NeuralProcessingTools

Introduction

This package contains tools for analyzing data recorded during electrophysiological experiments using multi-channel extra cellular electrodes.

Installation

pip install git+https://github.com/grero/DataProcessingTools
pip install git+https://github.com/grero/NeuralProcessingTools

Usage

A complete example

Here is an example of how to compute raster and psth for a list for a list of cells and step through plots of both using PanGUI

import DataProcessingTools as DPT 
import NeuralProcessingTools as NPT 
import numpy as np
import os
import PanGUI

# change this to wherever you keep the data hierarchy
datadir = os.path.expanduser("~/Documents/workingMemory")

# get all the cells for one session
with DPT.misc.CWD(os.path.join(datadir, "Whiskey/20200106/session02")):
    cells = DPT.levels.get_level_dirs("cell")

# gather rasters and PSTH for these cells, for the error trials
bins = np.arange(-300, 1000.0, 10)
with DPT.misc.CWD(cells[0]):
    raster = NPT.raster.Raster(-300.0, 1000.0, "stimulus1", "reward_on", "stimulus1",
                               redoLevel=1, saveLevel=0)
    psth = NPT.psth.PSTH(bins, 10, trialEvent="stimulus1", sortBy="stimulus1", trialType="reward_on",
                         redoLevel=1, saveLevel=0)
for cell in cells[1:]:
    with DPT.misc.CWD(cell):
        praster = NPT.raster.Raster(-300.0, 1000.0, "stimulus1", "reward_on", "stimulus1",
                                    redoLevel=1, saveLevel=0)
        raster.append(praster)
        ppsth = NPT.psth.PSTH(bins, 10, trialEvent="stimulus1", sortBy="stimulus1", trialType="reward_on",
                              redoLevel=1, saveLevel=0)
        psth.append(ppsth)

app = PanGUI.create_window([raster, psth], cols=1, indexer="cell")

See this notebook for more usage examples.