Evidence map›Paper›PMID 37315846›Full record

ArticleJournal of neuroscience methods2023

AxonQuantifier: A semi-automated program for quantifying axonal density from whole-mounted optic nerves.

Micalla G Peng, Jonathan Lee, Wilson Ho, Timothy Kim, Petcy Yao, Sasha Medvidovic, Basheer Alas, Vivian Wu, Margaret M Runner, Kimberly K Gokoffski

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of neuroscience methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
1.1field-weighted citation impact, top 24% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 1 country.

Micalla G PengDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Jonathan LeeDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Wilson HoDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Timothy KimDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Petcy YaoDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Sasha MedvidovicDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Basheer AlasDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Vivian WuDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA.
Margaret M RunnerDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA; Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, USA; Associated Retinal Consultants, PC, Department of Ophthalmology, Oakland University William Beaumont School of Medicine, Royal Oak, MI, USA.
Kimberly K GokoffskiDepartment of Ophthalmology, Keck School of Medicine, USC Roski Eye Institute, University of Southern California, Los Angeles, CA, USA. Electronic address: kimberly.gokoffski@med.usc.edu.
University of Southern California · USSouthern California Eye Institute · US

Funding

Ophthalmic Therapeutics Engineering CoreP30EY029220 · NEI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI Sarah F Hamm-Alvarez · 2018 to 2026
$6.5M
In vivo Application of Electrical Fields Directs Retinal Ganglion Cell Axon RegenerationK08EY031797 · NEI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI GOKOFFSKI, KIMBERLY K · 2020 to 2023
$862k
NEI NIH HHS K08 EY031797NEI NIH HHS P30 EY029220
6 · The paper itself

Abstract

backgroundHere, we present a semi-automated method for quantifying retinal ganglion cell (RGC) axon density at different distances from the optic nerve crush site using longitudinal, confocal microscopy images taken from whole-mounted optic nerves. This method employs the algorithm AxonQuantifier which operates on the freely available program, ImageJ. NEW

methodTo validate this method, seven adult male Long Evans rats underwent optic nerve crush injury followed by in vivo treatment with electric fields of varying strengths for 30 days to produce optic nerves with a wide range of axon densities distal to the optic nerve crush site. Prior to euthanasia, RGC axons were labelled with intravitreal injections of cholera toxin B conjugated to Alexa Fluor 647. After dissection, optic nerves underwent tissue clearing, were whole-mounted, and imaged longitudinally using confocal microscopy. COMPARISON WITH EXISTING

methodsFive masked raters quantified RGC axon density at 250, 500, 750, 1000, 1250, 1500, 1750, and 2000 µm distances past the optic nerve crush site for the seven optic nerves manually and using AxonQuantifier. Agreement between these methods was assessed using Bland-Altman plots and linear regression. Inter-rater agreement was assessed using the intra-class coefficient.

resultsSemi-automated quantification of RGC axon density demonstrated improved inter-rater agreement and reduced bias values as compared to manual quantification, while also increasing time efficiency 4-fold. Relative to manual quantification, AxonQuantifier tended to underestimate axon density.

conclusionsAxonQuantifier is a reliable and efficient method for quantifying axon density from whole mount optic nerves.

Indexed as

Optic NerveOptic Nerve InjuriesAnimalsAxonsDisease Models, AnimalMaleNerve CrushNerve RegenerationRatsRats, Long-EvansRetinal Ganglion CellsAxonNeuroprotectionNeuro-regenerationOptic nerveQuantificationRetinal ganglion cell

Identifiers

PMID37315846
PMCPMC10330882
OpenAlexW4380354169

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.