Code

Internal open-source software

Code developed by yours truly. Feel free to become a contributor!

PyCaAn (Python):

Toolbox for extracting tuning curves using a novel information theory approach, extract manifolds, model and decode neural activity,... all this using a simple and reproducible parametric approach that supports single session, batch processing, and open file standards!

Decoding behavior from calcium imaging data (python, MATLAB):

Code (and companion paper) to decode behavior from microendoscopic calcium imaging recordings

Miniscope analysis (MATLAB):

Pipeline to process, register, and extract data from calcium imaging recordings

PIMPN (Python):

Notebook to process, register, and extract data from calcium imaging (cloud support via Google Colab). Includes a pretrained model for deep learning analysis of behavior

Code for Etter et al., 2023 (python, MATLAB)

External open-source software

Code developed by others that I strongly recommend checking out!

RatInABox

Awesome suite to simulate animal exploration and associated neural representations! Very well written and easy to modulate/augment for use cases.

DeepLabCut:

A classic, deep-learning tool to track animal poses (individual limbs).

Caiman:

A Python toolbox for extracting calcium and voltage imaging video in 1- and 2-photon setups.