MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures

Whitehead, M. J., McCanney, G., Willison, H. J. and Barnett, S. C. (2019) MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures. Bioinformatics, (doi:10.1093/bioinformatics/btz403) (PMID:31095292) (Early Online Publication)

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Abstract

MyelinJ is a free user friendly ImageJ macro for high throughput analysis of fluorescent micrographs such as 2D-myelinating cultures and statistical analysis using R. MyelinJ can analyse single images or complex experiments with multiple conditions, where the ggpubr package in R is automatically used for statistical analysis and the production of publication quality graphs. The main outputs are percentage (%) neurite density and % myelination. % neurite density is calculated using the normalise local contrast (NLC) algorithm, followed by thresholding, to adjust for differences in intensity. For % myelination the myelin sheaths are selected using the Frangi vesselness algorithm, in conjunction with a grey scale morphology filter and the removal of cell bodies using a high intensity mask. MyelinJ uses a simple graphical user interface and user name system for reproducibility and sharing that will be useful to the wider scientific community that study 2D-myelination in vitro.

Item Type:Articles
Status:Early Online Publication
Refereed:Yes
Glasgow Author(s) Enlighten ID:McCanney, George and Whitehead, Mr Michael and Willison, Professor Hugh and Barnett, Professor Susan
Authors: Whitehead, M. J., McCanney, G., Willison, H. J., and Barnett, S. C.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:16 May 2019
Copyright Holders:Copyright © 2019 The Authors
First Published:First published in Bioinformatics 2019
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
632341MRC Doctoral Training Grant 2013/14, 2014/15 and 2015/16George BaillieMedical Research Council (MRC)MR/K501335/1MVLS GRADUATE SCHOOL
709171The basis of agonist and antagonist function at Free Fatty Acid receptor 2Graeme MilliganBiotechnology and Biological Sciences Research Council (BBSRC)BB/J013854/1RI MOLECULAR CELL & SYSTEMS BIOLOGY
722551Pathophysiological factors in the diagnosis and treatment of the Guillain-Barre syndromesHugh WillisonWellcome Trust (WELLCOTR)202789/Z/16/ZIII -IMMUNOLOGY