Welcome to NAPE Center Calcium Imaging Analysis Documentation Site!

Welcome to the University of Washington Center for Neurobiology of Addiction, Pain, and Emotion (NAPE) 2-photon calcium imaging analysis documentation website. Here we provide comprehensive documentation and guidelines for using the preprocessing and analysis tools for deep brain, GRIN-lens 2-photon calcium imaging.

Custom code and documentation were written by Zhe Charles Zhou and Tanish Kapur.

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Contents

• Anaconda, Jupyter Notebook, SIMA Installation Guide
  • Starting Anaconda and installing an environment
  • Using jupyter notebook to edit and run (SIMA) code
  • Troubleshooting
• Installation of suite2p on Windows
• Suite2p Preprocessing Pipeline
• Suite2p Segmentation Parameter Explanations and Demos