fluorescence-monitoring

Fluorescence monitoring plugin for Pioreactor systems: interfaces with Arduino for excitation LED control and automates spectrometer measurements.

How to Install the Plugin

1. Ensure you have the latest version of Python and pip:

   sudo apt install python3 python3-pip

2. To make the spectrometer work, you need libusb, pyusb, and rgbdriverkit.

   2.1. Install libusb:

   sudo apt install libusb-1.0-0-dev

   2.2. Install pyusb:

   pip3 install pyusb

   2.3. Install matplotlib (for graphs):

   sudo apt install python3-matplotlib

   2.4. Install the spectrometer driver:

   • Copy the folder pyrgbdriverkit-0.3.7 to the Pioreactor.
   • Navigate to the folder containing setup.py and execute:

   sudo pip3 install .

3. Create udev rules.

   For the spectrometer:

   sudo nano /etc/udev/rules.d/99-spectrometer.rules

   Add the following line:

   SUBSYSTEM=="usb", ATTRS{idVendor}=="276e", ATTRS{idProduct}=="0208", MODE="0666"
   

   For the Arduino:

   sudo nano /etc/udev/rules.d/99-arduino.rules

   Add the following line:

   SUBSYSTEM=="tty", ATTRS{serial}=="393D99A6EA0D4AE8", SYMLINK+="arduino"
   

   Save the file and reload udev rules:

   sudo udevadm control --reload-rules
   sudo udevadm trigger

   Disconnect and reconnect the devices to apply the new rules.

4. Place the fluorescence_monitoring.py file in the plugins folder.

5. Add the corresponding .yaml files in ui/Jobs, ui/Charts, and/or ui/Automations as needed.

6. Modify the config.ini file for charts:

   Add the following section:

   [ui.overview.charts]
   # show/hide charts on the PioreactorUI dashboard
   # 1 is show, 0 is hide
   implied_growth_rate=1
   implied_daily_growth_rate=0
   fraction_of_volume_that_is_alternative_media=0
   normalized_optical_density=1
   raw_optical_density=1
   temperature=1
   intensity_700nm_excitation_655nm_chart=1
   intensity_658nm_excitation_655nm_chart=1
   intensity_700nm_excitation_620nm_chart=1
   intensity_658nm_excitation_620nm_chart=1
   intensity_700nm_excitation_595nm_chart=1
   intensity_658nm_excitation_595nm_chart=1
   intensity_700nm_excitation_527nm_chart=1
   intensity_658nm_excitation_527nm_chart=1
   intensity_700nm_excitation_450nm_chart=1
   intensity_658nm_excitation_450nm_chart=1
   intensity_700nm_excitation_405nm_chart=1
   intensity_658nm_excitation_405nm_chart=1