REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-Mouse CD31 (1:1000)	Abcam	Cat# ab124432 RRID: AB_2802125
Rabbit anti-Rat IBA1 (1:1000)	Wako	Cat# 019-19741 RRID: AB_839504
Goat anti-Rabbit IgG, HRP-conjugated (1:2000)	Cell Signaling Technology	Cat# 7074 RRID: AB_2099233
Chemicals, peptides, and recombinant proteins
Opal 520 Reagent Pack	Akoya Biosciences	Cat# FP1487001KT
Opal 570 Reagent Pack	Akoya Biosciences	Cat# FP1488001KT
Opal 690 Reagent Pack	Akoya Biosciences	Cat# FP1497001KT
RNAscope 3-Plex Positive Control Probe-Mm	ACD	Cat# 320881
RNAscope 3-Plex Negative Control Probe-Mm	ACD	Cat# 320871
RNAscope probe-Mm-Pecam1	ACD	Cat# 316721
RNAscope probe-Mm-Aif1-C3	ACD	Cat# 319141-C3
RNAscope probe-Mm-Cx3cr1	ACD	Cat# 314221
10% Neutral Buffered Formalin	Cancer Diagnostics	Cat# FX1000
Sterile Pharmaceutical Grade Saline	Vet One	Cat# NDC 13985-807-50
Heparin	Sagent Pharmaceuticals	Cat# NDC 25021-400-30
Phosphate Buffered Saline	Rocky Mountain Laboratories
Trizma Base	Sigma-Aldrich	Cat# T6066-1KG
Bovine Serum Albumin	Calbiochem	Cat# 12659
ProLong Glass Antifade Mountant	Invitrogen	Cat# P36980
Tween-20	BIO-RAD	Cat# 1706531
Critical commercial assays
RNAscope Multiplex Fluorescent Reagent Kit v2	ACD	Cat# 323100
Experimental models: Organisms/strains
RML mice, (2–12 months), male or female	Rocky Mountain Laboratories	N/A
B6.129P2(Cg)-Cx3cr1tm1Litt/J (Cx3cr1GFP) mice, (6–12 weeks), male or female (CX3CR1 KO mice)	JAX	Cat# 005582
B6.129(Cg)-Ccr2tm2.1lfc/J (Ccr2RFP) mice, (6–12 weeks), male or female (CCR2 KO mice)	JAX	Cat# 017586
B6.129(Cg)F1-Cx3cr1tm1LittCcr2tm2.1lfc mice, (6–12 weeks), male or female (CX3CR1 heterozygous mice)	Rocky Mountain Laboratories	N/A
Software and algorithms
Fiji (ImageJ)	Schneider et al. (2012)	https://imagej.net/software/fiji/
SVI Huygens Essential	Scientific Volume Imaging	https://svi.nl/HomePage
Other
ImmEdge Hydrophobic Barrier Pen	ACD	Cat# 310018
HybEz II Hybridization System	ACD	Cat# 321710
TOMO Adhesion Microscope Slides	Matsunami	Cat# TOM-11/90
Vegetable Steamer, 5.5 quart	Hamilton Beach	Model 37530A
Tissue Tek staining dish	Sakura Finetek	Cat# 4457
Tissue Tek slide holder	Sakura Finetek	Cat# 4465
Fine Scissors	Fine Science Tools	Cat# 14958-11
Spring Scissors	Fine Science Tools	Cat# 15024-10
Graefe Forceps	Fine Science Tools	Cat# 11050-10
Dumont #7 Forceps (fine)	Fine Science Tools	Cat# 11271-30
Nikon Eclipse Ti2 fluorescence microscope	Nikon	https://www.microscope.healthcare.nikon.com/products/inverted-microscopes/eclipse-ti2-series
Nikon SMZ1500 stereomicroscope (dissection microscope)	Nikon	https://www.microscopyu.com/museum/model-smz1500-stereomicroscope