Table 3.

Summary of optical clearing techniques used in injury and diseases of the nervous system studies.

		Specimen	Species	Age	Technique	Cell Type/Structure/Marker	Citation
Injury	Nerve	Sciatic nerve	Rat/Tg Rat	Adult	THF	Individual axons	Jung et al, 2014
		Whole DRG Spinal cord	Tg Mouse	Adult	BABB	DRG neurons, neuronal nuclei, small C fibres	West and Bennett, 2019
	Spinal Cord	Spinal cord	Tg Mouse	2–18M	THF	Axonal boutons, neurons, microglia, astrocytes	Ertürk et al, 2012
		Spinal cord	Mouse/Tg Mouse	1-2D	CLARITY	DRGs, motor neurons, NECAB1+ neurons, dendrites	Zhang et al, 2014
		Spinal cord	Tg Mouse/Rat/Macaque	6-9W/5Y	3DISCO THF BABB	Axon collaterals and fibers, fibroblasts, astrocytes, motor and sensory neurons	Soderblom et al, 2015
	Retina	Whole Tissue	Tg Mouse	Adult	THF BABB	RGC axons	Luo et al, 2014
		Whole Tissue	Tg Mouse	6-8W	iDISCO	RGC axons	Bray et al, 2017
	Brain	Whole Brain	Mouse	10–12W	3DISCO	Blood vessels, capillaries, endothelial cells	Lugo-Hemandez et al. 2017
		Brain	Tg Mouse	Adult	CLARITY	oligodendrocytes, microglia, astrocytes, neuronal nucleolus and nuclear envelope	Gaire et al, 2018
		Dura mater	Human	3D-36W. 2Y	Glycerol & Mannitol	Dura, blood vesssels	Cheshire et al., 2015
		Brain	Rats	P90	SeeDB	Embryonic stem cells, cell bodies, neurons	Nudi et al.. 2015
		Whole & Section Brain	Tg Mouse	~3M	THF & DBE	Dendritic spines, immune cells (microglia, cerebral lymphocytes), astrocytes	Ertürk et al., 2016
		Brain	Tg Mouse	6W	PACT	Glial cells- astrocytes, microglia	Merkel et al.. 2017
		Brain	Tg Mouse	2-4M	THF & BABB	Endothelial cells, blood vessels	Assis-Nascimento et al., 2016
		Whole Brain	Mouse	8-10W	CLARITY	Peptides, commissural fibers	Mann et al., 2016
		Whole Brain	Tg Mouse	8-10W	CLARITY	Axons, Node of Ranvier, flanking paranodes, cell nuclei, cell membranes	Marion et al., 2018
	Ischemic model (Cerebral artery	Whole Brain	Tg Mouse	10W	CLARITY	Vessel endothelium, tight junction protien (Claudin-5	Zhang et al., 2018
	Hypoxic Injury	Brain	Rats	7D	CLARITY	Neurofilaments	Lee et al., 2017
Disease	Alzheimer’s	Brain	Mouse/Tg Mouse	8-19W/ 9-24M	ScaleS AbScale ScaleSQ	Aβ plaques, neuronal nuclei, neurons, synapse regions, blood vessels, dendrites, axon terminals, neurites, microglia	Hama et al, 2015
		Brain hemispheres Brain	Tg Mouse/Human	4.4-37M	iDISCO ClearMap	Aβ plaques, microglial aggregates, axon filaments, blood vessels, cell nuclei, tau, neurofibrillary tangles	Liebmann et al, 2016
		Brain hemispheres	Tg Mouse	8-34M	iDISCO+	Somatodendritic tau, neurons	Fu et al, 2016
		Brain	Tg Mouse	4-80W/15M	UbasM CUBIC uDISCO ScaleS SeeDB	Aβ plaques, dendritic spines; motor, sensory, and central neurons	Chen et al, 2017
		Brain hemisphere	Tg Mouse	1-6M	CUBIC Scale S4	Aβ aggregates, neurons, glia	Tanaka et al, 2018
		Brain	Mouse/Tg Mouse	4-6W/25M	CUBIC	Aβ plaques, neurons, neurites, dendritic spines, blood vessels	Vints et al, 2019
		Brain	Tg Mouse	90 ± 5D/6, 9M	iDISCO uDISCO	Hyperphosphorylated tau, protein aggregates	Detrez et al, 2019
		Brain	Mouse/Tg Mouse	6M	CLARITY	Aβ plaques, microglia, astrocytes, vascular endothelium, GFAP positive cells	Martorell et al, 2019
	PD	Brain	Mouse/Rat/Human	12W	CLARITY	Lewy body-like inclusions, neurofilament, neuronal soma, monoaminergic neurones and fibers, axonal processes, microglia	Liu et al, 2016
	DMD	Whole Body	Mouse/Tg Rats	8W	CUBIC	Calcium deposits, nuclei, intestinal villi and folia	Bozycki et al, 2018
	Viral	Whole Brain	Zebra Fish	4-7DPF	CLARITY	Microvasculature, endothelial cells	Passoni et al, 2017
	Glioma	Whole Brain	Tg Zebra Fish	1-14M	CLARITY	GFP malformations	Mayrhofer et al, 2017
	MtD	Brain	Mouse/Human	12M	CLARITY	Mitochondrial proteins, porin, neurofilament H, myelin, calbindin and parvalbumin interneurons, purkinje cell bodies, axons, mitochondria, vascular network	Phillips et al, 2016

PD, Parkinson’s disease; DMD, Duchenne muscular dystrophy; MtD, Mitochondrial disease; Tg, transgenic or reporter; DRG, dorsal root ganglia; M, months of age; D, days of age; W, weeks of age; Y, years of age.