In the notebook we provide an example workflow to combine the FISSA and Suite2p methods.
This repository mainly functions to provide environment files to run this notebook on Binder. For the most up-to-date code and extensive documentation on FISSA, see the FISSA repository.
You can view the notebook on GitHub, download it to your local machine, or interact with it in your web browser on Binder. Note that launching a Binder session can take 10 minutes.
This notebook can also be run on your own machine. To do so, you will need to:
- Download a copy of this repository, unzip it, and cd into the
fissa-suite2p-exampledirectory. - Create a new conda environment with
conda env create --file .binder/environment.yml. - Activate the environment with
conda activate suite2p-fissa. - Start up a Jupyter notebook server to run our notebooks
jupyter notebook.
If you're new to Jupyter notebooks, here is an approachable tutorial.
Unless otherwise stated in individual files, all code is Copyright (c) 2015–2021, Sander Keemink, Scott Lowe, and Nathalie Rochefort. All rights reserved.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.