pMAT (Photometry Modular Analysis Tool)

Version 1.3 BETA is now available!!!

• Spike detection protocol!
• Bug fixes
• Accompanying YouTube videos
• Increased Mac compatibility (We're not Mac folks here in the Barker Lab, so bear with us).
• MAC USERS: PLEASE USE VERSION 1.3 FOR ALL OF THE BUG FIXES!

What is pMAT?

Fiber Photometry is a tool for neural imaging of calcium or neurotransmitter dynamics. Many commercial systems exist for recording data, but analysis software is lacking across the field. Here we've introduced an open-source analysis package that can be used widely to standardize analysis approaches.

Basic Workflow 🧑‍💻

Sample Data 🧪💾

Below are links to sample data files from either Tucker Davis Technologies (TDT) or a generic comma-separated value ('.CSV') format. These files provide examples of how files should be formatted for use in pMAT and can also be used when learning to process data in pMAT.

• Tucker-Davis Technologies sample data 💾
• Comma separated values (CSV) sample data 💾

YouTube Video Tutorials 🎞️

• ⭐⭐⭐Training Playlist for new users⭐⭐⭐

Single topic videos:

• Installing pMAT as an independent application
• Installing pMAT for MATLAB
• Loading TDT data into pMAT
• Loading Other data formats into pMAT as a CSV file
• pMAT Options Module tutorial
• pMAT Export Data Module tutorial
• pMAT Plot Trace Data Module tutorial

MORE VIDEOS COMING SOON!!! STAY TUNED!!!

Planned Updates 📜

Check back or get in touch with us regarding future updates

• [x] Spike Detection
• [ ] Import function for Neurophotometrics Data
• [ ] Import function for FIP systems
• [ ] Compatibility with other open-source platforms (e.g., SimBA)
• [ ] Control channel-free detrending algorithms.
• [ ] Increased compatibility with TDT features (e.g., Behavioral notes).

License 📃

This project is licensed under the GNU Lesser General Public License v3.0. Note that the software is provided "as is", without warranty of any kind, express or implied.

Some notable details ‍💻

• Developed and tested in Windows on MATLAB 2019a and 2020a.
• A special thank you to John Woodward, who has helped us troubleshoot Mac compatibility (MATLAB version only).
• MATLAB Runtime 9.8 and above have worked for standalone installation
• Installation time is typically around 10 minutes (not including MATLAB installation).

References 📜

• Pre-print: pMAT: An Open-Source, Modular Software Suite for the Analysis of Fiber Photometry Calcium Imaging
• The original scripts behind the GUI can be found here for those interested in writing their own MATLAB code

Contributors 👨‍🔬👩‍🔬

• David Barker
• David Estrin
• Carissa Bruno
• Chris O'Brien
• Svetlana Bryant
• Jennifer Mejaes
• Carina Pizzano