The multi-electrode array technique (MEA) produces a high quantity of data relating to excitable cell activity. This data can often be complex and time-consuming to analyse in a reproducible manner. Furthermore, limited resources are available to calculate burst parameters for individual electrodes as opposed to the whole well. The MEAanalysis package provides functions which can assist with MEA data analysis and exploration at the single electrode level, through downstream visualisation of electrode burst list files produced by AxIS Navigator 3.6.2 software (Axion BioSystems), whilst enabling comparison of bursting parameters between different time intervals. This package has been designed to be compatible with 12- and 24- well MEA plates.
The package can be installed from gitHub using devtools::install_github("egordon2/MEA-analysis-package/MEAanalysis") or by cloning the repository (https://github.com/egordon2/MEA-analysis-package). Once the package is installed it can be loaded using the library("MEAanalysis") command. It is possible the user will need to update existing packages to conform with the package dependencies, however they should be notified of this in the terminal. Once the package is installed it can be loaded using the library(“MEAanalysis”) command.
If the user requires workflow vignettes to be included in the package then they should run the devtools::install_github(“egordon2/MEA-analysis-package/MEAanalysis”, build_vignettes = TRUE) command during installation, ensuring the build_vignettes argument is included. These vignettes can then be viewed directly in R studio using the vignette(package=“MEAanalysis”) command.
MEAanalysis functions utilise electrode burst files exported from the AxIS Navigator 3.6.2 software (Axion BioSystems) as their input. This analysis needs to be carried out prior to the below workflows. To view information on how to do this, as well as the specific parameters used in the example workflows, click here.
The following example workflows have been included to demonstrate how this package may be used to analyse MEA data:
1) To create a bar chart visualisation of either number of bursts, number of spikes per burst, burst duration, and mean inter-spike interval within a burst for single electrodes click here.
2) To create a bar chart visualisation of either average number of bursts, number of spikes per burst, burst duration, and mean inter-spike interval within a burst for each well click here.
3) To create a heatmap visualisation of the well average synchrony index recorded by an MEA click here.
For more information on the individual function arguments please see the associated help pages. This can be done using the following code: help(package = "MEAanalysis")
This package is still in the development phase. Please send any feedback you may have to emily.gordon@wadham.ox.ac.uk so it can be incorporated into later versions of the package.