OptoReader repository for software package to run the OptoReader, hardware files, and modeling scripts.
The OptoReader can be run using a computer and two Arduino Micros with the following provided code files:
OptoPlate_topArduino.ino - Arduino code to control the stimulation plate. Takes in experiment stimulation settings, controls the 96 stimulation and optical density LEDs, and communicates with the reading plate for optical density measurements.
PlateReader_bottomArduino.ino - Arduino code to control the reading plate. Takes in experiment reading settings, controls the 96 excitation LEDs and photosensors, and communicates with the stimulation plate for optical density measurements.
OptoReader_Protocol.py - Python code to take in inputs from the graphical user interface, keep track of experiment timing, and communicate with Arduinos to initiate readings and calibrate the optical density LEDs.
GUI.py - Python code creating a graphical user interface to take in user experiment inputs including stimulation settings, reading settings, feedback control, and experiment timing.
To run the OptoReader, first upload OptoPlate_topArduino.ino to the stimulation (top) plate Arduino and upload PlateReader_bottomArduino.ino to the reading (bottom) Arduino. Note the port name for each Arduino. If necessary, rename the port name from the preset COM11 and COM12 in OptoReader_Protocol.py. Finally, run GUI.py to open the graphical user interface and enter your experiment settings. Ensure that the image files blue_logo.png and optologo_small.png and the Python file OptoReader_Protocol.py are saved in the same folder as GUI.py.
Includes files for our 3D-printed parts Bottom_Adaptor.stl and Top_Adaptor.stl. These files include the 3D model of the top adaptor and bottom adaptor, that fit each pcb board to a microwell plate.
Includes schematic files for our printed circuit boards (PCBs) PlateReader.kicad_pcb and optoPlate96.kicad_pcb. These can be sent directly to a company that provides printed circuit boards. The board components are soldered directly onto the boards.
Files for our fluorescence calibration modeling include FirstFit.m and Fluorescence_Calibration_Curve.m. These files use our device’s fluorescence readings at different known concentrations to fit each well to a fluorescent calibration curve.