For the preliminary version of this code, please refer to https://github.com/kzapfe/CSDA
A video representing the detection of centers of mass and tracing of center-of-mass trajectories over time.
This methodology provides a means to define the center of mass of sinks and sources in time at high spatiotemporal resolution in brain slices, which can aid in inferring information transmission.
Using CSD analysis, a disjoint component analysis allows for the dissection of restricted synaptic activation that is obscured by high-voltage electrographic elements. Subthreshold activity, not overtly detected with voltage recordings, can also be better defined and traced in a quantitative manner.
The following codes contain the methods described in the article:
- Zapfe, K.W.P., Romero-Maldonado, I., Gutiérrez, R., High Resolution Detection of Stationary and Evolving 2D-Current Source Density within Neuronal Microcircuits, 2024. (under review for publication)
Created with data extracted from High-Density Multielectrode Arrays (HD-MEAs, 3Brain) using slices of rodent hippocampal tissue.
This code is released under GPL-3.0.
- This software was developed specifically for high-density multielectrode arrays 3Brain BIOCAM X
These notebooks and modules were developed and tested in Julia (versions 1.7.2 and 1.10.2) using Jupyter Notebooks and text editors, across Linux distributions and Windows 10. We recommend using Julia 1.10.x to ensure compatibility with the latest dependencies.
All packages and functions are properly described at the beginning of each module or notebook.
- Install Julia 1.10.x
Visit julialang.org/download to download and install Julia.
Note
You can also check out Julia's previous versions at julialang.org/downloads/oldreleases.
- Clone the repository
git clone https://github.com/LBitn/Hippocampus-HDMEA-CSDA.git- Install the dependencies
Open Julia and run the following commands to install the Julia kernel package for Jupyter Notebooks:
using Pkg
Pkg.add("IJulia");If you already have Jupyter on your computer, this process will add a Julia kernel for Jupyter. Then, you can start Jupyter Notebook as usual by running jupyter notebook in the terminal.
Alternatively, you can let IJulia install and manage its own Jupyter setup. To do this, type the following at the Julia
using IJulia
notebook();- Angel Vazquez Flores: Parameter optimization, testing
- Francisco Victorio Santiago: Testing and suggestions
- Isabel Romero Maldonado: Code and data analysis
- Jorge Antonio Hernández García: Testing and suggestions
- Karel Zapfe Aguilar: Author of the concept and source code
- Luis Reynaldo Ramos González: Testing and optimization
- Rafael Gutiérrez Aguilar: Conceived and designed research
Dr. R. Gutiérrez is based at Department of Pharmacobiology, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional. Please contact the following e-mail: rafagut@cinvestav.mx