REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Paraformaldehyde 16% aqueous solution	Electron Microscopy Sciences	Cat#15700
PBS 10x	Corning	Cat#46-013-CM
Sucrose	Fisher Scientific	Cat#AC177140050
Tissue-Tek OCT Compound	Sakura Finetek	Cat#4583
Fluoro-Gel mounting medium	Electron Microscopy Sciences	Cat#17985-11
Neurotrace 500/525 (1:200)	Thermo Fisher Scientific	Cat#N21480
Neurotrace 640/660 (1:200)	Thermo Fisher Scientific	Cat#N21483
DAPI (1:1000)	Thermo Fisher Scientific	Cat#D1306
Experimental models: Organisms/strains
C57BL/6J mice, adult (25–90 weeks old), males and females	The Jackson Laboratory	Stock#000664
Deposited data
3D SC reference atlas p56	Fiederling et al. (2021)	https://data.mendeley.com/datasets/4rrggzv5d5/1
SpinalJ example dataset: processed files	This protocol	https://data.mendeley.com/datasets/mkc37w4rrv/1
SpinalJ example dataset: raw files (1/6)	This protocol	https://data.mendeley.com/datasets/dsn9kggdpx/1
SpinalJ example dataset: raw files (2/6)	This protocol	https://data.mendeley.com/datasets/mrbjz83xf6/1
SpinalJ example dataset: raw files (3/6)	This protocol	https://data.mendeley.com/datasets/dfyvhrh4cd/1
SpinalJ example dataset: raw files (4/6)	This protocol	https://data.mendeley.com/datasets/43ky5by55m/1
SpinalJ example dataset: raw files (5/6)	This protocol	https://data.mendeley.com/datasets/xdj4kxkvnp/1
SpinalJ example dataset: raw files (6/6)	This protocol	https://data.mendeley.com/datasets/4hx2cj4j67/1
SpinalJ video tutorial	This protocol	https://data.mendeley.com/datasets/63m34hg3pt/1
SpineRack .stl print file	Fiederling et al. (2021)	https://doi.org/10.5281/zenodo.5177185 Also available through: https://github.com/felixfiederling/SpinalJ/blob/main/SpineRack.stl
Software and algorithms
Cura v4.8	Ultimaker	https://ultimaker.com/software/ultimaker-cura
Fiji (ImageJ)	Schindelin et al. (2012)	https://fiji.sc/
SpinalJ	Fiederling et al. (2021)	https://doi.org/10.5281/zenodo.5177185 Also available through: https://github.com/felixfiederling/SpinalJ
Attenuation Correction	Biot et al. (2008)	https://imagejdocu.tudor.lu/plugin/stacks/attenuation_correction/start#attenuation_correction
TurboReg	Thévenaz et al. (1998)	http://bigwww.epfl.ch/thevenaz/turboreg/
MultiStackReg	Thévenaz et al. (1998)	http://bradbusse.net/sciencedownloads.html
3D Viewer	Schmid et al. (2010)	https://imagej.nih.gov/ij/plugins/3d-viewer/
Elastix	Klein et al. (2010)	https://elastix.lumc.nl/download.php
Ilastik	Berg et al. (2019)	https://www.ilastik.org/
NIS-Elements JOBS	Nikon Instruments	https://www.microscope.healthcare.nikon.com/en_EU/products/software/nis-elements/nis-elements-jobs
JOBS settings for imaging	Fiederling et al. (2021)	https://doi.org/10.5281/zenodo.5177185
Other
Ultimaker3 3D printer (or equivalent)	Ultimaker	https://ultimaker.com/de/3d-printers/ultimaker-3
PVA filament	Ultimaker	Cat#9731
Truncated embedding mold Peel-A-Way(R) T12	Polysciences	Cat#189861
Cryostat	Leica Biosystems	CM3050S or equivalent
Disposable microtome blades	Sakura Finetec	Cat#4685
Microscope slides, Fisherbrand Superfrost Plus	Fisher Scientific	Cat#12-550-15
Wheaton dish	DWK Life Sciences	Cat#900200
Slide Scanning Microscope e.g., Nikon AZ100 Multizoom	Nikon Instruments	Model AZ100, discontinued
Automated slide feeder	Prior Scientific Inc.	Model PL-200
Andor Zyla camera	Oxford Instruments	Model Zyla 4.2 sCMOS