Journal article
Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ
Scientific reports, Vol.6(1), 26559
05/26/2016
DOI: 10.1038/srep26559
PMCID: PMC4881014
PMID: 27226405
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.
Details
- Title: Subtitle
- Automated Axon Counting in Rodent Optic Nerve Sections with AxonJ
- Creators
- Kasra Zarei - Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USATodd E Scheetz - Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USAMark Christopher - Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USAKathy Miller - Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USAAdam Hedberg-Buenz - Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USAAnamika Tandon - Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USAMichael G Anderson - Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USAJohn H Fingert - Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USAMichael David Abràmoff - Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA 52242, USA
- Resource Type
- Journal article
- Publication Details
- Scientific reports, Vol.6(1), 26559
- DOI
- 10.1038/srep26559
- PMID
- 27226405
- PMCID
- PMC4881014
- NLM abbreviation
- Sci Rep
- ISSN
- 2045-2322
- eISSN
- 2045-2322
- Publisher
- England
- Grant note
- R01 EY019112 / NEI NIH HHS R01 EY018825 / NEI NIH HHS R01 EY023187 / NEI NIH HHS I01 RX001481 / RRD VA R01 EY023512 / NEI NIH HHS R01 EY018853 / NEI NIH HHS I01 CX000119 / CSRD VA R01 EY017673 / NEI NIH HHS
- Language
- English
- Date published
- 05/26/2016
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Molecular Physiology and Biophysics; Ophthalmology and Visual Sciences
- Record Identifier
- 9983806386602771
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