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.
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
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
Follow the links below for step by step tutorials on how to install anaconda (python), the environment with the prerequisites, and run the code:
The main jupyter notebook script for the preprocessing pipeline (main_parallel.ipynb) resides in the napeca folder. The main Bruker/tiff prepreprocessing script is in the napeca/prepreprocess folder.
- SIMA - Adapted motion correction algorithm; Kaifosh et al., 2014
- Zhe Charles Zhou - Initial work - Zhou NAPE UW
- Tanish Kapur - Initial sphinx setup - Tanish Kapur
- Alex De Lecea - Documentation Development - Alex De Lecea
If the code and resources outlined here are helpful to your project, we encourage you to cite/acknowledge the UW NAPE Imaging Core. Thank you!
This project is licensed under the MIT License - see the LICENSE.md file for details