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README.md

Spatially structured perisomatic inhibition organized along polarized fast-spiking interneuron axons

How to setup the python environment

It is recommended to use Anaconda to create a virtual environment with the necessary dependencies. With anaconda, it is a one button install. After cloning the repository and changing into the root folder, type

conda env create -f environment.yml

This creates an environment called interneuron_polarity, which can be activated via

conda activate interneuron_polarity

To run the scripts, you also need to make the repository folder available in the python path (requires conda--build)

conda develop .

How to run the simulation

The entire process is split in three main scripts: run, analysis and plotting. We use pypet to organize our simulations and save intermediate results.

Simulate the spatial networks

The simulation is setup and run via

cd scripts/spatial_network/perlin_map
python run_simulation_perlin_map.py

This script also contains the relevant parameter settings such as network size or the form of the interneuron axons. To allow exceution of the script in a reasonable time, we reduced the number of input maps that are tested . In the script, you find instructions to make the full run. After the script has successfully finished, you find the output in the data folder.

Analysis of the network activity

A preliminary analysis of the simulated data is done by running

python preliminary_analysis_perlin_map.py

To run both simulation and preliminary analysis

python run_and_analyze_perlin.py

Generate plots

The final analysis and figure generation is done by

python final_analysis_and_plotting_perlin_map.py

Supplemental figure

For the supplement figure, a pinwheel map is used as an alternative input map. The run, analyse and plot scripts are organized in the same manner but found in the folder scripts/spatial_network/supplement_pinwheel_map.

Additional Ressources

The simulation saves the generated data in a hdf5-file. Since the full parameter exploration used for the model section of the paper requires significant time to run, the generated data set can also be downloaded from the following location. When the pre-simulated dataset is used, only the figure script needs to be executed to get the results of the data analysis. Note that the save file will be overwritten when the simulation is started again.

Download location with following content:

  • Full perlin data set: spatial_network_perlin_map.hdf5
  • Full pinwheel data set: spatial_network_pinwheel_map.hdf5
  • Pregenerated pinwheel maps: precalculated_pinwheel_maps.hdf5
datacite.yml
Title Spatially structured inhibition defined by polarized parvalbumin interneuron axons promotes head direction tuning
Authors Peng,Yangfan;Institute for Neurophysiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany;ORCID:0000-0002-0317-1353
Barreda Tomas,Federico J.;Institute for Integrative Neuroanatomy, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
Pfeiffer,Paul;Institute for Theoretical Biology, Humboldt – Universität zu Berlin, 10115 Berlin, Germany;ORCID:0000-0001-5324-5886
Drangmeister,Moritz;Institute for Theoretical Biology, Humboldt – Universität zu Berlin, 10115 Berlin, Germany;ORCID:0000-0002-5947-162X
Schreiber,Susanne;Institute for Theoretical Biology, Humboldt – Universität zu Berlin, 10115 Berlin, Germany;ORCID:0000-0003-3913-5650
Vida,Imre;Institute for Integrative Neuroanatomy, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany;ORCID:0000-0003-3214-2233
Geiger,Jörg R. P.;Institute for Neurophysiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt – Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
Description Anatomical organization of an inhibitory cortical microcircuit suggests an intrinsic compass supporting spatial navigation.
License Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References
Funding
Keywords Neuroscience
Presubiculum
Structured Inhibition
Spatial Network Model
Resource Type Software