FISSA Suite2p Example

July 26, 2021 · View on GitHub

|Binder|

FISSA Suite2p Example

In the notebook we provide an example workflow to combine the FISSA <fissa_>_ and Suite2p <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 <fissa_>_ repository.

You can view <suitehtml_>_ the notebook on GitHub, download <suitedown_>_ it to your local machine, or interact with it in your web browser on Binder <suitebind_>_. Note that launching a Binder session can take 10 minutes.

.. _fissa: https://github.com/rochefort-lab/fissa .. _suite2p: https://suite2p.readthedocs.io/ .. _suitebind: https://mybinder.org/v2/gh/rochefort-lab/fissa-suite2p-example/master?filepath=Suite2p%20example.ipynb .. _suitehtml: https://rochefort-lab.github.io/fissa-suite2p-example/Suite2p%20example.html .. _suiteview: https://github.com/rochefort-lab/fissa-suite2p-example/blob/master/Suite2p%20example.ipynb .. _suitedown: https://raw.githubusercontent.com/rochefort-lab/fissa-suite2p-example/master/Suite2p%20example.ipynb

This notebook can also be run on your own machine. To do so, you will need to:

  1. Download a copy of this repository <download_repo_>_, unzip it, and cd into the fissa-suite2p-example directory.

  2. Create a new conda environment with conda env create --file .binder/environment.yml.

  3. Activate the environment with conda activate suite2p-fissa.

  4. Start up a Jupyter notebook server to run our notebooks jupyter notebook.

If you're new to Jupyter notebooks, here is an approachable tutorial_.

.. _download_repo: https://github.com/rochefort-lab/fissa-suite2p-example/archive/master.zip .. _an approachable tutorial: https://www.datacamp.com/community/tutorials/tutorial-jupyter-notebook

License

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/.

.. |Binder| image:: https://mybinder.org/badge_logo.svg :target: suitebind_ :alt: Open in Binder