title: Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ.
abstract: We have developed a publicly available tool, AxonJ, which quantifies the axons in optic nerve sections of rodents stained with paraphenylenediamine (PPD). In this study, we compare AxonJ's performance to human experts on 100x and 40x images of optic nerve sections obtained from multiple strains of mice, including mice with defects relevant to glaucoma. AxonJ produced reliable axon counts with high sensitivity of 0.959 and high precision of 0.907, high repeatability of 0.95 when compared to a gold-standard of manual assessments and high correlation of 0.882 to the glaucoma damage staging of a previously published dataset. AxonJ allows analyses that are quantitative, consistent, fully-automated, parameter-free, and rapid on whole optic nerve sections at 40x. As a freely available ImageJ plugin that requires no highly specialized equipment to utilize, AxonJ represents a powerful new community resource augmenting studies of the optic nerve using mice.
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Kasra
authors.initials: K
authors.lastname: Zarei
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.|Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.
authors.forename: Todd E
authors.initials: TE
authors.lastname: Scheetz
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.|Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Christopher
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.
authors.forename: Kathy
authors.initials: K
authors.lastname: Miller
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Veterans Affairs, Iowa City VA Medical Center, 601 Highway 6 West, Iowa City, IA 55242, USA.|Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Hedberg-Buenz
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.
authors.forename: Anamika
authors.initials: A
authors.lastname: Tandon
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.|Department of Veterans Affairs, Iowa City VA Medical Center, 601 Highway 6 West, Iowa City, IA 55242, USA.|Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Anderson
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.
authors.forename: John H
authors.initials: JH
authors.lastname: Fingert
authors.affiliation: Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.|Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA.|Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA.|Department of Veterans Affairs, Iowa City VA Medical Center, 601 Highway 6 West, Iowa City, IA 55242, USA.|Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Michael David
authors.initials: MD
authors.lastname: Abràmoff
mesh_terms: D000465:Algorithms; D000818:Animals; D001369:Axons / Q000473:pathology*; D002452:Cell Count; D004195:Disease Models, Animal; D005901:Glaucoma / Q000473:pathology*; D006801:Humans; D051379:Mice; D009900:Optic Nerve / Q000473:pathology*; D010655:Phenylenediamines; D013194:Staining and Labeling
chemical_list: D010655:Phenylenediamines; C029728:4-phenylenediamine