notebooks for workshop on analyzing data from the two-photon mesoscope

This repository contains a collection of Jupyter notebooks, alongside sample data, for demonstrating some basic analyses of mesoscope data. It includes basic data processing and conversion using the mesoscope package, as well as analysis of both low magnification and high magnification data using thunder, thunder-extraction, and thunder-registration.

You can use Binder to run a hosted version of this tutorial. Just click this badge.

To run these notebooks locally, first make sure you have a recent version of Python 3 — we highly recommend using Anaconda, a distribution of Python that comes bundled with common scientific computing libraries.

Then clone this repository by typing

git clone https://github.com/freeman-lab/mesoscope-workshop

And inside the folder mesoscope-workshop type

pip install -r requirements.txt

Which will install all the dependencies.