By: Jonathan Fookes

Design

A probe was built as described in this build guide. The following data was returned from the sensor. This probe is was designed by Dongjun Lee and Jonathan Fookes using the previous design from Brett Stoddard.

Methods

Because our probe was designed with an Ethernet connection, we created a PCB with an eight pin connector that sat directly on top of our Adafruit Feather M0 with Lora capabilities. Instead of using an NPN mosfet similar to the one used in the Orchid Test, a voltage regulator kept the voltage across the heater at a steady 3.3 V. These device was fully integrated with the LOOM interface for easy setup and implementation, as laid out in our LOOM implementation guide. The electronics were run with two batteries: 12 V, 2 AH to power the heater in pulses, and a 3.7 V, 2.5 AH battery to power the M0.

Similar to the Orchid Test, analog values were recorded by the board’s dedicated analog in pins. As per default, these readings were 10-bit although the M0 chip has the capability to do 12-bit ADC (detailed in this link), therein increasing the theoretical precision four-fold. These raw values were logged onto an SD card.

The waterproof enclosure was built to contain the fully constructed circuit and each of the batteries. Even though the tree was too far away from the lab to successfully transmit and received LORA data, there is space for an antenna and LORA can be set up using the LOOM interface if desired. The waterproof Ethernet connector is where the probe can connect to the circuitry, ensuring a secure connection. A hot glue gun was used to add an extra waterproof seal.

Energy Saving: The Power Problem

Our design uses heat pulses in order to save energy. Given the current models and code for both the TDM and HRM sapflux measuring methods, we conducted a current draw test with the batteries we had on hand to see if our designs will be able to run continuously in the field for 2 weeks as requested.

TDM Probe

Current Draw:  20.88 to 20.91 mA while on, 0.13 mA while off (not negligible)

TDM heater Pulse: 4 minute pulse every 30 minutes, aka 8 minutes an hour, 192 minutes per day. This is 3.2 hours.

The TDM probe uses: 67 mAh per day(Heater on) + 2.7mAh per day(Heater off) ~= 70mAh per day. The TDM heater probe can be on for 28.5 days with a 2,000 mAH battery.

TDM base

Assume we measure SHT31D + probe temperatures + soil moisture

M0 Current draw: 25 mA in Idle, and +130mA when measuring and transmitting data. (25mA * 24h per day) + (130mA * 48sec per day)  = 600 mAh(idle) + 1.73mAh(Transmit data) = 601.73 mAh per day. The M0 can run for 16.6 days when we use a 3.7V 10,000mAh battery.

HRM Probe

Current Draw: 225 to 237 mA

HRM Heater pulse: 2.5 sec on and 2.5 sec off. It works on 2 minutes every 30 min, aka 2 minutes an hour, 48 minutes(0.8 hours) per day. 180 mAh to 190 mAh per day. The HRM heater can run for 10.5 days when we use a 12V 2,000mAh battery. For 2 weeks test, we need higher capacity of battery.

HRM base

M0 Current draw: 25 mA in Idle, +130mA when measuring and transmitting data, and 156 mA when relay switch is on.

Relay switch is on for 2.5sec and off for 2.5 sec. It works on 2 minutes every 30 min, aka 2 minutes an hour, 48 minutes(0.8 hours) per day. (156mA *0.8h per day) + (25mA *23.2h per day) + (130mA * 48sec per day)  = 124.8mAh(Relay on) + 580mAh(Relay off and idle) + 1.73mAh(Transmit data) = 706.53mAh per day. The M0 can run for 14 days when we use a 3.7V 10,000mAh battery.

TDM Test: Return of the Data

After a couple of failed test runs, we were finally able to graph data using our TDM probe. We used the Dynamax data calculation example from their website and created the following graph for the sap flow in a wild Cherry tree for about

The trend of this data is consistent and promising!

We have a two-week long test of our TDM probes coming up in the following weeks, where we will be able to show more conclusively if our probes are providing accurate sap flow data.

HRM Test: The Phantom Data

Our first HRM test was a success, however we are still working on a method to calculate sap flow from the data we have collected. Below is the data we collected in the wild cherry tree. We are continuing to work with the Heat Ratio equation to plot Sap Flow in grams per hour with respect to time.

This plot shows all of the data points we measure on our HRM test. The y-axis is degrees Celsius. Because we collected data every 15 minutes during this test, the x-axis is time, and represents X*(15 minutes)

Here we have the difference between the temperatures of the two probes you see in the first graph. The y-axis is still in degrees Celsius and the x-axis shows time of day.

While we do not have calculations for Sap Flow yet, we know that a lower difference means that there is an increase in sap movement up the trunk of the tree, and a higher difference means less. We can infer this from the Heat Ratio Equation. The HRM difference data shows that the lowest difference occurs between ~11:30am and 7:00pm. This is consistent with our TDM data, shown in the section above. While our TDM measuring method is more complete and can render Sap Flow calculations, we are confident that our HRM measuring method can be used to produce accurate readings as well.

Our TDM probe prototype in the wild cherry tree! (8/03/2018)

Our HRM probe prototype in the wild cherry tree! (8/16/2018)

What’s next for the Sap Flow Team?

Now that we have gathered promising data from a tree, we will be deploying both our TDM and HRM prototypes in an orchard, where we will attempt to gather data for two weeks continuously. More on this to come!

By: Brett Stoddard

Plant Data!

Design

A probe was built as described in this build-guide. The following data was returned from the sensor.

Methods

An Adafruit Feather M0 with Lora capabilities was used to take measurements from the sap flow sensor. It activated an NPN mosfet that was connected in series with the +battery the heater probe and ground (or -battery).

Analog values were recorded by the board’s dedicated analog in pins. As per default, these readings were 10-bit although the M0 chip has the capability to do 12-bit ADC (detailed in this link). This would increase the theoretical precision four-fold and is something that should be investigated in the future. These raw values were logged onto an SD card. The electronics were run off of a 4AH battery until it died (after around days).

Additionally, an Adafruit SHT31-D breakout board was wired up and placed in the enclosure to provide ambient temperature values that also recorded day-night cycles.

In order to make the setup water resistant, electrical tape was wound around any electrical connections, the probes were covered in silicone conformal coating, and the microcontroller and battery were placed in a waterproof box, the DriBox.

Results

The following graph was determined from the plant data. As you can see, there is a cyclic pattern happening, with the temperature differential. However, there are also several large “spikes” in the data. Talking with the greenhouse manager, it turns out that the timing of those spikes corresponds directly with the time he waters the plants. Best guest, water either cooled down one of the probes or got into the connections and acted as a short briefly before evaporating. The full raw data can be downloaded here.

To determine the exact temperatures from the two probes, two equations were used. The first one was a simple voltage divider equation to get the resistance of the thermistor. From the resistance, the thermistor beta equation was used to determine the temperature. The beta value for the beta value of the thermistor used (link here) was determined from its product datasheet. Unfortunately, the exact equations used were removed when I saved the file as its native CSV format after editing it in excel instead of saving it in an excel format (learn from my mistakes!).

Code

The code used for this project can be found here: https://github.com/stoddabr/SapFlux

By: Brett Stoddard

Abstract

This post will provide step by step instructions on how to build your own thermal dissipation sap flow sensor. Seperate blog posts fully explain the what a thermal pulse sap flow sensor does, the idea behind this design, and the code involved (coming later).

Index

1. Order parts
2. Solder probes
3. Apply thermal epoxy
4. Wire it up
5. Program microcontroller
6. Install in a plant.

Step 0: Required Tools

Before jumping into the project, it’s important to mention that this project requires a few specialty devices to make.

• Soldering iron station
• Tweezers
• A computer with Arduino IDE installed

Step 1: Order Parts

Below are two different bills of materials (BOM) that contain all that is required to build one of these sensors. The files for the pcb board can be found in a zip file here. To edit, you will need to download Eagle by Autodesk as well as a few part libraries including my personal library of Eagle PCB parts. A The total sensor cost is estimated to be $20.

Additionally, an Adafruit Feather M0 Lora is needed with a 3.7 volt battery (suggested 4AH) for the sake of this build guide ($34.95 + $19.99 resp.). It also requires an SD card breakout to save data in nonvolatile memory ($7.50).

The Feather M0 can be substituted for any micro controller with analog-in pins with some changes to the code to accommodate these new pins (mentioned briefly in Step 4) and if a different voltage batter is used, you should take a look at this blog post and change the heater resistor value.

When ordering the electronic parts I would highly suggest you buy spare parts, especially any 0603 resistors (I baked those into the single sensor BOM). It’s important to note the tolerance of the bias resistor (line 5), a lower tolerance can be used if it is calibrated for (a later blog post should talk about this).

Step 2: Solder Probes

Once you’ve received all the parts, it’s time to break out the soldering iron, tweezers, and reading glasses (optional) to tackle the most difficult step of this build: soldering on US0603 sized resistors. Soldering these on is a major test of patience even for veteran electrical engineers, but not impossible for first-time solders. Here are a few tips and tricks that should help: article from build-electronic-circuits.com, video from Engenuics Technologies.

For the current design, three resistors need to be soldered: two thermistors and one low-ohm heater resistor. I find it helpful to mark which one is which immediately after soldering with some nail polish so I don’t get them confused because they look identical.

After the tiny resistors are in place on the end of the probe, its time to move down and solder on connectors on all the probes, 100K ohm bias resistors on the thermistor probes, and “short” the bias resistor on the heater probes using a large clump of solder on the 0603 pads (circled in red below). Use a multimeter to make sure all solder points are good and that the probe resistor is not shorted. The temperature probe should have a resistance of ~100k (this will vary based on temperature). The heater probe should have a resistance of 50 ohms (or whatever heater ohm is chosen).

As kind of a placeholder, the current connectors on the probes are 90 deg female headers. Eventually it would be a good idea to add a waterproof connector onto the ends; I’ve had my eye on TE’s DEUTSCH DTF13-3P for a while for this purpose.

Step 3: Apply Thermal Epoxy

The next step involves the thermal epoxy. This is used in order to evenly spread out the effect of the heat pulse and to get better contact when inserted into a tree bore-hole. This is best applied using a 3D printed mold. Ideally, this would be printed on a high resolution SLA printer because of the small size of the mold. Formlab’s Form 2 was used to make the molds in the images; it provides up to 0.025 mm layer size. It’s also suggested that mold release spray be used on the inside of the mold to help the epoxy from sticking.

The epoxy in the BOM is a two part epoxy with a curing time of 45 minutes. To use, squeeze out equal parts from the A and B syringes and mix this well with a mixing stick before applying this to the inside of the mold. Put the mold on the tip of the probe so that the resistor is centered and press down. Gently wipe away any excess epoxy. Wait at LEAST 45 minutes before removing the mold, suggested overnight. Make sure that disposable gloves are used during this step.

After the epoxy is set, gently wipe with sandpaper to remove any major impurities. Next, coat the entire probe with silicone conformal coating with two coats, letting dry completely in between. This will seal the epoxy to prevent plant moisture from seeping in and changing the properties of the probe over time. It will also waterproof the rest  of the board. Make sure to avoid getting and silicone in the connector.

Step 4: Wire Things Up

The probes should be wired to the board as shown to work with the current code.

If you’re feeling savvy, feel free to play around with what pins are used. It’s important that the probes output goes to an analog in pin on the M0 (A0 to A5 shown below). The trigger can be moved to any pin, provided that the code is updated to match.

The heater probes could be attached to the 3.3V output pin (identified by “3V”) in order to further stabilize the power delivered as battery voltage decreases as it dies but the 3.3V should always be the same. However, this would reduce the energy efficiency of the system as the 3.3V output pin goes through the M0’s internal voltage regulator which burns off the excess voltage as heat. Also, the 3.3V supply has a max supply of 500mA which is near the current draw of a single heater probe.

Step 5: Program the Microcontroller

The code for the basic program described in this build guide is posted at this link. A future blog post will walk through the important functions. Further in the future, a stand alone library and/or incorporation with project Loom is planned.

If you’ve never used an Feather M0 before, check out these two pages on Adafruit’s tutorial:

• Arduino IDE Setup
• Programming with Arduino IDE

If you’ve never programmed in Arduino before (or ever), I would highly recommend reading though a few of the fundamental tutorial pages on the Arduino website until you grasp basic the basic concepts and idea of what Arduino is. Linked here.

Step 6: Install in Plant

This part of the process will change slightly based on what plant this is being installed into.

In order to to ensure that the probes are properly spaced, a 3D printed guide should be used. This version has a 7mm spacing between the probes. Future tests should test with different probe spacing. This doesn’t need to be as precise as the thermal epoxy mold; I used a Lulzbot Taz 5.

Insert the probes into their respective holes in the guide with the heater in the middle. Turn all of the PCB boards to face the thin side of the guide such that all the boards are parallel and facing to the same side (not up or down); this will help to deliver the heat pulse to the thermistors symmetrically. Optionally, use epoxy/superglue to fix them in place.

If you’re installing in a tree, holes will need to be drilled into the wood at a proper diameter (~2.75 mm) using an additional “guide”. As of now (6/11/2018) these have not been tested in a tree. 

View fullsize

Based on preliminary tests it should take about a day for the temperature to regulate and good data to start coming in. A later blog post will go into further detail on best practices for installing in different plants (especially trees) after some more tests are conducted. Potential things include: installing all probes in the north side of plants to avoid the sun (south if you’re on the wrong side of the world), filling any drill hole cavity with thermal grease via a syringe prior to inserting the probes (improve contact with the tree) and filling the end of the hold with putty/glue to seal it.

If you have any questions or suggestions for this design please please please reach out to me, Brett, at stoddabr@gmail.com. Happy building!

By: Brett Stoddard

One metric for plant health is simply how “hydrated” the xylem is. This can be an indication of how much water the plant has been drinking and could change if it is living in a stressful environment.

This sensor would be very similar to capacitance sensors used to measure volumetric water content (VWC) in the soil. An open sourced implementation of that is the Gravity Capacitance Soil Moisture Probe which is from DFRobot. It uses the TLC555I pulse generator to generate a signal which passes through a transmission line (on a pcb) that is immersed in the soil. Depending on the VWC of the water, the properties of that embedded transmission line changes.

For the tree implementation, the transmission line would go along a probe similar to the one used for the thermal sap flow sensor.

By: Brett Stoddard

Intro

By far the most annoying part of designing a thermal sap flux probe sensor is the “thermal” part. Without a proper heat pulse, there is no sensor. The problem is generating heat requires raw energy. According to my calculations, the heater makes up ~99% of the total energy requirements for this sensor. One of the goals of this project is to make the sap flow sensor as energy efficient as possible which will require a lot of testing to find the most efficient way to send out a heat pulse.

The Knobs

To find that maximum efficiency, there are a couple of design “knobs” that can be adjusted to find the maximum efficiency. Unfortunately, due to the short amount of time on this project, not all of these are going to be tested. Here is a list with what I believe are going to be the most important factors first:

• Energy Delivered (joules)
• Time of Pulse (second)
• Depth into Tree (inches from the edge of the tree’s cambium)
  • There’s a possibility that a “wrap” sensor could be possible like Dynamax’s Dynagague which uses thermojunctions on a flexible PCB
• Size of the Probe

The *IDEAL* Physics

I’ve put together a simple spreadsheet of a few different heater resistance values. Since this sensor is primarily being designed to integrate into other OPEnS Lab projects (namely the Evaporometer) a 3.7 voltage supply is assumed (uses 3.3V logic but runs off of a 3.7V battery, the heater will draw power from the battery).

Linked here is a google sheets file that I’ve been using to estimate the heat increase of the tree directly around the probe, and calculate the power requirements from the total resistance of the heater. 

One thing that should be noted when finalizing the resistance: the wattage rating for the resistor. There exists a lot of SMT resistors on the market, Digikey lists near 50 thousand, however, only a small minority possess the wattage requirements to provide that much heat (this can be seen in the “wattage” column of the attached table). If a resistor is chosen that does not satisfy the wattage requirements it will most likely fail. If a specific resistance is desired that is not available at this wattage, two identical resistors can be placed together in series, essentially halving this wattage requirement.

The temperature delta was calculated assuming that the heat capacitance of sapwood is 8 joules/C. This is an estimation. Further research into the exact heat capacitance of sapwood should be conducted.

By: Brett Stoddard

Background

Thermal sap flux (or flow) sensors have been popular amongst environmental sensing experts since the mid-20th century. They measure the velocity of sap through the stem or trunk of a plant using an array of heaters and temperature sensors.

A modern sap flow variant, proposed by Grainer, is made up of two temperature sensing probes directly above and below a heater probe—all spaced evenly. When a measurement is taken, the heater probe turns on and emits a heat pulse for several seconds. Then the temperature difference between the upper and lower probe is recorded. The temperature difference over time can be used to track sap flow (the specifics of this will be talked about in a later blog post).

Goal

To construct a sap flux sensor using surface mount technology (SMT) which can be manufactured using an entirely automated setup given a pick-and-place machine but can still be made by hand by a person with adept soldering skills.

Challenges

The biggest challenge for this project is minimizing the width of the probes. Inserting any foreign object into the xylem of any plant will alter how sap flows through it. As such, minimizing the size of the probe is critical to accurate measurements. Current commercial probes have diameters of around 1.5mm (http://dynamax.com/products/transpiration-sap-flow/tdp-sap-velocity-thermal-dissipation-probe).

Limitations in commercial PCB etching process are a limiting factor in the minimum size of these probes. Also, if a sufficiently small probe size is achieved, the number of plant types this can be used on increases. For example, a large probe may only be used on trees of a sufficient diameter while a smaller one could be used on crops such as corn.

Method

To design the PCB designs for sap flow probes, Eagle CAD was used. Sparkfun has a solid tutorial on learning the basics of PCB design (https://learn.sparkfun.com/tutorials/using-eagle-schematic). OSHPARK is a popular PCB vendor that is easy to order from and so their DRC was used for this project (http://docs.oshpark.com/design-tools/eagle/design-rules-files/). Using these limitations, a PCB probe diameter of ~2.5 mm was achieved.

For the temperature sensor probe thermistors were chosen to be the sensor component. Thermistors were chosen because of their high level of sensitivity when compared to other sensors. Thermistors act as variable resistors that alter their resistance based on their temperature. The main drawback to using thermistors is that their output is not linear, but rather follows a logarithmic curve and so they are difficult to work with. For this probe, a voltage ladder was used to retrieve the resistance of the thermistor as shown in the schematic in the results section.

The heater element consists of a 50 ohm, US0603 footprint resistor with a 0.38 wattage rating. A future blog post will go more in-depth on how the resistance was calculated.

To maximize contact with the plant’s xylem, thermal epoxy was used in a mold around all three PCB probes. This was designed in SolidWorks 2017 and printed on a FormLabs Form 2 SLA printer for maximum resolution. The inside of this mold was coated in mold release spray to prevent the thermal epoxy from sticking to it. After the epoxy was sufficiently dried, a layer of silicone conformal coating was applied to waterproof each of the probes.

To control the sensor, a microcontroller with built-in ADC’s (here an Adafruit M0 Trinket) was used. The output pins on the temperature sensors were connected to the analog inputs of the microcontroller. An NPN transistor sat between a voltage source and the heater and was controlled by an output pin on the microcontroller.

Results

Images of the final PCB are shown below. It uses standard US0603 footprint resistors.

The bill of materials used is below.

A future blog post will go into a more detailed, step-by-step tutorial on how to build your own! It will also have finalized design files and best pracitces.

Room for Improvement

As with any project design, there are a multitude of ways that this could be improved. A few ideas with good potential are listed below in no particular order:

• Linearizing voltage output using a parallel thermistor configuration
• A/D conversion on the probe sensor to avoid signal loss across the line
• Housing to protect the temperature probes from solar radiation
• Insulation to protect the probes from ambient temperature fluxes

References

In order that they appear:

1. Dynamax TDR Probes http://dynamax.com/products/transpiration-sap-flow/tdp-sap-velocity-thermal-dissipation-probe
2. Sparkfun Eagle Tutorial https://learn.sparkfun.com/tutorials/using-eagle-schematic
3. OSHPARK DRC for Eagle http://docs.oshpark.com/design-tools/eagle/design-rules-files/

External Links

In no particular order:

• Adafruit 12 bit ADC forum post
• Feather Lora RFM95 Adafruit tutorial
• Evaporimeter blog

By: Brett Stoddard

To test the probe described in my previous blog post, I deposited the probes in a banana plant I had handy.

How I built the probes by inserting heater wire and type T thermocouples into hypodermic needles. More resources can be found in my last post and in the following paper by Davis et al. Post here. Paper here. 

The graph result of the test is below:

As you can see, the top probe was not reading the correct temperature. This was probably an issue with the accuracy because it remained surprisingly precise meaning that the results shouldn’t be completely discarded. Daily trends are evidence that the sensor could be working somewhat. This is nowhere near the accuracy I intend to get with my final design.

However, there definitely is something interesting going on here. The data was recorded over an interval of three days. Examining the Differential plot, there seem to be roughly three major up-and-downs that PROBABLY are related to the day-night cycles of photosynthesis.

By: Brett Stoddard

Before I got started designing the SMT sap flow, I built and tested the probe sap flow sensor popularized by Grainer. This design popular with researchers probably because of its inexpensive BOM ( ~$10/sensor ) and promisingly low labor ( 1 hour/sensor ) which puts the total price at ( ~$60/sensor ).

When I replicated several of these probes I found significant difficulty in making them. The 36 gauge wires are especially difficult to work with and the nichrome wire heater probe was almost impossible to wind to a high enough resistance. For the 7 I built, only 2 were usable enough to record meaningful data. This is not a process I would recommend to anyone.

Here is the BOM used by Camden Lowrance in his University of Georga thesis in 2014 and the simplified one I created for this project. Camden’s includes a base station and mine does not.

The biggest difference is that I used a thermocouple amplifier chip instead of building my own. This greatly simplified the design and made fabrication a lot easier. I chose an Adafruit Universal Thermocouple Amplifier MAX31856 Breakout board. I made sure to set it to the Type-T setting. Adafruit has an excellent guide on how to use one of these on their website here.

Posted by Brett Stoddard

By: Brett Stoddard

Thermal sap flow sensors were initially proposed in the paper [German paper] in [date of german paper] by [german paper author]. Since then, several key improvements have created a sensor that semi-popular amongst researchers. However, their current high price point has reduced adoption.

A good case study for the modern state of commercial thermal sap flow sensors is Dynagague. Their probe style sap flow sensor which costs around $300-500 for a single sensor and an additional cost of ~$400 for the datalogger.

By using a few tricks in the design, we at the OPEnS Lab in contribution with [Friend of Trees] hope to design a sap flow sensor that costs less an $100 to produce including labor (priced at $50/hour) that meets the same performance at Dynagague. I plan to do this by redesigning almost everything to incorporate modern SMT manufacturing techniques open sourced communication protocols.

Here is an image of the rough schematic for the build.

This is the BOM for the first draft design. The raw eagle design documents can be found at [https://github.com/stoddabr/sapflow/tree/master].

To open them you will have to download my parts library from [https://github.com/stoddabr/EaglePCB].