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pMAT (Photometry Modular Analysis Tool)

License: LGPL v3

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.

YouTube Video Tutorials 🎞️

Single topic videos:

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

Planned Updates 📜

Check back or get in touch with us regarding future updates

  • 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 📜

Contributors 👨‍🔬👩‍🔬

About

Fiber Photometry Modular Analysis Tool Suite

Resources

Readme
GPL-3.0 license
Activity

Stars

44 stars

Watchers

4 watching

Forks

9 forks
Report repository

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Packages

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GitHub - djamesbarker/pMAT: Fiber Photometry Modular Analysis Tool Suite · GitHub
Skip to content
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pMAT (Photometry Modular Analysis Tool)
License: LGPL v3
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.
YouTube Video Tutorials 🎞️
Single topic videos:
MORE VIDEOS COMING SOON!!! STAY TUNED!!!
Planned Updates 📜
Check back or get in touch with us regarding future updates
  •  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 📜
Contributors 👨‍🔬👩‍🔬
About
Fiber Photometry Modular Analysis Tool Suite
Resources
Readme
GPL-3.0 license
Activity
Stars
44 stars
Watchers
4 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

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GitHub - djamesbarker/pMAT: Fiber Photometry Modular Analysis Tool Suite · GitHub
Skip to content
BranchesTags
Repository files navigation
pMAT (Photometry Modular Analysis Tool)
License: LGPL v3
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.
YouTube Video Tutorials 🎞️
Single topic videos:
MORE VIDEOS COMING SOON!!! STAY TUNED!!!
Planned Updates 📜
Check back or get in touch with us regarding future updates
  •  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 📜
Contributors 👨‍🔬👩‍🔬
About
Fiber Photometry Modular Analysis Tool Suite
Resources
Readme
GPL-3.0 license
Activity
Stars
44 stars
Watchers
4 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

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GitHub - djamesbarker/pMAT: Fiber Photometry Modular Analysis Tool Suite · GitHub
Skip to content
BranchesTags
Repository files navigation
pMAT (Photometry Modular Analysis Tool)
License: LGPL v3
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.
YouTube Video Tutorials 🎞️
Single topic videos:
MORE VIDEOS COMING SOON!!! STAY TUNED!!!
Planned Updates 📜
Check back or get in touch with us regarding future updates
  •  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 📜
Contributors 👨‍🔬👩‍🔬
About
Fiber Photometry Modular Analysis Tool Suite
Resources
Readme
GPL-3.0 license
Activity
Stars
44 stars
Watchers
4 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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GitHub - djamesbarker/pMAT: Fiber Photometry Modular Analysis Tool Suite · GitHub
Skip to content
BranchesTags
Repository files navigation
pMAT (Photometry Modular Analysis Tool)
License: LGPL v3
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.
YouTube Video Tutorials 🎞️
Single topic videos:
MORE VIDEOS COMING SOON!!! STAY TUNED!!!
Planned Updates 📜
Check back or get in touch with us regarding future updates
  •  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 📜
Contributors 👨‍🔬👩‍🔬
About
Fiber Photometry Modular Analysis Tool Suite
Resources
Readme
GPL-3.0 license
Activity
Stars
44 stars
Watchers
4 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - djamesbarker/pMAT: Fiber Photometry Modular Analysis Tool Suite · GitHub
Skip to content
BranchesTags
Repository files navigation
pMAT (Photometry Modular Analysis Tool)
License: LGPL v3
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.
YouTube Video Tutorials 🎞️
Single topic videos:
MORE VIDEOS COMING SOON!!! STAY TUNED!!!
Planned Updates 📜
Check back or get in touch with us regarding future updates
  •  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 📜
Contributors 👨‍🔬👩‍🔬
About
Fiber Photometry Modular Analysis Tool Suite
Resources
Readme
GPL-3.0 license
Activity
Stars
44 stars
Watchers
4 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

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(function(){
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var __m = "*";
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GitHub - djamesbarker/pMAT: Fiber Photometry Modular Analysis Tool Suite · GitHub
Skip to content
BranchesTags
Repository files navigation
pMAT (Photometry Modular Analysis Tool)
License: LGPL v3
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.
YouTube Video Tutorials 🎞️
Single topic videos:
MORE VIDEOS COMING SOON!!! STAY TUNED!!!
Planned Updates 📜
Check back or get in touch with us regarding future updates
  •  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 📜
Contributors 👨‍🔬👩‍🔬
About
Fiber Photometry Modular Analysis Tool Suite
Resources
Readme
GPL-3.0 license
Activity
Stars
44 stars
Watchers
4 watching
Forks
9 forks
Report repository
Releases
Packages
Contributors
Languages

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GitHub - djamesbarker/pMAT: Fiber Photometry Modular Analysis Tool Suite · GitHub
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pMAT (Photometry Modular Analysis Tool)
License: LGPL v3
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.
YouTube Video Tutorials 🎞️
Single topic videos:
MORE VIDEOS COMING SOON!!! STAY TUNED!!!
Planned Updates 📜
Check back or get in touch with us regarding future updates
  •  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 📜
Contributors 👨‍🔬👩‍🔬
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Fiber Photometry Modular Analysis Tool Suite
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