Welcome to HeureCa !
A modular data processing pipeline designed for analysing 2-photon calcium imaging and electrical stimulation experiments created for Hyperstim. This site contains detailed documentation for the analysis pipeline
📖 What You'll Find Here
- Setup: Step-by-step instructions to set up and run the pipeline.
- Descriptions: Overview of the available Python modules and functions.
🔬 About the Project
This pipeline supports the analysis of multi-session two-photon imaging experiments, including:
- Extraction and preprocessing of MESc TIFF files
- Suite2p-based ROI detection and signal extraction
- Automated activation analysis and visualization
- ROI tracking across sessions using CellReg
Technologies Used
- Python 3.9, Suite2p
- MATLAB with CellReg
- Anaconda for environment management
- MkDocs for documentation
Commands for MkDocs development
mkdocs new [dir-name]- Create a new project.mkdocs serve- Start the live-reloading docs server.mkdocs build- Build the documentation site.mkdocs -h- Print help message and exit.mkdocs gh-deploy- Deploy the documentation to GitHub Pages.
Use the sidebar navigation or the links above to get started.