PCB impedance

Projet Fungi

The goal of this project is to measure the impedance of bags containing mycelium in order to observe how mycelium growth influences impedance. With this information, we aim to determine whether the mycelium is fully developed in the bags or if there are areas with little or no growth.

Operation

The idea is to measure the impedance of the mycelium over several weeks to observe its evolution. Each measurement consists of a frequency sweep from 1 kHz to 100 kHz, taken every 5 minutes.

The measurements from the Evaluation Board (EVAL-AD5940BIOZ) are retrieved via UART by a Raspberry Pi. The Raspberry Pi then synchronizes this data with Google Drive, making the measurements accessible from anywhere.

The measurement process is triggered by the Raspberry Pi. The reason for this is that up to four boards can be placed on the same bag, and the Raspberry Pi coordinates the measurements from each board to prevent interference.

Material used

• Precision Impedance Analyzer - Agilent 4294A
• ECG Electrodes
• 4 x Bio-Electric Evaluation Board - EVAL-AD5940BIOZ
• Raspberry pi model 3B+

Installation / Configuration

Flashing the Evaluation Board

The first step is to install the Keil IDE to compile and program the Evaluation Board by following this setup guide: https://wiki.analog.com/resources/eval/user-guides/eval-ad5940/tools/keil_setup_guide

The code used to program the evaluation board is located in the following folder: Fungi/EVAL-AD590ELCZ_Pain/ad5940-examples-master/ad5940-examples-master/examples/AD5940_BIA

This code is based on the official repository: https://github.com/analogdevicesinc/ad5940-examples

With this code, the evaluation board performs a frequency sweep to measure impedance only when it receives a trigger signal on pin GP4 from the Raspberry Pi.

Raspberry Pi Configuration

The Raspberry Pi runs two Python scripts in the background, located in:
Fungi/EVAL-AD590ELCZ_Pain/python_Code

• com_ports.py
• Measurement_synchronization.py

The first script retrieves data from each COM port to which the four AD5940 boards are connected. It stores the data in CSV files, one per COM port, in the folder: Fungi/EVAL-AD590ELCZ_Pain/python_Code/Measurement

The second script sends trigger pulses to the GP4 pins of the four evaluation boards to start measurements. It also coordinates measurements between the boards to avoid interference. Additionally, it synchronizes the data in the Measurement folder with a measure_impedance folder on Google Drive using rclone.

Python Installation

• Install Python 3 and pip:

sudo apt update && sudo apt upgrade -y
sudo apt install python3 python3-pip -y

• Create and activate a virtual environment:

python3 -m venv mon_env
source mon_env/bin/activate

• Install required libraries:

# Library for serial communication
pip install pyserial
# Library to control Raspberry Pi GPIO
pip install RPi.GPIO

Google Drive Remote Configuration

To synchronize the local Measurement folder with a remote folder on Google Drive, install and configure rclone:

# Install rclone
sudo apt install rclone
# Configure rclone
rclone config

Create Services to Run Python Scripts

The two python scripts (com_ports.py and Measurement_synchronization.py) are run as background services on Linux. This ensures they start automatically when the Raspberry Pi powers on. The service files are located in: /etc/systemd/system

• read_ports.service : Runs com_ports.py

[Unit]
Description=Measurement System (Serial)
After=network.target

[Service]
ExecStart=/home/fr1boise/Documents/Fungi/EVAL-AD590ELCZ_Pain/python_Code/.venv/bin/python3 /home/fr1boise/Documents/Fungi/EVAL-AD590ELCZ_Pain/python_Code/com_ports.py
WorkingDirectory=/home/fr1boise/Documents/Fungi/EVAL-AD590ELCZ_Pain/python_Code
Restart=always
RestartSec=5
User=fr1boise

PrivilegesStartOnly=true

[Install]
WantedBy=multi-user.target

• measure_syncro.service : Runs Measurement_synchronization.py

[Unit]
Description=Measurement System (Synchronisation)
After=network.target

[Service]
ExecStart=/home/fr1boise/Documents/Fungi/EVAL-AD590ELCZ_Pain/python_Code/.venv/bin/python3 /home/fr1boise/Documents/Fungi/EVAL-AD590ELCZ_Pain/python_Code/Measurement_synchronization.py
WorkingDirectory=/home/fr1boise/Documents/Fungi/EVAL-AD590ELCZ_Pain/python_Code
Restart=always
RestartSec=5
User=fr1boise

PrivilegesStartOnly=true

[Install]
WantedBy=multi-user.target

• Commands to enable and start a service:

sudo systemctl enable name.service
sudo systemctl start name.service

EVAL-AD777xFMCZ - Electrophysiological measurement

• ad777.service : Runs the ad777 executable

[Unit]
Description=Electrophysiological measurement (AD777)
After=network.target

[Service]
ExecStart=/home/fr1boise/Documents/Fungi/ADC/AD777_code/ad777
WorkingDirectory=/home/fr1boise/Documents/Fungi/ADC/AD777_code/
Restart=always
RestartSec=5
User=root

[Install]
WantedBy=multi-user.target

• sync_ADC.sh : Script to synchronize data on Google Drive

#!/bin/bash

mkdir -p /home/fr1boise/Documents/Fungi/adc_snapshot

rsync -a --delete --inplace \
/home/fr1boise/Documents/Fungi/ADC/AD777_code/Measurement_ADC/ \
/home/fr1boise/Documents/Fungi/adc_snapshot


rclone copy /home/fr1boise/Documents/Fungi/adc_snapshot gdrive:mesure_ADC \
  --transfers=4 \
  --fast-list \
  --drive-use-trash=false

Tailscale

Installation

• Enable ssh server

sudo raspi-config

• Installation:

curl -fsSL https://tailscale.com/install.sh | sh

• start the Tailscale client

sudo tailscale up --ssh

if it don't work :

sudo tailscale up --force-reauth

• connect to raspberry

ssh fr1boise@100.98.6.121

• Transfer file from Raspberry Pi to Laptop (Laptop and Raspberry must be added to tailscale)

scp /home/fr1boise/Documents/Fungi/adc_snapshot/channel0 beuns/@100.91.175.60:/home/beuns/Documents