Clusters of cooperative ion channels enable a membrane potential-based mechanism for short-term memory

Paul Pfeiffer 6007674046 ignore pycharm files 4 years ago
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scripts 4197d0d449 automatic generation of a report 4 years ago
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README.md

Clusters of cooperative ion channels enable a membrane potential-based mechanism for short-term memory

This data repository holds the dynamic clamp recordings and analysis scripts to test whether cooperative ion channels could produce persistent activity in perirhinal cortex neurons.

Overview

Recordings

Cells were patchclamped and the dynamic clamp was used to emulate the presence of multiple clusters of cooperative ion channels. in the membrane.Succesive current pulses were used to test for persistent activity and graded persistent activity.

Analysis

The stimulation protocols were categorized according to the number of pulses and whether the pulses were de- or hyperpolarizing. Then recordings with increasing (respectively decreasing) levels of persistent activity were labelled as successful trials.

Structure of the repository

The repository is structured as follows

  • recordings: each folder in here corresponds to a recording session from the recording software RELACS
  • metadata: contains a mapping of cells to the above recording sessions and a manually created blacklist of protocols that are excluded from the analysis
  • scripts: python scripts to read in the recordings, analyse the firing rates and generate a report
  • out: contains the automatically generated pdf report with an overview of all cells and plots of each stimulation

How to rerun the analysis

Tested in Linux

  1. Install python dependencies e.g. via conda
   conda env create -f environment.yml 
  1. Run analysis and generate the report
   make all