CO2 Soil Respiration Chamber

1 Nano's documentation of camara-respiración-suelo
2 UROŠ new CO2 soil chambers
3 Testing and hacking the SCD 41
4 Testing the soil chamber at the beach
5 CO2 soil chambers
6 Test Measurements @ Yogyakarta / Lifepatch
7 Soil Geeking @ Lifepatch with Matt
- 7.1 Testing trials in lifepatch garden
- 7.2 Visit to Pak Paning's permaculture farm
8 Early Experiments
9 More about CO2 sensors:
10 References

Developed during the RandeLab Soil Retreat as part of the HUMUS.Sapiens research phase and discussed on the forum. Continued during UROS (UROŠ - Ubiquitous Rural Open Science Hardware) in Maribor, 2021.

Nano's documentation of camara-respiración-suelo

https://gitlab.com/nanocastro/camara-respiracion-suelo

Also discussed on the GOSH forum here: https://forum.openhardware.science/c/projects/camara-de-respiracion-de-suelo/56

UROŠ new CO2 soil chambers

Based on FeatherS2 and new SCD41 Sensor sponsored by Sensirio. We'd like to thank here again for the Sensirion eval-kit donated to the UROŠ project and we are looking forward to receive more sensor chips and manufacture our own UROŠ break-out boards, see below.

FeatherS2 version using arduino libraries

See the first test code on github

Electronic Materials and links:

ESP-32 FeatherS2 (USB-C & circuitpython native support and many other features)
- https://feathers2.io/
Sensirion's SCD41 CO2 sensor
- https://sensirion.com/products/catalog/SCD41/
- See our own brk-out board below, thanks to the sponsoring by Sensirion
- Or you can purchase other brk-out: https://www.adafruit.com/product/5190
OLED diyplay, 0.96inch, I2C, Yellow/Blue ,SSD1306
- https://github.com/adafruit/Adafruit_SSD1306
BMP280 pressure and temperature sensor
- https://www.bosch-sensortec.com/products/environmental-sensors/pressure-sensors/bmp280/
Dallas DS18x20 temperature sensor waterproof probe
- https://www.aliexpress.com/item/32467815969.html
LiPo battery with connector to FeatherS2 board
(on-board BOOT) 1 small button
1 big red button
LEDs

... what else? speaker?

Wiring diagram

Software

Installing the ESP-32 and firmware

https://randomnerdtutorials.com/installing-the-esp32-board-in-arduino-ide-windows-instructions/
test your system, blink something. mbe pre-installed bootloader for circuitpython. press boot / rest to go into bootmode and upload from arduino IDE
the first time, you might have to press "reset" button manually, later it should "Hard resetting via RTS pin..."
See the code on our new github. Look for the newest file under software/ESP32-S2.
Making more logos is easy to! check this online converter.

Send and receive data via Serial

The data is sent in the following format:

Each line is timestamped (in sec, could be also in millis)
data rate can be modified. At the moment BMP280 is read every 200 millis, SCD41 every 5000 millis, DS18b20 every 30sec
Maybe some delays here and there. Still needs optimization
3 values from SCD41:
- CO2 (ppm)
- Temperature (ºC)
- Humidity (%)
3 values from BMB280:
- Pressure (Pa) (could be also sent in hPa?)
- Altitude (calculated in meter above sea level, calibrated with: #define SEA_LEVEL_PRESSURE 1010.0f // sea level pressure 1013.25
- Temperature (ºC)
1 value from soil temperature probe (DS18b20)
- ** Temperature (ºC)

TimeSec: 256	CO2: 419	Temp: 31.09	Hum%: 76.58	BMB-Pres: 98763	Alti: 188.50	BMP-Temp: 30.14	SoilTemp: n.c.
TimeSec: 256	CO2: 419	Temp: 31.09	Hum%: 76.58	BMB-Pres: 98763	Alti: 188.50	BMP-Temp: 30.14	SoilTemp: n.c.
TimeSec: 257	CO2: 419	Temp: 31.09	Hum%: 76.58	BMB-Pres: 98763	Alti: 188.52	BMP-Temp: 30.13	SoilTemp: n.c.
TimeSec: 257	CO2: 419	Temp: 31.09	Hum%: 76.58	BMB-Pres: 98763	Alti: 188.52	BMP-Temp: 30.13	SoilTemp: n.c.

You can reveive the data for testing in the Arduino IDE, and it should look as following:

You can also receive the data in a serial plotter, i suggest for example the tauno-serial plotter

The regosh team in Mendoza has been working on a python based serial plotter dedicated to soil respiration measurements. See their gitlab for more details.

Optimizing display and usability

PVC chamber for field-use

Building the chamber

Standard PVC piping (4 inch / 10 cm diameter)
Standard PVC covers/lids (4 inch / 10 cm diameter)
Aviation connectors, 5 pin
Aviation connectors, 3 pin (for external soil temperatur probe)
small computer fan, 5-12V (has to run on very low rpm)

Testing and hacking the SCD 41

<< CO2 Soil Respiration Chamber#UROŠ new CO2 soil chambers

Comparing the different Sensors

https://gitlab.com/nanocastro/camara-respiracion-suelo/-/blob/master/Docs/CO2%20sensor%20performance%20test.md

Circuit Python and FeatherS2

See some first notes and experiments here: https://mega.hackteria.org/index.php/s/AzikGk77wAdPdqg

Mbe add even another VOC sensor?

With all the libraries and examples prepared by sensirion and Adafruit, it was easy to connect it all together using the FeatherS2 and CircuitPython. A first prototype is connected and working.

First measurements look promising, very stable, relatively fast response times. The library is very easy to use, auto-calibration has to be turned off. During the start of the code you can adjust a temperature_offset to calibrate the temp sensor. Additionally you have to adjust the pressure or altitude to where you are doing the measurement, altitude offset (default hardware is 0m). First experiments show that this is pretty crucial, details will have to explored and discussed with the sensirion tech team.

Testing and hacking the SCD 41

Checking the PCB and the footprint to plan our own reflowing of PCB

Opening up the sensor

What is inside? As described on the sensirion product page, the new sensor works on the "photo-accoustic effect". So it's similar, but also a different method, than other NDIR sensors.

It's pretty easy to understand what's under the hood for the SCD41. There is a signal-processor, to read and control the sensor components and communicate to the outside via I2C, there is the "classic" SH40 temperature & humidity sensor, and now... There is an IR emmiter with a dedicted filter on it and a MEMS microphone. Everything is enclosed within a small metal case, with a hole to the outside world and a particle filter stuck onto it.

Photoacoustic effect is the generation of acoustic waves as a result of light absorption in a material. As an example, consider a laser beam that is passed through a gas sample, which is enclosed in a cell of a constant volume. The laser energy absorbed by the sample molecules leads to local heating of the gas, which causes a pressure increase. If the optical excitation of molecules is done periodically, by modulating the laser power or frequency, also the pressure change is periodic. This acoustic wave at the modulation frequency can be detected with a microphone. The microphone signal is directly proportional to the absorbed power, which makes it possible to determine the concentration of absorbing molecules in the sample. Taken from this source on laser spectroscopy

Designing UROŠ - CO2 brkout PCB

PCB (printed circuit board) breakout board for CO2 sensor (SCD41), NEO-pixel (WS2812B) and I2C interface (JST-SH4)

Designed with open source software: Kicad, Inkscape and svg2shenzhen

The files "as ordered" are available on github: https://github.com/GenericLab/UROS-CO2_brkout

It arrived!!!

UROŠ - CO2 brkout PCB reflow soldering

We managed to reflow a first working version of our own PCB!!!

Just un-flowed from the original Sensirion break-out board using our nice little reflow hotplate. Cos we didn't have proper reflow solder paste, we just tinned all the pads with normal solder, and wigged it off to create a very thin flat layer of solder on all the copper for the SCD41 sensor. Then mounted the sensor and back onto the hotplate, using 220 / 250 °C, and after it seemed to have settled down into the molten solder, we took the board off and cooled it down.

Then we soldered the remaining parts, some resistors for pull-up on the I2C channel, LED and a NeoPixel on the backside.

Wiring it up, connecting the I2C connection and the extra wire for the neo-pixel.... It works!!

Minting UROŠ - CO2 brkout as NFT on OpenSea

Go to OpenSea NFT marketplace

Serial Plotter and how to get dedicated soil resp data

Started to use this tool tauno-serial-plotter to plot data and export .png or .csv for further analysis / storage.

Testing the soil chamber at the beach

See all data on dusjagr's public channel: https://thingspeak.com/channels/1718702

CO2 soil chambers

BambooBox

Further developments during dusjagr's residency at Lifepatch June - August 2018

Teensy Code

See RandeLab repo on GitHub

results on our-sci

https://app.our-sci.net/#/survey/by-form-id/build_Randen-Soil-Chamber-Measurement-with-the-Soil-Chamber-built-at-Randelab_1525625829

using this script: https://gitlab.com/our-sci/measurement-scripts/tree/master/mh-z16-randen

PVC pipe Chambers

Wiring diagram

RandeChamber aka Kilju Chamber

Failed PCB...

Test Measurements @ Yogyakarta / Lifepatch

Respiration measurement Lifepatch rooftop

1st measurement, late afternoon

2nd measurement, noon

Respiration measurement Lifepatch frontyard

1st measurement around noon

Tibor's rice experiment

CO2 absorbtion with NaOH crystals

Beach Sand | dried and rewetted

Soil Geeking @ Lifepatch with Matt

Great opportunity to do some testing and sharing of protocols with Matthew Daniel from Global Urban Forest. This turned out to be a great little gathering of overlapping networks from GOSH, our-sci, hackteria and the local soil, gardening and permaculture geeks around Lifepatch.