REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
DiI (1,1’-Dioctadecyl-3,3,3′,3′-Tetramethylindocarbocyanine Perchlorate)	Invitrogen, USA	Cat# D282
Loctite super glue	Henkel, Germany	401
Silicon elastomer	World Precision Instruments, USA	Kwik-Cast
32% paraformaldehyde (PFA)	Electron Microscopy Science, USA	32% PFA solution
Oxidized agarose	Merck KGaA, Germany	Type-I agarose
Sodium borohydride	Merck KGaA, Germany	NaBH4,
Self-curing denture acrylic	Kulzer, Germany	Paladur
Self-curing denture acrylic (transparent)	LANG, USA	Ortho-Jet
Deposited data
Dataset and MATLAB analysis code	This study	https://doi.org/10.5281/zenodo.4720013
Allen Mouse Common Coordinate Framework version 3	Wang et al., 2020	http://help.brain-map.org/display/mousebrain/API
Experimental models: organisms/strains
Mouse: B6.129S2-Emx1 < tm1(cre)Krj > /J	The Jackson Laboratory	JAX: 005628
Mouse: B6.Cg-Tg(Camk2a-tTA)1Mmay/DboJ	The Jackson Laboratory	JAX: 007004
Mouse: B6.Cg-Igs7 < tm143.1(tetO-RcaMP1.07)Hze > /J	The Jackson Laboratory	JAX: 030217
Mouse: STOCK Vip < tm1(cre)Zjh > /J	The Jackson Laboratory	JAX: 010908
Mouse: B6.Cg-Gt(ROSA)26Sor < tm9(CAG-tdTomato)Hze > /J	The Jackson Laboratory	JAX: 007909
Mouse: B6;129S-Gt(ROSA)26Sor < tm32(CAG-COP4∗H134R/EYFP)Hze > /J	The Jackson Laboratory	JAX: 024109
Mouse: B6.Cg-Tg(Slc32a1-COP4∗H134R/EYFP)8Gfng/J	The Jackson Laboratory	JAX: 014548
Mouse: C57BL/6 wild type	Janvier (France)	C57BL/6JRj
Mouse: B6.FVB(Cg)-Tg(Adora2a-cre)KG139Gsat/Mmucd	Mutant Mouse Resource & Research Centers	MMRRC: 036158
Software and algorithms
MATLAB R2020a	MathWorks, USA	SCR_001622
Klusta	Rossant et al., 2016	https://github.com/kwikteam/klusta
Two-photon microscopy control software	Vidrio Technologies, USA	ScanImage 2017b
Extension for serial sectioning in 2-P tomography	Han et al., 2018	BakingTray; https://github.com/SainsburyWellcomeCentre/BakingTray
ARAtools	Han et al., 2018	https://github.com/SainsburyWellcomeCentre/ara_tools
StitchIt	Han et al., 2018	https://github.com/SainsburyWellcomeCentre/StitchIt
MaSIV	Han et al., 2018	https://github.com/SainsburyWellcomeCentre/masiv
Other
32-channel silicon probe	NeuroNexus,USA	A1x32-Poly2-10mm-50 s-177
Optrode	NeuroNexus, USA	A1x32-Poly3-10mm-50 s-177-OA32,
Digital headstage	Blackrock Microsystems, USA	CerePlex M32
Data acquisition system	Blackrock Microsystems, USA	CerePlex Direct
470-nm high power LED	Thorlabs, USA	M470F3
Blue Laser	GMP SA, Switzerland	MBL-F-473/200mW
High speed camera	Optronis, Germany	CL 600 X 2/M
16-bit monochromatic sCMOS camera	Hamamatsu Photonics, Japan	ORCA FLASH4.0v3,
567-nm LED	Luxeon, Canada	SP-01-L1
563/9-nm band pass filter	Semrock, USA	563/9 BrightLine HC
645/110 band pass filter	Semrock, USA	645/110 ET Bandpass
588-nm dichroic mirror	Chroma, USA	Beamsplitter T 588 LPXR
Nikkor 50 mm f/1.2 lens	Nikon, Japan	50 mm f/1.2
50 mm video lens	Navitar, USA	50 mm f/1.4
473 nm multimode fiber-coupled laser	Thorlabs, USA	S1FC473MM
2D Galvo System	Thorlabs, USA	GVS202
Shortpass beamsplitter	Semrock, USA	F38-496SG
High-precision X/Y/Z stage	Physik Instrumente, Germany	X/Y: V-580 Z: L-310
High-precision piezo objective scanner	Physik Instrumente, Germany	PIFOC P-725
500 – 550 nm bandpass filter	Chroma, USA	ET525/50
580 – 630 nm bandpass filter	Chroma, USA	ET605/70
A 16x water immersion objective lens	Nikon, Japan	LWD 16x/0.80W; MRP07220
Vibratome for 2-P tomography	Leica, Germany	VT1000S
Vibratome for conventional histology	Leica, Germany	VT 100