SymBioSense Plant Biologger
The "Growing symbiotic new senses for humans" experiment continues to progress and in this labnote I'm happy to introduce the main sensing piece of this project, the SymBioSense plant biologger.
"Devices worn by wild animals that record their location, and in some cases their behavior and environmental conditions, are known as biologgers. They have vastly increased our knowledge of animal movements and generated data on their use of space that have led to numerous conservation applications."
For this experiment I propose a Plant Biologger. That is, a device worn by plants that record parameters about their state and/or activity. Wearable sensors for plants signals and hysiology have been increasing in number and diversity and for this experiment I have compiled a set of sensors that will be used for the monitoring of an Epipremnum aureum for an extended period of time. Some of these sensors have been extensively used with plants, demonstrating their effectiveness. Others are purely experimental and shall be tested in regards what they can tell about the plant. Together, they form what I've been calling the SymBioSense. All data is sent to a dedicated database for further ML analysis and haptics integration. Below is a list detailing each one of the sensors, with a breakdown of their electronic inner workings.
---CODE CURRENTLY RUNNING IN THE SYMBIOSENSE---
---LIVE WEBAPP WITH SYMBIOSENSE DATA---
Tested Sensors
1) InterComUnit Sensor - Resistance sensor
The ICU is the sensor I have worked with for the longest time. From breadboard protopying to naming and circuit printing I have used it with a varied of different plants (in different parts of plants, and different probes) and have developed an empirical intuition around it. Technically speaking, it consists of a 10kOhm resistor connected to ground and to the middle of a cable. The same cable has one of its ends connected to an analog port in a microcontroller. The other end is left open as a probe. Another cable is connected to the power supply of the same microcontroller. And the other end of this power cable functions as a probe as well. I use these two probes to close the circuit. When I connect them to different bodies, like a plant, I get fluctuating readings via analogread().
Here's a detailed explanation of how it works:
When the probes are not touching anything (or each other), the circuit is open. This means that no current can flow from the microcontroller's power supply, through the resistor, and back to the microcontroller's ground. In this state, the voltage at the analog port (where one end of the resistor is connected) is 0V, because it's directly connected to ground.
When you touch the probes to something conductive (like your body or a plant), you're closing the circuit. Now, current can flow from the power supply, through the resistor, through the object you're touching, and back to the microcontroller's ground. The amount of current that flows depends on the total resistance in the circuit, which is the sum of the 10kOhm resistor and the resistance of the object you're touching (they are connected in series).
The microcontroller's analog port measures the voltage across the 10kOhm resistor. According to Ohm's Law (V = I*R), the voltage across the resistor is equal to the current through it times its resistance. Because the current depends on the resistance of the object you're touching, the voltage at the analog port will change when you touch the probes to different objects.
The
analogRead()function in your microcontroller's programming language reads the voltage at the analog port and returns a value proportional to it. This value will be higher when the object you're touching has lower resistance (allowing more current to flow and creating a higher voltage across the resistor), and lower when the object has higher resistance.
So, the fluctuating readings you're seeing represent the varying resistance of the different objects you're touching with the probes. This could be influenced by many factors, including the object's inherent electrical properties, its moisture content (water is a good conductor), and the size and position of the area you're touching with the probes.
For plants, experience has told me that this sensor is more suitable for the roots.
2) Galvanometer - Biodata Sonification
This one is perhaps the most widely used plant sensor in existence. Initially conceived as the Midi Sprout by Data Garden and Sam Cusumano (electricity for progress), it has taken the market as the PlantWave. In essence, this functions as a Galvanometer "capable of reading microfluctuations in conductivity across the surface of a plant's leaf". It does so via a 555 timer chip:
"The 555 Timer output is a variable width square pulse, which is measured using an Interrupt INT0. Variations in the width of the pulse shows changes in conductivity measured across the electrodes of the 555 Timer."
The 555 timer IC is a versatile component that can be configured in several modes, one of which is the astable mode. In this mode, the 555 timer oscillates continuously, producing a square wave output. The frequency of this oscillation is determined by external components, specifically resistors and capacitors.
For the 555 timer in astable mode, the frequency f is given by:
f=1.44/(R1+2R2)×C1
Where:
R1 is the resistance between pins 7 (Discharge) and 8 (VCC).
R2 is the resistance between pins 7 (Discharge) and 6 (Threshold).
C1 is the capacitor connected between pin 2 (Trigger) and ground.
In electricity for prorgress' setup:
R1 is ta 100k resistor.
R2 is the resistance between the electrodes snaps to the plants leaves
C1 is a 4700pF capacitor.
As the resistance between the electrodes changes (due to different objects or varying conditions of the same object), R2 in the formula changes. This, in turn, changes the frequency f of the 555 timer's oscillation.
Sam himself has designed the SymBioSense printed circuit board, integrating the galvanometer and the ICU into one unity.
3) Capacitive Soil Moisture Sensor
This is a very well known sensor for soil moisture. So much so that researchers reverse engineered how modules of this type work.
Unlike resistive soil moisture sensors that measure the resistance between two electrodes to determine the moisture content, capacitive sensors measure the changes in capacitance in the soil due to moisture content. Here's a breakdown of how this sensor works:
TL555I CMOS Timer: The TL555I is a CMOS version of the classic NE555 timer IC. The CMOS version can operate at higher frequencies and consumes less power compared to its older counterpart. In this sensor, the TL555I is set up to produce a high-frequency oscillation, in this case, 1.5MHz.
Capacitance Change: The probe, when inserted into the soil, forms one plate of a capacitor, with the soil (and the moisture within) acting as the dielectric, and the other plate being the surrounding ground. As the moisture content in the soil changes, the dielectric constant of the soil changes, which in turn changes the capacitance of this "soil capacitor."
Effect on Oscillation: The change in capacitance due to moisture affects the characteristics of the oscillation produced by the TL555I. Specifically, it affects the peak amplitude of the oscillation.
Peak Voltage Detector: This part of the circuit converts the oscillating waveform into a DC voltage. It captures the peak value of the oscillation, which varies based on the capacitance (and therefore the moisture content).
Reading by MCU: The DC voltage output from the peak detector is then read by an analog-to-digital converter (ADC) on a microcontroller (MCU). As the moisture increases, the DC voltage output decreases, and this inverse relationship can be calibrated and processed by the MCU to provide a meaningful moisture reading.
4) Adafruit BME680 - Temperature, Humidity, Pressure and Gas Sensor
This combo sensor is taking care of environmental measurements for the experiment.
"this precision sensor from Bosch can measure humidity with ±3% accuracy, barometric pressure with ±1 hPa absolute accuracy, and temperature with ±1.0°C accuracy." "it contains a small MOX sensor. The heated metal oxide changes resistance based on the volatile organic compounds (VOC) in the air, so it can be used to detect gasses & alcohols such as Ethanol, Alcohol and Carbon Monoxide and perform air quality measurements."
Experimental Sensors
Now I'll talk about two sensors that, as far as I know, have never been used for plant monitoring, even though they are well established sensors for humans. I'm very curious about what insights they might yield in regards to the Epipremnum aureum due to their inner workings.
5) Pulse Sensor
The Pulse Sensor is an open-source hardware project developed by Joel Murphy and Yury Gitman. It's primarily designed to measure heart rate in humans by detecting the pulse from the fingertip or earlobe. The sensor uses the ambient light sensor from Avago (APDS-9008) and a green super bright reverse mount LED from Kingbright (AM2520ZGC09). In this way, it is able to detec changes in light reflection when blood pumps through human tissues.
While plants don't have a pulsating circulatory system like humans, they do have various physiological processes that might cause subtle changes in light reflection, absorption, or transmission via water movement. Monitoring these changes could provide insights into the plant's health, hydration level, or other physiological activities.
It's uncertain what insighs will be drawn from the use of this sensor, but preliminary tests have shown the it does capture varying signals when attached to plants. Therefore, it will be interesting to correlate these to the other established sensors, so as to decypher possible patterns occoring within the plant. Therefore, I hope to use the pulse sensor in the plant's stalk.
Email exchanges with Joel Murphy have encourage this approach. In his words:
"Your project and plan sound very intriguing, experimental, and futuristic! The best advice we can give you is to be experimental!"
6) MyoWare
The other experimental sensor in the SymBioSense Plant Biologger is the MyoWare Muscle Sensor. it is designed to detect the electrical activity of muscles, commonly known as electromyography (EMG). When muscles contract, they produce electrical signals that can be detected and measured. The MyoWare sensor amplifies and processes these signals, making them suitable for interfacing with electronics.
When considering its application to plants, it's important to note that while plants don't have muscles they produce action potentials and other electrical signals in response to environmental stimuli and due to processes like photosynthesis, and cell signaling. It's possible that the MyoWare sensor could detect some of these electrical signals, openning up windows into the realm of plant electrophysiology. But again, this is a rather experimental approach and the correlatoin between the myoware signals and the other sensors (as well as observable phenomena) will tell whether or not it tell us significant things about the plant. Just like the galvanometer, the myoware will be used in the plant's leaves.
Next Steps
So these are the sensor I'll be primarily working with for the continuation of this experiment. For those who have been following this journey from the beginning, the SymBioSense as presented here concludes a chapter by integrating the initial hardware granted by differente people and organizations for this experiment into a single sensing unity. Preliminary tests have been conducted and the whole sensor unity currently stands as one, sending data every 3 senconds to a dedicated database via wifi.
The next step is the beginning of a larger data collection sub-experiment. This will be done with an Epipremnum aureum for an extended period of time. Alongside the collected data I will be taking daily notes and pictures on the development of the plant, towards the creation of a "quasi-annotated dataset". Such data will be further analysed with the help of sulf-supervised ML algorithms for the automatic discovery and labeling of patterns in the plant's activity. In parallel, the same data will be sent to the haptic bracelet which I'll be constantly wearing. Such combination will hopefully allow for the comparison between my own impressions on the state/activity of the plant versus that of the artificial intelligence.
Stay tunned for these next steps.
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