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, 35(21), pp. 4528-4530. (doi: 10.1093/bioinformatics/btz403) (PMID:31095292) (PMCID:PMC6821319)
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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 |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Whitehead, Mr Michael and Willison, Professor Hugh and Barnett, Professor Susan and McCanney, George |
Authors: | Whitehead, M. J., McCanney, G., Willison, H. J., and Barnett, S. C. |
College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity |
Research Centre: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Immunobiology |
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 35(21): 4528-4530 |
Publisher Policy: | Reproduced under a Creative Commons License |
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