REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat anti-guinea-pig IgG Secondary Antibody, Alexa 555	Thermo Fisher Scientific	Cat# A-21435; RRID: AB_2535856
Goat anti-mouse IgG Secondary Antibody, Cy5	Thermo Fisher Scientific	Cat# A-10524; RRID: AB_2534033
Goat anti-mouse IgG Secondary Antibody, Alexa 555	Thermo Fisher Scientific	Cat# A21424; RRID: AB_141780
Goat anti-rabbit IgG Secondary Antibody, Alexa 555	Thermo Fisher Scientific	Cat# A21429; RRID: AB_2535851
Goat anti-rabbit IgG Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-11008; RRID: AB_143165
Guinea-pig polyclonal anti-Cre recombinase Antibody	Synaptic Systems	Cat# 257 004; RRID: AB_2782969
Mouse monoclonal anti-Calretinin Antibody	Swant	Cat# 6B3; RRID: AB_10000320
Mouse monoclonal anti-GFAP Antibody	Synaptic Systems	Cat# 173 111; RRID: AB_10640333
Mouse monoclonal anti-Parvalbumin Antibody	Swant	Cat# PV-235; RRID: AB_10000343
Mouse monoclonal anti-Prox1 Antibody	Thermo Fisher Scientific	Cat# P21936; RRID: AB_2539823
Rabbit polyclonal anti-GFP Antibody	MBL	Cat# MBL-598; RRID: AB_591819
Rabbit polyclonal anti-IBA1 Antibody	Synaptic Systems	Cat# 234 003; RRID: AB_10641962
Rabbit polyclonal anti-Synaptoporin Antibody	Synaptic Systems	Cat# 102 003; RRID: AB_2619748
Chemicals, Peptides, and Recombinant Proteins
2,4,6-Tris(dimethylaminomethyl)phenol (DMP-30)	Electron microscopy sciences	Cat# 13600
2,3-Dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonamide disodium salt (NBQX)	HelloBio	Cat# HB0443
2-Dodecenylsuccinic acid anhydride (DDSA)	Serva	Cat# 20755.02
5-fluoro-2′-deoxyuridine	Sigma Aldrich	Cat# F0503
Acetone	Electron microscopy sciences	Cat# 10015
Alexa Fluor 555 streptavidin conjugate	Thermo Fisher Scientific	Cat# S32355; RRID: AB_2571525
Basal Medium Eagle (BME)	Thermo Fisher Scientific	Cat# 41010026
Biocytin hydrochloride	Sigma-Aldrich	Cat# B1758
Chicken Plasma	Sigma Aldrich	Cat# P3266
Cytosine β-D-arabinofuranoside hydrochlorine	Sigma Aldrich	Cat# C6645
D-APV: D-(-)-2-Amino-5-phosphonopentanoic acid	Tocris Bioscience	Cat# 0106
DAPI: 4′,6-Diamidine-2′-phenylindole dihydrochloride	Sigma-Aldrich/Roche	Cat# 10236276001
Di-Sodium hydrogen phosphate dihydrate	Merck	Cat# 1.06580.1000
Gelatin from cold water fish skin	Sigma Aldrich	Cat# G7041
Gey’s Balanced Salt Solution (GBSS)	Sigma Aldrich	Cat# G9779
GlutaMAX Supplement	Thermo Fisher Scientific	Cat# 35050061
Glycidether 100	Serva	Cat# 21045.02
Goat Serum	GIBCO	Cat# 16210-072
Hank’s Balanced Salt Solution, Ca2+, Mg2+ (HBSS)	Thermo Fisher Scientific	Cat# 24020091
Horse serum	GIBCO	Cat# 16050122
Kynurenic acid	Sigma-Aldrich	Cat# K3375
Lead (II) Nitrate	Merck	Cat# 1.07398.0100
Methylnadic anhydride (MNA)	Serva	Cat# 29452.02
Mounting glue: Aqua-Poly/Mount	Polysciences	Cat# 18606-20
Osmium tetroxide	Electron microscopy sciences	Cat# 19132
Paraformaldehyde (PFA)	Serva	Cat# 31628.02
Picrotoxin	Tocris Bioscience	Cat# 1128
Poly-L-lysine	Sigma Aldrich	Cat# P8929
Protein A (ProtA) coupled to 10 / 15 nm gold particles	Cell Microscopy Core Products, University Medical Center Utrecht, the Netherlands	N/A
Sodium citrate dihydrate	Calbiochem	Cat# 567446
Sodium dihydrogen phosphate monohydrate	Merck	Cat# 1.06346.0500
Tannic Acid 0.1%	Sigma Aldrich	Cat# 403040-100G
Tetrodotoxin	Tocris Bioscience	Cat# 1078
Thrombin from bovine plasma	Sigma Aldrich	Cat# 1.12374
Tissue-Tek O.C.T. Compound	Sakura	Cat# 4583
Triton X-100	Roche	Cat# 10789704001
Uranyl Acetate	SPI Supplies	Cat# 2624
Uridine	Sigma Aldrich	Cat# U3750
Experimental Models: Organisms/Strains
Mouse: Tg(Dock10-Cre)#Stl	Kohara et al., 2014	RRID: MGI:6117432
Mouse: Nex-Cre (Neurod6tm1(cre)Kan)	Goebbels et al., 2006	RRID: MGI:2668659
Mouse: Ai32 (Gt(ROSA)26Sortm32(CAG-COP4∗H134R/EYFP)Hze)	Madisen et al., 2012	RRID: MGI:5013789
Software and Algorithms
Diffraction PSF 3D plugin	Bob Dougherty	https://imagej.net/Diffraction_PSF_3D
Fiji	Schindelin et al., 2012	https://fiji.sc; RRID:SCR_002285
GraphPad Prism 8	GraphPad Software	https://www.graphpad.com; RRID: SCR_002798
IgorPro 6.3.7.2	Wavemetrics	https://www.wavemetrics.com; RRID: SCR_000325
ImageJ	National Institutes of Health	https://imagej.nih.gov/ij; RRID: SCR_003070
IMOD software	Kremer et al., 1996	https://bio3d.colorado.edu/imod/; RRID: SCR_003297
Interactive Deconcolve 3D plugin	Bob Dougherty	https://imagej.net/Iterative_Deconvolve_3D; RRID: SCR_016246
iTEM software (Version 5.1)	Olympus Soft Imaging Solutions GmbH	N/A
Leica LAS AF	Leica Microsystems	https://www.leica-microsystems.com; RRID: SCR_013673
Patch Master v2x53/ Pulse v8.80	HEKA / Harvard Bioscience	https://www.heka.com; RRID: SCR_000034
SerialEM software	University of Colorado, Boulder, Colorado, US; Mastronarde, 2005	https://bio3d.colorado.edu/SerialEM/; RRID:SCR_017293
Other
Cryostat	Leica	RRID:SCR_016844
EPC 10 double patch clamp amplifier	HEKA Elektronik	RRID:SCR_018399
JEM 2100 (200 kV)	Jeol	N/A
LED ENGIN LZ series λ 460 nm	Leica	N/A
LED, fiber-coupled KSL2/ KSL 70	Rapp Optoelectronic	N/A
Leica EM ACE600	Leica	N/A
Leica EM AFS2	Leica	N/A
Leica EM ICE	Leica	N/A
Leica EM TRIM2	Leica	N/A
Leica EM UC7 Ultramicrotome	Leica	RRID:SCR_016694
Leo912 (80 kV)	Zeiss	N/A
Orius SC1000 camera	Gatan	N/A
TCS-SP5 Confocal Microscope	Leica	N/A
Tissue chopper	McIlwain	RRID:SCR_015798
Sharp:eye CCD camera	Tröndle, TRS	N/A