Automated Cell Culture Pump Control System

A web-based control system for managing peristaltic pumps in cell culture experiments using Arduino-controlled hardware and a Flask backend, running on a Raspberry Pi 4 with touchscreen display.

This project explores automated cell culture techniques. Check out the video below for a demonstration:

Overview

This project provides a web interface to control and monitor peristaltic pumps for cell culture experiments. It consists of:

• A Flask backend API for handling web requests
• Arduino-controlled peristaltic pumps
• Serial communication between the backend and Arduino
• Raspberry Pi 4 with Elecrow touchscreen display for local control

Hardware Requirements

• Raspberry Pi 4 Model B
• Elecrow 5" Touchscreen Display
• Arduino Mega 2560 (or compatible)
• Peristaltic pumps for liquid handling
• USB cables for Arduino connection

Software Setup

Raspberry Pi Setup

1. Install Raspberry Pi OS (64-bit)
2. Connect the Elecrow touchscreen display
3. Configure display settings:
   • Set correct DPI in /boot/config.txt
   • Enable touchscreen driver

Backend Setup

1. Create and activate a Python virtual environment:

python -m venv backend/venv
source backend/venv/bin/activate  # On Windows: backend\venv\Scripts\activate

2. Install required Python packages:

pip install flask flask-cors pyserial

3. Configure Arduino port:
   • Edit backend/app.py and set the correct arduino_port
   • For Windows: use COM port (e.g., "COM3")
   • For Linux: use ttyACM port (e.g., "/dev/ttyACM0")

Arduino Setup

1. Open Arduino IDE

2. Install required libraries:

   • LiquidCrystal_I2C

3. Upload the Arduino code from Arduino/pump_control1.ino

Running the System

Starting the Backend

cd backend
python app.py

The Flask server will start on http://localhost:5000

Arduino Connection

The system will automatically attempt to connect to the Arduino. You should see connection messages in the terminal.

API Endpoints

Endpoint	Method	Description
/	GET	Check server status
/control	POST	Send control commands to Arduino
/status	GET	Get current system status

Troubleshooting

• Arduino Connection Issues:

  1. Ensure Arduino is properly connected
  2. Check the port configuration in app.py
  3. Verify Arduino is uploading code correctly

• Serial Communication Errors:

  1. Check baud rate settings (9600)
  2. Ensure no other programs are using the serial port
  3. Try restarting both the Arduino and the Flask server

• Touchscreen Issues:

  1. Verify display is properly connected
  2. Check touchscreen calibration
  3. Ensure correct display resolution is set

Safety Notes

• Always ensure proper sterilization procedures are followed
• Regularly check system connections and hardware
• Implement emergency stop procedures for safety

Contributing

1. Fork the repository
2. Create a feature branch
3. Commit your changes
4. Push to the branch
5. Create a Pull Request

License

MIT License - feel free to use this code for your cell culture projects!

Relevant Documents

OneDrive with Resources: Link 1

Link 2

OneDrive with PSD:Link 1(https://imperiallondon-my.sharepoint.com/:w:/g/personal/da1322_ic_ac_uk/EXKUht7OnVdJsqrV60ub2PAB3-0p0oUdjwzsyK82-7Xsmw?e=OTsWRL )