sje30/epameadev repository overview

⁠EPAmeadev

This is the repository to accompany our 2016 paper freely available at http://dx.doi.org/10.1177/1087057116640520⁠

Characterization of Early Cortical Neural Network Development in
Multiwell Microelectrode Array Plates

Ellese Cotterill, Diana Hall, Kathleen Wallace,
William R Mundy, Stephen J Eglen, Timothy J Shafer

Journal of Biomolecular Screeing (2016)

You are free to use any of the data or resources in this repository. We do request however that if you use this material, you cite the above paper in any work that you publish.

⁠Data files

The data files for this project are stored in allH5Files⁠. They are stored in the HDF5 format as outlined in our 2014 paper⁠. Our analysis package, sjemea⁠ can read in these files as follows:

library(sjemea)
s = h5.read.spikes("allH5Files/CO_20140212_MW1007-51_DIV12_00_001.h5")
fourplot(s)

These are the first multi-well datasets that we have published, so some of the data in the HDF5 fields has not previously been documented. The new fields include:

1. /dose dosage of any drug (not used here) to each well.
2. /treatment any manipulation performed to a well (all "control" in this study).

⁠Analysis code

Our analysis was done in R, using mostly standard packages. See the files in analysis_code⁠ for details. You will need to change the file analysis_code/well_analysis.R⁠ so that the following variable points to the correct location of the data:

mea.data.dir <- "~/EPAmeadev/tree/master/allH5Files"

⁠TODO

1. Push to zenodo when ready.

⁠Docker

work in progress.