pyPhotometry

Open source, Python based, fiber photometry data acquisition.


Acquisition board

Overview

pyPhotometry is system of open source hardware and software for neuroscience fiber photometry data acquisition, consisting of an acquisition board and graphical user interface.

pyPhotometry supports data aquisition from two analog and two digital inputs, and control of two LEDs via built in LED drivers with an adjustable 0-100mA output. The system supports time-division multiplexed illumination which allows fluoresence evoked by different excitation wavelengths to be independenly readout from a single photoreciever signal. Assembled acquisition boards are available from the OpenEphys store

For questions about the pyPhotometry system contact the google group.

pyPhotometry hardware, software and documentation repositories are on GitHub.

The pyPhotometry manuscript has validation experiments characterising system performance, and information about the multiplexed illumination acquisition modes. If you use pyPhotometry in a publication, please cite it.

If your experiments involve behavioural tasks, you may be interested in pyPhotometry's sister project pyControl, a Python based system for controlling behavioural experiments.


Getting started

Dependencies

pyPhotometry has the following dependencies:

  • Python 3
  • pyserial
  • numpy
  • pyqt5
  • pyqtgraph

On a windows machine that does not already have Python installed, the simplest way to install Python is to download an installer from python.org. To ensure you can run Python files (including the pyControl GUI) by double clicking on them, select the options 'Add Python to PATH', 'Add Python to environment variables', and 'Associate files with Python' during installation. Note; selecting these options when installing Python will cause the Python version you are installing to take precedence over any other version of Python installed on the computer, so may break previous Python based workflows on the computer.

Once you have a working Python 3 installation on the computer, run the windows command prompt (cmd.exe) as an administrator and enter the following commands to install the required packages:

python -m pip install numpy
python -m pip install pyserial
python -m pip install pyqt5
python -m pip install pyqtgraph

pyPhotometry has been tested primarily on Windows 10 but in principle should be cross platform.

Installation

Download the latest version of pyPhotometry as a zip file from the releases page.

Unzip the file and you will have the following folder structure:

- GUI               # Graphical user interface code.
- uPY               # Code that runs on the Micropython Microcontroller.
- tools             # Tools for importing pyPhotometry data.
- data              # Default data directory.
pyPhotometry_GUI.py # Python script to launch the GUI.

Hardware

The acquisition board can be purchased from the Open Ephys store for €350 or built from components. Assembly instructions for a red/green photometry system are provided in the hardware user guide.

Running an experiment

Connect a pyPhotometry acquisition board to the computer with a USB cable.

Load the GUI by running the file pyPhotometry_gui.py.

Select your aqusition board using the Serial port drop down menu and connect to the board with the connect button.

Select the data acquisition mode, for more information see the GUI user guide.

Press Start to start data acquisition.

Adjust the LED currents (and photoreciever gain if applicable) to bring the signals into the center of the 0 - 3.3V range covered by the analog inputs. Signals that exceed 3.3V it will be clipped. If the signal is very low the signal to noise ratio will be less good. When adjusting the LED current it is recommended to use the 'two colour continous' acquisition mode as this mode does not use baseline subtraction so the signal you see is the raw photoreciever voltage.

To record data enter a subject ID and data directory and press Record.

For information on opening data files generated by pyPhotometry see Importing data.

If you encounter problems take a look at the troubleshooting page or contact the google group.

System testing

If you are new to pyPhotometry, we recomend doing the following steps to build understanding of the signals, and test your optical setup is working as expected.

  1. Put the system in 'Two colour continuous' mode and wave the fiber tip around, you should see the signal levels go up and down as the tip is oriented towards and away from light sources in the room.

  2. Put the system in 'One colour time division' or 'Two colour time division' mode, depending on your whether you are using one or two phototdetectors. These modes use background subtraction, i.e. they subtract the signal level with the LED off from the value with the LED on, to remove the influence of background illumination. Therefore when you move the tip around the signal should stay constant (though if you point the fiber tip at a bright light, the background subtracted signal may drop to zero due to the raw signal saturating).

  3. Even using background subtraction, and with nothing in front of the patch cord, the signal will not be zero due to autofluorescence from the patch cords themselves. The brightness of the autofluorescence depends on the illumination intensity and wavelength (shorter wavelengths typically evoke more autofluorescence). Increase and decreace the LED currents and check that the corresponding signal levels change.

  4. Touch the tip of the patch cord onto a sheet of white paper, you should see the signal levels go up due to fluorescence of the paper.

If the above steps look good you are ready to try and record brain signals.