Overview

Repository for the analysis of electrophysiological data after spike sorting. Analyses are focused to single cell medial prefrontal cortex (mPFC) activity during an auditory delayed comparison working memory task (Parametric Working Memory, PMW) in rats. Moreover, they are inspired by those done by Romo ... Brody et al. 1999 in macaques.

Highlights

• functions for aligning kilosort spike sorting output with Bdata SQL tables containing behavioral data
• flexible python code for exploratory visualizations of neural activity during stimulus and delay period conditioned on multiple features
• inspired by the Spykes library & rewritten with updated python syntax & seaborn visuals

Steps

• (1) Align spike and behavioral data (\kilosort_bdata_alignment)
• (2) Import to python (io_utils.py)
• (3) Visualization and analyses (plotting_utils.py)

Usage

git clone  https://github.com/Brody-Lab/jbreda_PWM_mPFC_analysis

conda create -n PWM_ephys python=3.7 pip numpy matplotlib scipy scikit-learn h5py pyqt cython pillow black seaborn jupyter statsmodels pydove

conda activate PWM_ephys
pip3 install jedi==0.17.2 # for tab complete bug

Tutorial

See the 2021_Tutorial.ipynb notebook for example usage.

Assumptions

(1) This repo is built as a continuation of the output from the jbreda_kilsort repository that was designed for analyzing wireless tetrode data in kilosort and uses the same file structure.

(2) Functions for spike & behavior alignment are written to be run after all sorting is done on a per animal basis. But, if needed, this could be easily changed