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SEBA - Simple Ephys-Behavior Analysis

SEBA is a small package that standardizes and automates exploratory analysis of electrophysiological data not only in combination with behavior but also any stimuli with recorded and synchronized timestamps.

It's based on the output of https://github.com/jenniferColonell/ecephys_spike_sorting for ephys data and https://github.com/JingyiGF/HERBS for probe tracing from histological images.

SEBA can import behavior annotation data from BehaView and BORIS (DLC2Action and SimBA will be added in future updates) and based on spike data and timestamps of behavior or stimuli it builds a comprehensive data structure which is then used in visualisation and further analysis.

Expected folder structure is:

  1. data_folder:
    • ephys_recording_1
    • ephys_recording_2
    • ephys_recording_3
    • ...

Each ephys_recording folder should contain results of an sglx_multi_run_pipeline.py run from ecephys_spike_sorting.

SEBA uses HERBS output to assign to each neuron obtained with ecephys_spike_sorting it's location and adds this information to cluster_info_good.csv - a file that contains only neurons labeled as good by both kilosort and the user.

Examples of plots that can be created using the package. Users can choose between plotting data for all neurons or only responsive neurons, plot based on z-score or firing rate and for between plotting combined results for all animals or plot data per animal.

Heatmaps of the neural acitvity per behavior:

Comparison heatmaps (same neuron response between behaviors/stimuli):

Comparison PSTH plots:

PSTH combined with a raster plot for resposivity verification:

Simple linear regression:

Summary heatmap structures vs behaviors/stimuli overlap (how many cells per structure encode a specific behavior):

Matrix visualising overlap of neurons per behavior/stimulus:

For workflow example check example_notebook

Installation:

conda create -n SEBA python=3.10
conda install git
conda install pip
git clone https://github.com/KonradDanielewski/SEBA
cd SEBA
pip install .

Developed by Konrad Danielewski, partially based on script by Kacper Kondrakiewicz https://github.com/KacperKon/EphysAnalysis