Dataset Information

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

ABSTRACT:

Summary

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 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 implementation

MyelinJ 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.

SUBMITTER: Whitehead MJ

PROVIDER: S-EPMC6821319 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

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

Whitehead Michael J MJ McCanney George A GA Willison Hugh J HJ Barnett Susan C SC

Bioinformatics (Oxford, England) 20191101 21

<h4>Summary</h4>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 usin ...[more]

PMID: 31095292

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Dataset Information

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

Summary

Availability and implementation

Supplementary information

Publications

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

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