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stg embedding

This repository contains code to reproduce every figure in

Mapping circuit dynamics during function and dysfunction

Installation and prerequisites

You will need MATLAB.

Download the following repositories and add them to your MATLAB path:

https://github.com/sg-s/stg-embedding
https://github.com/sg-s/srinivas.gs_mtools
https://github.com/sg-s/crabsort
https://github.com/KlugerLab/FIt-SNE

Data

The raw data is >30TB and getting it into your hands is not easy. Instead we provide reduced data consisting of spiketimes, metadata and various annotations. This should allow you to reproduce every figure in the paper.

To get the data, download it from Zenodo.

How to regenerate figures

  1. First, download the code and add to path (see above).
  2. Then, download the data and put it in a folder called "reduced-data" within your "stg-embedding" folder. You will have to create this if needed.
  3. Then, navigate to the paper-figures folder and run any script to generate that figure. For example, to generate Figure 2, run: fig_embedding.

License

GPL v3

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Embedding spike times from a small neural circuit to map how collective dynamics change under different conditions

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