Direct Extraction of Signal and Noise Correlations from Two-Photon Calcium Imaging of Ensemble Neuronal Activity

This repository is the official implementation of 'Direct Extraction of Signal and Noise Correlations from Two-Photon Calcium Imaging of Ensemble Neuronal Activity'.

Requirements

This code was originally implemented in MATLAB R2017B. However, it should run in most versions without a problem.

Instructions

1. Download all the codes in a single directory
2. Run the script main.m

Results

Following these steps will regenerate the Figures (Figure 2) and results outlined in the Simulation study 1, in the Results section.

Contents

The tasks performed by each MATLAB function are explained in detail in their headers and comments. In summary:

1. main.m : Master script
2. generate_signals.m: Generates the simulated data
3. proposed_estimation_procedure.m: The implementation of the proposed iterative procedure
4. performance_evaluation.m: Used for Hyper-Parameter tuning
5. redblue.m: colormap for correlation plots
6. spike_deconvolution_FCSS.m: Generates the deconvolved spikes for two-stage estimates