Dunnart neural activity analysis

Jupyter notebook and Python code for the analysis of neuronal ensembles and travelling waves in the cerebral cortex of the fat-tailed dunnart from calcium imaging data, as published in our study:

Suárez, R. et al. Cortical activity emerges in region-specific patterns during early brain development. Proceedings of the National Academy of Sciences 120, e2208654120 (2023), doi: 10.1073/pnas.2208654120.

 

Overview

This repository contains:

• The Jupyter notebook dunnart_analysis.ipynb which runs the complete pipeline for analysing the calcium imaging data, generating results and rendering figures for our published study.
• Custom modules called from the notebook including:
  • caimaging/tools for extracting neural activity from 2D calcium imaging data using an ROI grid.
  • fcnetwork/ggm,networkviz and stats for estimating functional connectivity between ROIs using Gaussian graphical modelling and qunatifying properties of neuronal ensembles and network structure.
  • wavetrack/wave_cc, wave_viz and direction_stats for tracking and analysing properties of travelling wave activity.

Installation and usage

To run the notebook (or use the custom functions on your own data):

1. Clone the repository.
2. Install the environment with conda using the included YAML file.

conda env create -f dunnart_analysis.yml

1. Download the data (see Data availability).
2. Set the datapath, scratchpath and figpath environment variables in the second code block of the notebook. The datapath must point to the raw-2p folder in the downloaded data. Create directories for figpath and scratchpath as necessary.
3. Run all cells in order.

Data availability

The data for this project are available for download at: https://doi.org/10.48610/5ccfb47

References

Please see the companion paper linked above for details of the methods and packages used in this code.

Citing this code

If you use or adapt our code or methods in your research, please cite the companion paper linked above or as shown here in BibTeX format:

@article{
doi:10.1073/pnas.2208654120,
author = {Rodrigo Suárez  and Tobias Bluett  and Michael H. McCullough  and Lilach Avitan  and Dylan A. Black  and Annalisa Paolino  and Laura R. Fenlon  and Geoffrey J. Goodhill  and Linda J. Richards },
title = {Cortical activity emerges in region-specific patterns during early brain development},
journal = {Proceedings of the National Academy of Sciences},
volume = {120},
number = {22},
pages = {e2208654120},
year = {2023},
doi = {10.1073/pnas.2208654120}
}

This repository was archived on Zenodo on the date of publication:

Questions

Please email michael.mccullough@anu.edu.au if you have questions about the code.