KISN-pancortical-kinematics

Data analyses for e-phys and 3D tracking experiments

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Code used to generate findings presented in "Behavioral decomposition reveals rich encoding structure employed across neocortex" (bioRxiv, 2022). The "Rat 3D Tracking & E-Phys KISN 2020 Dataset", generated for the purposes of this project, can be downloaded at figshare.

To run the code, download the data and clone the repository in a virtual environment with the installed packages listed in the file requirements.txt. Installation time should be under one minute.

Prerequisites

• Python 3.9 (and add it to top of PATH)
• git (and add it to PATH)

Installation and updating

Clone repository with command below.

git clone https://github.com/bartulem/KISN-pancortical-kinematics.git

For example, to plot spiking cross-correlation examples, one would run:

from make_example_plots import PlotExamples
PlotExamples(cch_data_dir='/.../noise_correlations/analyses',
             area_file='synaptic_AA.json',
             cell_pair_id='imec0_cl0185_ch087-imec0_cl0192_ch093',
             sp_profiles_csv=sp_profiles_csv,
             save_dir='/.../Downloads',
             save_fig=False,
             fig_format='svg').plot_spiking_cch(add_prob=True,
                                                fig_size_of_choice=True,
                                                to_normalize=True,
                                                plot_pair_position=False)

Developed and tested in PyCharm 2021.3.3 on Windows 10, Ubuntu 20.04 and 22.04 LTS.