christianepedersen / nape_imaging_analysis

UW NAPE Imaging Preprocessing and Analysis

UW NAPE Imaging Analysis/Preprocessing

Welcome to the UW NAPE (Neurobiology of Addiction, Pain, and Emotion) Center's calcium imaging analysis repository. You will find code for preprocessing calcium imaging (primarily 2-photon, GRIN lens-based deep brain imaging) data.

Image created by Morgan Alexander

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

Python 2.7
h5py==2.10.0
future==0.14.3
numpy==1.16.5
Pillow==6.2.0
scikit-image==0.14.5
scikit-learn==0.20.4
scipy==1.2.2
Shapely==1.6.4.post2

Installing

Follow the link below for a step by step tutorial on how to install anaconda (python), the environment with the prerequisites, and the sima code:

• Docs Install Guide

Built With

• SIMA - Adapted motion correction algorithm; Kaifosh et al., 2014

Authors

• Zhe Charles Zhou - Initial work - Zhou NAPE UW
• Tanish Kapur - Initial sphinx setup - Tanish Kapur

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments