23120-500; CAS: 10049-21-5
Sodium phosphate, dibasic anhydrous	DOT Scientific	DSS23100-1000; CAS: 7558-79-4
Sodium borohydride, powder, ≥ 98.0%	Sigma-Aldrich	452882-25G; CAS: 16940-66-2
Sodium tetraborate decahydrate	Honeywell/Fluke	31457-500G; CAS: 1303-96-4
Boric acid	Sigma-Aldrich	B0394-500G; CAS: 10043-35-3
Experimental models: Organisms/strains
C57BL/6J mice Age: Postnatal day 67; Sex: Male and female	Jackson Laboratory	Strain #: 000664; RRID:IMSR_JAX: 000664
nNOS-CreER (B6;129S-Nos1tm1.1(cre/ERT2)Zjh/J) mice Age: 8 weeks old Sex: Male and female	Jackson Laboratory	Strain #: 014541; RRID:ISMR_JAX: 014541
Ai14 (B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J) mice Age: 8 weeks old Sex: Male and female	Jackson Laboratory	Strain #: 007914; RRID:ISMR_JAX: 007914
PDGFRβ-Cre mice Age: 8 weeks old Sex: Male and female	Gift from Volkhard Linder Laboratory at the Maine Medical Center; Cuttler et al.6	N/A
Software and algorithms
Fiji/ImageJ	Schindelin et al.7	https://imagej.nih.gov/ij/; RRID: SCR_003070
VasoMetrics ImageJ macro	McDowell et al.8	https://pubmed.ncbi.nlm.nih.gov/33654670/
Elastix	Klein et al.9	https://elastix.lumc.nl/; RRID: SCR_009619
MATLAB	Mathworks	https://www.mathworks.com/products/matlab.html; RRID: SCR_001622
Python	Python	https://www.python.org/
Anaconda	Anaconda	https://www.anaconda.com/products/distribution
Ubuntu	Canonical Ltd.	https://ubuntu.com/
Spyder	Spyder IDE	https://www.spyder-ide.org/
TensorFlow	Google	https://www.tensorflow.org/
STPT imaging reconstruction algorithm	Wu et al.1	ZenodoData: https://doi.org/10.5281/zenodo.6517732 and https://github.com/yongsookimlab/TracibleTissueCyteStitching
Vascular tracing algorithm based on STPT imaging	Wu et al.1	ZenodoData: https://doi.org/10.5281/zenodo.6517732 and https://github.com/yongsookimlab/MiceBrainVasculatureTracer
Machine learning based cell counting algorithm	Wu et al.1	ZenodoData: https://doi.org/10.5281/zenodo.7477393 and https://github.com/yongsookimlab/Multi_resolution_DLNN_Cell_Counting and https://kimlab.io/data_share/files/NVU_young/Code_S3_Multi_resolution_DLNN_Cell_Counting.zip
Other
Bottle-top vacuum filter (neck size = 45 mm, capacity = 500 mL, diameter = 75 mm, pore size = 0.2 μm)	Thermo Fisher Scientific/Nalgene	Cat#28199-307
Custom-made brain embedding platform	Yongsoo Kim Lab	N/A
Custom-made embedding molds (1 × 1 × 1 in.)	Yongsoo Kim Lab	N/A
Micro-Adson Forceps	Fine Science Tools	Item no. 11018-12
Graefe Forceps	Fine Science Tools	Item no. 11050-10
Fine scissors – large loops	Fine Science Tools	Item no. 14040-10
Surgical scissors – serrated	Fine Science Tools	Item no. 14007-14
Iris spatula	Fine Science Tools	Item no. 10093-13
Insulin syringe, U-100 Micro-Fine IV, 28 Gauge, 1cc, 1/2″	BD Biosciences	Cat#329424
Hypodermic needle, precision glide needle only, 25 gauge, 1″	BD Biosciences	Cat#305125
20× Olympus XLUMPLFLN20XW Objective, 1.00 NA, 2.0 mm WD	Thorlabs	Part number: N20×-PFH
TissueCyte 1000	TissueVision, Inc.	N/A
Chameleon Ultra II Laser	Coherent	Serial: GDP.1117782.2667
Piezo amplifier/servo controller	Physik Instumente (PI)	E-665.S0
Stabilizer - laminar flow isolation system	Newport	S-2000
RS 2000 Optical Table Top - sealed hole table top with tuned damping	Newport	RS 2000
All-purpose super glue	Krazy Glue	KG92548R
Two-part epoxy and resin	Gorilla Glue	Cat#4200101
Superfrost microscope slides	Fisher Scientific	Cat#12-544-7
Neodymium magnets (10 × 4 × 2 mm)	MIN CI	20120000
2-hole stainless steel injector blades for vibratome	Lutz	Part # I-015004
Peristaltic pump	Ismatec	Cat#EW-78018-02
Peristaltic pump	Welch	Model 3100