Reconstruction and simulation of an entire column of the cerebellar cortex

Required steps to reproduce De Schepper et al. 2022

Installing the full software environment

This step is not always required, to simply reproduce the plots from the available datasets, this can be skipped.

pip install -r requirements.txt --only-binary=":all:"

If you're planning to use MPI, also install mpi4py:

pip install mpi4py

Usage

1. Plot all figures

python plot

2. Plot specific figures

python plot figure1 figure2

The figure names correspond to the filenames without the suffix

3. Build the static image files

python build [format]

The default format is EPS.

Obtaining the data

You can obtain an already reconstructed version of the network model at https://doi.org/10.5281/zenodo.7230288 and save it as /networks/balanced.hdf5. Otherwise you can reconstruct it yourself by downloading the morphologies as morphologies.hdf5 running:

bsb -v=4 -c=configs/balanced.json compile

To replicate the figures, you require certain result files in exact locations inside of the results folder. These files are available as datasets on Zenodo, here is a list of URLs for each plot:

• feedforward_jitter: https://doi.org/10.5281/zenodo.7230239 (place in: results/single_impulse/sensory_burst)
• feedforward: https://doi.org/10.5281/zenodo.7230798, https://doi.org/10.5281/zenodo.7230830, https://doi.org/10.5281/zenodo.7230836 (place in: results/clamp)
• goc_nspos, goc_sync*: https://doi.org/10.5281/zenodo.7231068 (place in: results)
• goc_nsync, goc_sync*: https://doi.org/10.5281/zenodo.7231161 (place in: results)
• goc_oscillations: https://doi.org/10.5281/zenodo.7231187 (place in: results/oscillations)
• grc_activation_overlap: Calcium signal datasets too large to be uploaded (1.44TB). Please reproduce using sensory_burst_calcium_dense.json.

Reproduce the results

In order to reproduce the results for yourself, install bsb==3.10.3 and use the balanced.hdf5 network to simulate the configuration files you can find in the configs folder. Place the result files for each config as dictated by this config-to-location list: