neuro-mine 0.3.0

Identifies the contribution of behavioural and stimulus parameters to nerual activity

Model Identification of Neural Encoding (MINE) 🧠💻

Welcome to MINE: your handy companion for processing neuronal response data! This program allows users to use MINE to train a flexible convolutional neural network (CNN) to analyze experimental datasets containing neural activity and corresponding predictors (e.g., behavioral responses).

Application:
- Any model organism
- Any type of predictor data (stimuli and/or behavior)
- Any type of response data (imaging or spikes)

Limitation:
- Data must be continuous in time, and time must be monotonically increasing (i.e., any discontinuity between epochs must be resolved prior to fitting)

Authors:
Dr. Martin Haesemeyer
Jamie Costabile
Dr. Kaarthik Balakrishnan
Sina Schwinn
Danica Matovic

Publication: Costabile JD, Balakrishnan KA, Schwinn S, Haesemeyer M. Model discovery to link neural activity to behavioral tasks. Elife. 2023 Jun 6;12:e83289. doi: 10.7554/eLife.83289. PMID: 37278516; PMCID: PMC10310322. https://elifesciences.org/articles/83289

GitHub Repository of Original Publication: https://github.com/haesemeyer/mine_pub
Lab Website: https://www.thermofish.org/

All code is licensed under the MIT license. See LICENSE for details.
© Martin Haesemeyer, Jamie D Costabile, Kaarthik A Balakrishnan, and Danica Matovic 2020-2025
Questions may be directed to [e-mail]

Quick Start

[1] Create an environment using Python v3.9

conda create -n mine python=3.9

[2] Activate new environment

conda activate mine

[3] Install MINE from PyPi

pip install neuro_mine

[4] Run program

Mine-gui

** to see possible command line prompts to customize the model, run the command:

Mine --help

.csv File Requirements:
- Predictor data must have time as the first column and it must be named 'time'; for optimal outputs, predictor columns should be meaningfully labelled (e.g., 'temperature' or 'left_paw') in the header
- Reponse data must have time as the first column and the responses must be in adjacent columns; column titles (a header) are supported but are not mandatory