In this repository, I provide a few scripts that I used to analyze and visualize calcium imaging data. The scripts are not fully polished, but functional(ish).
OpenField_Analysis.py This script is intended for the analysis of open field experiment data. It includes functions for loading, processing, and analyzing the data.
- Firing rate
- PSTH
- Place cells
- speed cells
- etc.
GUI_Explore_OpenField_Data.py This script provides a graphical user interface for exploring open-field data. It is built with qt. The GUI is still a work in progress, but I hope it gives a idea of what I am trying to achieve.
data/E8KO_1234 This file is an example dataset that can be used to test the functionality of the GUI and the analysis script. It contains synthetic data (generated with RatInABox toolbox) structured similarly to typical open field experiment datasets. Results_OLM_Ca_Events.pkl can be visualized with the GUI.
Requirements :
- pandas
- numpy
- PyQt5
- pyqtgraph
- matplotlib
- pathlib
- scipy
- pynapple
- tqdm