Table 1.1. ex vivo Axon Tracing Studies.

This table summarizes the studies obtained from our search. Aspects such as tracer used, tissue used, fixative, location, temperature, incubation solution, incubation duration, sectioning method, distance, and microscope used were all assessed from the studies in order to assist in comparing them.

Author/year	Tracer	Animal	Fixative	Location of Tracer/Tools	Incubation Temperature	Incubation Solution	Incubation Duration	Sectioning Method	Length Traced	Visualization
Auclair et al. 1993	DiI and DiA Crystals	13/14 day albino rat embryos	4% PFA	5–10 Crystals placed at C3 level of spinal cord to study brain stem. Method of insertion not specified.	37°C	4% PFA	2–4 months	Cryostat	Unclear	Epifluorescence Microscope
Baier et al. 1996	DiI and DiO	Zebrafish larvae	4% PFA	DiI and DiO injected using an apparatus to visualize retinotectal projection. DiI injected into temporal-ventral region and DiO injected into nasal-dorsal region	Room temperature	Unclea	Overnight	Unclear	Unclear	Fluorescence Microscope
Buhl 1989	Lucifer Yellow	Cats	4% PFA	Visual cortex	4°C	Unclear	Unclear	Vibratome	Unclear	Electron Microscope
Ceranik et al. 1999	DiI	Pre-natal and post-natal rats	4% PFA	Crystals placed on entorhinal cortex	Room temperature	4% PFA	3–6 weeks	Coronal sections 80–100 μm with vibratome	Unclear	Epifluorescence microscope/Confocal Laser Scanning Microscope
Chen et al. 2006	DiI and DiO	Adult Female Sprague Dawley Rats	4% PFA	Developed own method for insertion using 2mm thick and 4 mm diameter disc with 10 pins in it and placed these discs on either side of the spinal cord section and coated with wax to prevent leakage of dye	37°C and Room Temperature	1% and 4% PFA	2–24 weeks	Longitudinal vibratome sections	Distance varied depending on conditions. 37°C traveled up to 8.89±.23 mm over 24 wks And DiO traveled up to 1.67±0.11 mm in 4 weeks	Laser Scanning Confocal microscope
Collinge et al. 1991	DiI	Hamster	4%PFA	Cochlea. Placed crystals with micropipette.	40°C	Unclear	18–42 days	Transversely cut sections either 75 or 100 μm	Unclear	Epifluorescence
Eide et al. 1997	DiI	Chicken Embryo	4% PFA	Dorsal Root Ganglion	37°C	4% PFA	4–400 days	Vibratome	Unclear	Fluorescence Microscope
Friedland 1996	Fast DiI	Rat	4% PFA 0.1 M PB	Upper Respiratory Tract	37°C	4% PFA and 0.1 M PB	1 week	Vibratome	5–10mm	Epifluorescence
Fritzsch 1990	DiI	Chicks	Unclear	Optic Nerve	21–25°C	2.5% formalin in 0.1M PB	4–28 weeks	Unclear	3 mm	Epifluorescence
Fritzsch et al. 2005	DiI, DiA, DiO, DiD, NeuroVue Maroon, NeuroVue Red, NeuroVue Green	Mice	4% PFA	Auditory Cortex, Inferior Colliculus, Saccule, Posterior Crista, Cerebellum, Brain Stem. NV has dye loaded filters	37°C	4%	24–96 hrs	Vibratome	Unclear	Epifluorescence
Haber. 1988	Horseradish peroxidase	Human	Unclear	Basal ganglia. Injected with a glass pipette	37°C and 4°C	Low calcium phosphate buffer or 10% glucose, 10% fetal bovine serum and 10% penicillin streptomycin	24 hrs	Microtome and vibratome	10mm from center of injection site	Unclear
Hofmann and Bleckmann 1999	DiI	Goldfish	4% PFA	Optic Nerve	6, 20, 30, 35, 40°C	4% PFA, or 1–4% glutaraldehyde with 1% CaCl2 and 3% potassium dichromate, or 1–4% glutaraldyhyde in PB with 0.1% EDTA	1 week to 2 months	Vibratome	Unclear	Fluorescence
Jensen-Smith	NeuroVue Emerald, NeuroVue Jade, NeuroVue Red, NeuroVue Maroon	Mice embryos	Neutral-buffered PF (NBPF).	Spinal Cord Nylon filter	37–60°C	4% NBPF	24, 48, and 96 hours	Vibratome	Unclear	Confocal
Kayeyama et al. 1987	HRP	Cats/goldfish	2.5% depolymerized PF and 1.5% glutaraldehyde	Central Nervous System. Inserted with a glass micropipette	4°C	0.1 M PB for the goldfish sections	1–2 weeks	Vibratome	1.5 mm	Electron microscope
Kikkawa 2007	DiI, DiO, DiD, NV Red, and Golgi-Cox	Rat/mouse/guinea pig	Unclear	Nylon filters for NV Red. Looked at cochlea	Unclear	Unclear	NV Red 7–10 days. Golgi-Cox 3 weeks. Carbocyanine dye 4 weeks	Vibratome	Unclear	Confocal or light or Fluorescence
Lukas 1998	DiI, DiO, DiA	Human cadavers and guinea pigs	4% PFA	Placed crystal with glass micropipette	37°C or 40°C	4% PFA	3 weeks to 1 year	Vibratome	≈29.2 mm in guinea pigs and 28.5mm in human fixed tissue for DiI	Epifluorescence
Linke 1995	DiI	Rat	4% PFA	Hippocamposeptal Projection	Unclear	4% PFA	4–12 weeks	Vibratome	Unclear	Fluorescent
Magoul 1994	DiI	Rat	4% PFA	Arcuate nucleus	37°C	4% PFA	5 months	Vibratome and microtome	Unclear	Epifluorescence
Makarenko 2005	DiI	Rat	4% PFA in 0.1M sodium phosphate buffer	Pituitary intermediate lobe	20°C	4% PFA	6–24 Months	Vibratome	Unclear	Fluorescent
Mastick 1996	DiI and DiO	Mouse	4% PFA 0.1M PB	Forebrain and Midbrain	37°C	4% PFA 0.1M PB	4–24 hour	Unclear	Unclear	Dissecting Microscope
Mufson 1990	DiI	Human	4% PFA	Hippocampal complex	20°C	4% PFA	6 months	Vibratome	8mm	Epifluorescence
Murphy et al. 2007	DiI oil and crystal form	Mice	4% PFA	Vagal innervations	Unclear	4% PFA	4–7 weeks	Unclear	2–3.5mm	Fluorescent
Richards et al. 1997	DiI dissolved in DMF	Rats	2% PFA and post fixed with 10% buffered formalin	Neocortex	RT	Unclear	>3 weeks	Vibratome	Unclear	Fluorescence
Soukup et al. 2009	NeuroVue Dyes	Mice	4% PFA	Inner ear	–	–	–	–	–	Confocal
Swift et al 2004	DiI, DiO, DiA, DiR crystals dissolved in ethanol	Human cadavers	10% formalin	Peripheral nerve tissue	RT	Unclear	Up to 48 hours	Vibratome	12 hrs-15.4mm 24 hrs-29mm 48 hrs-53.7	Unclear
Zec 2001	DiI	Human	4% PFA in 0.1 M PB with .05% Sodium Azide and 4% sucrose	Nucleus paragigantocelluaris lateralis	20°C	Same as fixative	8.5–15.5 months	Unclear	Unclear	Fluorescent