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

Michael J Whitehead,George A Mccanney,Hugh J Willison,Susan C Barnett,Robert Murphy

doi:10.1093/bioinformatics/btz403

Michael J Whitehead, George A Mccanney + Show 3 more

Open Access

https://doi.org/10.1093/bioinformatics/btz403

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Journal: Bioinformatics	Publication Date: May 16, 2019
Citations: 29	License type: CC BY 4.0

Affiliation: University of Glasgow

Abstract

SummaryMyelinJ 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 normalize local contrast 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.Availability and implementationMyelinJ is freely available at https://github.com/BarnettLab/MyelinJ. For statistical analysis the freely available R and the ggpubr package are also required. MyelinJ has a user guide (Supplementary Material) and has been tested on both Windows (Windows 10) and Mac (High Sierra) operating systems.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

Myelin is an essential component of the central nervous system (CNS) and its degeneration is associated with spinal cord injury and several CNS diseases, most notably multiple sclerosis (Goldenberg, 2012)
The MyelinJ ImageJ plugin we have developed is a freely available ImageJ (Schindelin et al, 2012) macro that allows for high throughput analysis of individual experiments or large studies
Myelinating cultures were made according to Sorensen et al (2008), demyelinated as described in McCanney et al (2019) and manual analysis of micrographs was performed according to Sorensen et al (2008)

Summary

Introduction

Myelin is an essential component of the central nervous system (CNS) and its degeneration is associated with spinal cord injury and several CNS diseases, most notably multiple sclerosis (Goldenberg, 2012). Myelinating cultures can be used as a high throughput screen for potential therapeutics that promote (re)myelination (McCanney et al, 2018, 2019). One of the main bottlenecks for these screens is the accurate high throughput quantification of myelin sheaths. The MyelinJ ImageJ plugin we have developed is a freely available ImageJ (Schindelin et al, 2012) macro that allows for high throughput analysis of individual experiments or large studies. User interface (GUI) and username system support reproducibility and sharing. This study has only tested MyelinJ using myelinating cultures, it is likely to be useful for analysing slice cultures (Hill et al, 2014) and tissue sections

Materials and methods

Background subtraction

Myelin sheath selection

Statistical analysis

Results

Conclusions