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kushalkolar committed Jul 16, 2020
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| <span> | <span> | <span> | <span> |
|--------|--------|--------|--------|
| PyPI | [![PyPI version](https://badge.fury.io/py/mesmerize.svg)](https://badge.fury.io/py/mesmerize) | Downloads | [![Downloads](https://pepy.tech/badge/mesmerize)](https://pepy.tech/project/mesmerize) |
| License | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | Maintenance | ![GitHub commit activity](https://img.shields.io/github/commit-activity/m/kushalkolar/MESmerize) |
| Documentation | [![Documentation Status](https://readthedocs.org/projects/mesmerize/badge/?version=master)](https://mesmerize.readthedocs.io/en/master/?badge=master) | Code analysis | [![Maintainability](https://api.codeclimate.com/v1/badges/950e956456b688c0886e/maintainability)](https://codeclimate.com/github/kushalkolar/MESmerize/maintainability) |
| Chat & Help | [![Gitter](https://badges.gitter.im/mesmerize_discussion/community.svg)](https://gitter.im/mesmerize_discussion/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) | Issue tracker | ![GitHub issues](https://img.shields.io/github/issues/kushalkolar/MESmerize) |
| License | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | Maintenance | [![GitHub commit activity](https://img.shields.io/github/commit-activity/m/kushalkolar/MESmerize)](https://github.com/kushalkolar/MESmerize/commits/master) |
| Documentation | [![Documentation Status](https://readthedocs.org/projects/mesmerize/badge/?version=master)](http://docs.mesmerizelab.org/en/master/?badge=master) | Code analysis | [![Maintainability](https://api.codeclimate.com/v1/badges/950e956456b688c0886e/maintainability)](https://codeclimate.com/github/kushalkolar/MESmerize/maintainability) |
| Chat & Help | [![Gitter](https://badges.gitter.im/mesmerize_discussion/community.svg)](https://gitter.im/mesmerize_discussion/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) | Issue tracker | [![GitHub issues](https://img.shields.io/github/issues/kushalkolar/MESmerize)](https://github.com/kushalkolar/MESmerize/issues) |

Mesmerize is a platform for the annotation and analysis of neuronal calcium imaging data. Mesmerize encompasses the entire process of calcium imaging analysis from raw data to interactive visualizations. Mesmerize allows you to create FAIR-functionally linked datasets that are easy to share. The analysis tools are applicable for a broad range of biological experiments and come with GUI interfaces that can be used without requiring a programming background.

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<img src="https://www.biorxiv.org/sites/default/files/site_logo/bioRxiv_logo_homepage.png" alt="manuscript on biorxiv" width="160"/>
</a>

## Video Tutorials!
We have recently created detailed video tutorials! The main tutorial series provides a quick overview that takes you from raw imaging data, to downstream analysis and interactive visualizations:\
https://www.youtube.com/playlist?list=PLgofWiw2s4REPxH8bx8wZo_6ca435OKqg

Additional videos on specific aspects of Mesmerize will be posted here:\
https://www.youtube.com/playlist?list=PLgofWiw2s4RF_RkGRUfflcj5k5KUTG3o_

More tutorial videos will be available soon.

## Installation

If you're familiar with anaconda or virtual environments, installation is as simple as:
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After installation simply call ``mesmerize`` from inside the virtual environment to launch it.

If you're unfamiliar with virtual environments, see the docs for more detailed instructions on all operating systems:
http://mesmerizelab.org/user_guides/installation.html
http://docs.mesmerizelab.org/en/master/user_guides/installation.html

#### Caiman
In order to use [CaImAn](https://github.com/flatironinstitute/CaImAn) features you will need to have [CaImAn](https://github.com/flatironinstitute/CaImAn) installed into your environment. See the Mesmerize installation instructions linked above for more details: https://mesmerize.readthedocs.io/en/master/user_guides/installation.html
In order to use [CaImAn](https://github.com/flatironinstitute/CaImAn) features you will need to have [CaImAn](https://github.com/flatironinstitute/CaImAn) installed into your environment. See the Mesmerize installation instructions linked above for more details: http://docs.mesmerizelab.org/en/master/user_guides/installation.html

Caiman is used for the following Viewer modules: CNMF, 3D CNMF, CNMFE, caiman motion correction and Detrend DFOF.

#### tslearn
In order to use tslearn features you will need ``tslearn~=0.2.2``. This can be installed via pip or conda, see the detailed installation instructions for more details: https://mesmerize.readthedocs.io/en/master/user_guides/installation.html
In order to use tslearn features you will need ``tslearn~=0.2.2``. This can be installed via pip or conda, see the detailed installation instructions for more details: http://docs.mesmerizelab.org/en/master/user_guides/installation.html

tslearn is used for KShape clustering, cross-correlation analysis, and some of the flowchart nodes

## Documentation
Documentation is available here: [http://www.mesmerizelab.org/](http://www.mesmerizelab.org/)
Documentation is available here: [http://docs.mesmerizelab.org/](http://docs.mesmerizelab.org/)

## Questions/Discussions

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