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Posts from the ‘Agriculture’ Category

Soil Moisture Sensors: Why TDR vs. Capacitance May Be Missing the Point

Time Domain Reflectometry (TDR) vs. capacitance is a common question for scientists who want to measure volumetric water content (VWC) of soil, but is it the right question?  Dr. Colin S. Campbell, soil scientist, explains some of the history and technology behind TDR vs. capacitance and the most important questions scientists need to ask before investing in a sensor system.

TDR vs. Capacitance

TDR began as a technology the power industry used to determine the distance to a break in broken power lines.

Clarke Topp

In the late 1970s, Clarke Topp and two colleagues began working with a technology the power industry used to determine the distance to a break in broken power lines.  Time Domain Reflectometers (TDR) generated a voltage pulse which traveled down a cable, reflected from the end, and returned to the transmitter. The time required for the pulse to travel to the end of the cable directed repair crews to the correct trouble spot. The travel time depended on the distance to the break where the voltage was reflected, but also on the dielectric constant of the cable environment.  Topp realized that water has a high dielectric constant (80) compared to soil minerals (4) and air (1).  If bare conductors were buried in soil and the travel time measured with the TDR, he could determine the dielectric constant of the soil, and from that, its water content.  He was thus able to correlate the time it took for an electromagnetic pulse to travel the length of steel sensor rods inserted into the soil to volumetric water content. Despite his colleagues’ skepticism, he proved that the measurement was consistent for several soil types.

TDR vs. Capacitance

TDR sensors consume a lot of power. They may require solar panels and larger batteries for permanent installations.

TDR Technology is Accurate, but Costly

In the years since Topp et al.’s (1980) seminal paper, TDR probes have proven to be accurate for measuring water content in many soils. So why doesn’t everyone use them? The main reason is that these systems are expensive, limiting the number of measurements that can be made across a field. In addition, TDR systems can be complex, and setting them up and maintaining them can be difficult.  Finally, TDR sensors consume a lot of power.  They may require solar panels and larger batteries for permanent installations. Still TDR has great qualities that make these types of sensors a good choice.  For one thing, the reading is almost independent of electrical conductivity (EC) until the soil becomes salty enough to absorb the reflection.  For another, the probes themselves contain no electronics and are therefore good for long-term monitoring installations since the electronics are not buried and can be accessed for servicing, as needed.  Probes can be multiplexed, so several relatively inexpensive probes can be read by one set of expensive electronics, reducing cost for installations requiring multiple probes.

Many modern capacitance sensors use high frequencies to minimize effects of soil salinity on readings.

Advances in Electronics Enable Capacitance Technology

Dielectric constant of soil can also be measured by making the soil the dielectric in a capacitor.  One could use parallel plates, as in a conventional capacitor, but the measurement can also be made in the fringe field around steel sensor rods, similar to those used for TDR.  The fact that capacitance of soil varies with water content was known well before Topp and colleagues did their experiments with TDR.  So, why did the first attempt at capacitance technology fail, while TDR technology succeeded? It all comes down to the frequency at which the measurements are made.  The voltage pulse used for TDR has a very fast rise time.  It contains a range of frequencies, but the main ones are around 500 MHz to 1 GHz.  At this high frequency, the salinity of the soil does not affect the measurement in soils capable of growing most plants.  

Like TDR, capacitance sensors use a voltage source to produce an electromagnetic field between metal electrodes (usually stainless steel), but instead of a pulse traveling down the rods, positive and negative charges are briefly applied to them. The charge stored is measured and related to volumetric water content. Scientists soon realized that how quickly the electromagnetic field was charged and discharged was critical to success.  Low frequencies led to large soil salinity effects on the readings.  This new understanding, combined with advances in the speed of electronics, meant the original capacitance approach could be resurrected. Many modern capacitance sensors use high frequencies to minimize effects of soil salinity on readings.  

TDR vs. Capacitance

NASA used capacitance technology to measure water content on Mars.

Capacitance Today is Highly Accurate

With this frequency increase, most capacitance sensors available on the market show good accuracy. In addition, the circuitry in them can be designed to resolve extremely small changes in volumetric water content, so much so, that NASA used capacitance technology to measure water content on Mars. Capacitance sensors are lower cost because they don’t require a lot of circuitry, allowing more measurements per dollar. Like TDR, capacitance sensors are reasonably easy to install. The measurement prongs tend to be shorter than TDR probes so they can be less difficult to insert into a hole. Capacitance sensors also tend to have lower energy requirements and may last for years in the field powered by a small battery pack in a data logger.   

In two weeks: Learn about challenges facing both types of technology and why the question of TDR vs. Capacitance may not be the right question.

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New Weather Station Technology in Africa-3

The Trans African Hydro and Meteorological Observatory (TAHMO) project expects to put 20,000 microenvironment monitors over Africa in order to understand the weather patterns which affect that continent, its water, and its agriculture. In the conclusion of our 3 part series, we  interview Dr. John Selker about his thoughts on the project.

TAHMO

The economics of weather data value may be going up because we’re reaching a cusp in terms of humanity’s consumption of food.

In your TEDx talk you estimate that US weather stations directly bring U.S. consumers  31 billion dollars in value per year. Can Africa see that same kind of return?

Even more.  The economics of weather data value may be going up because we’re reaching a cusp in terms of humanity’s consumption of food.  Africa, one could argue, is the breadbasket for this coming century.  Thus, the value of information about where we could grow what food could be astronomical.  It’s very difficult to estimate.  One application of weather data is crop insurance.  Right now, crop insurance is taking off across Africa. The company we’re working with has 180,000 clients just in Kenya.  When we talked about 31 billion dollars in the U.S., that is the value citizens report, but you need to add to that protection against floods, increased food production, water supply management, crop insurance and a myriad of other basic uses for weather data.  In Africa, the value of this type of protection alone pays for over 1,000 times the cost of the weather stations.

Another application for weather data is that in Africa, the valuation of land itself is uncertain. So if, because of weather station data, we find that a particular microclimate is highly valuable, suddenly land goes from having essentially no value to becoming worth thousands of dollars per acre.  It’s really difficult to estimate the impact the data will have, but it could very well end up being worth trillions of dollars.  We have seen this pattern take place in central Chile, where land went from about $200/hectare in 1998 to over $3,000/ha now due to the understanding that it was exceptionally suited to growing pine trees, which represented a change in land value exceeding $3 billion.

Does the effect of these weather stations go beyond Africa?

There’s limited  water falling on the earth, and if you can’t use weather data to invest in the right seeds, the right fertilizer, and plant at the right time in the right place, you’re not getting the benefit you should from having tilled the soil.  So for Africa the opportunity to improve yields with these new data is phenomenal.  

In terms of the world, the global market for calories is now here, so if we can generate more food production in Africa, that’s going to affect the price and availability of food around the world.  The world is one food community at this point, so an entire continent having inefficient production and ineffective structures costs us all.

TAHMO

If we can generate more food production in Africa, that’s going to affect the price and availability of food around the world.

You’re collecting data from Africa. Is it time to celebrate yet?

I think this is going to be one of those projects where we are always chilling the champagne and never quite drinking it.  It is such a huge scope trying to work across a continent.  So I would say we’ve got some stations all over Africa, we’re learning a lot, and we’ve got collaborators who are excited.  We have reason to feel optimistic.  It will be another five years before I’ll believe that we have a datastream that is monumental.  Right now we’re still getting the groundwork taken care of.  By September of this year we expect to have five hundred of stations in place, and then two years from now, over two thousand. This will be a level of observation that will transform the understanding of African weather and climate.

TAHMO

This is a project of hundreds of people across the world putting their hands and hearts in to make this possible.

How do you deal with the long wait for results?  

In science there is that sense you get when you want to know something, and you can see how to get there.  You have a theory, and you want to prove it.  It kind of captures your imagination.  It’s a combination of curiosity and the potential to actually see something happen in the world: to go from a place where you didn’t know what was going on to a place where you do know what’s going on.  I think about Linus Pauling, who made the early discoveries about the double helix.  He had in his pocket the X-ray crystallography data to show that the protein of life was in helical form, and he said, “In my pocket, I have what’s going to change the world.”  When we realized the feasibility of TAHMO, we felt much the same way.”  

Sometimes in your mind, you can see that path: how you might change the world.  It may never be as dramatic as what Pauling did, but even a small contribution has that same excitement of wanting to be someone who added to the conversation, who added to our ability to live more gracefully in the world.  It’s that feeling that carries you along, because in most of these projects you have an idea, and then ten years later you say, “why was it that hard?”  

Things are usually much harder than your original conception, and that energy and curiosity really helps you through some of the low points in your projects.  So, curiosity has a huge influence on scientific progress.  Changing the world is always difficult, but the excitement, curiosity, and working with people, it all fits together to help us draw through the tough slogs.  In TAHMO, I cannot count the number of people who have urged us to keep the effort moving forward and given a lift just when we needed it most.  This is a project of hundreds of people across the world putting their hands and hearts in to make this possible.  Having these TAHMO supporters is an awesome responsibility and concrete proof of the generosity and optimism of the human spirit.

Learn how you can help TAHMO.

New Weather Station Technology in Africa (Part 2)

Weather data improve the lives of many people. But, there are still parts of the globe, such as Africa, where weather monitoring doesn’t exist (see part 1). John Selker and his partners intend to remedy the problem through the Trans African Hydro Meteorological Observatory (TAHMO).  Below are some challenges they face.

weather station

TAHMO aims to deploy 20,000 weather stations across the continent of Africa in order to fill a hole that exists in global climate data.

Big Data, Big Governments, and Big Unknowns

Going from an absence of data to the goal of 20,000 weather stations offers hope for positive changes. However, Selker is still cautious. “Unintended consequences are richly expressed in the history of Africa, and we worry about that a lot. It’s an interesting socio-technical problem.”  This is why Selker and others at TAHMO are asking how they can bring this technology to Africa in a way that fits with their cultures, independence, and the autonomy they want to maintain. 

TAHMO works with the government in each country stations are deployed in; negotiating agreements and making sure the desires of each recipient country are met. Even with agreements in place, the officials in each country will do what is in the best interest of the people: a gamble in countries where corruption is a factor which must be addressed. Selker illustrates this point by recalling an instance in 1985 when he witnessed a corrupt government official take an African farmer’s land because the value had increased due to a farm-scale water development project.

Most TAHMO weather stations are hosted and maintained by a local school, making it available as an education tool for teachers to use to teach about climate and weather. Data from TAHMO are freely available to the government in the country where the weather station is hosted, researchers who directly request data, and to the school hosting and maintaining the weather station. Commercial organizations will be able to purchase the data, and the profits will be used to maintain and expand the infrastructure of TAHMO.

weather station

Selker says it’s all about collaboration.

Terrorism, Data, and Open Doors

“When I wanted to go out and put in weather stations, my wife simply said, ‘no, you will not go to Chad.’ … because it is Boko Haram central,” Selker says.

The Boko Haram— a terrorist organization that has pledged allegiance to ISIS— creates an uncommon hurdle. Currently the Boko Haram is most active in Nigeria, but has made attacks in Chad, Cameroon, and Niger.

Selker also mentioned similar issues with ISIS, “When ISIS came through Mali, the first thing they did is destroy all the weather stations. So they have no weather data right now in Mali.” Acknowledging the need for security, he adds, “we’re  completing the installation of  eight stations [in Mali] in April.”

“We have good contacts [in Nigeria] and they’re working hard to get permission to put up stations right now in that area. We’ve shipped 15 stations which are ready to install. With these areas we can’t go visit, it’s all about collaboration. It’s about partners and people you know. We have a partnership with a tremendous group of Africans who are really the leading edge of this whole thing.”

weather station

Most TAHMO weather stations are hosted and maintained by a local school.

A Hopeful Future

Despite the challenges of getting this large-scale research network off the ground, Selker and his group remain hopeful.  About his weather data he says, “It’s not glamorous stuff, you won’t see it on the cover of magazines, but these are the underpinnings of a successful society.”

Selker optimistically adds, “We are in a time of incredible opportunity.”

Learn more about TAHMO

Next Week:  Read an interview with Dr. John Selker on his thoughts about TAHMO.

New Weather Station Technology in Africa

Weather data, used for flight safety, disaster relief, crop and property insurance, and emergency services, contributes over $30 billion in direct value to U.S. consumers annually. Since the 1990’s in Africa, however, there’s been a consistent decline in the availability of weather observations. Most weather stations are costly and require highly trained individuals to maintain. As a result, weather stations in African countries have steadily declined over the last seventy years. Oregon State University’s, Dr. John Selker and his partners intend to remedy the problem through his latest endeavor— the Trans African Hydro Meteorological Observatory (TAHMO).

weather stations

Weather data improve the lives of many people. But, there are still parts of the globe where weather monitoring doesn’t exist.

Origins of TAHMO

TAHMO is a research-based organization that aims to deploy 20,000 weather stations across the continent of Africa in order to fill a hole that exists in global climate data. TAHMO originated from a conversation between Selker and Dr. Nick van de Giesen from Delft University of Technology while doing research in Ghana. Having completed an elaborate study on canopy interception at a cocoa plantation in 2006, they hit a “data wall.” There was virtually no weather data available in Ghana, a problem shared by most African countries. This opened the door to what would later become TAHMO.

weather stations

The majority of weather stations are being installed at local schools where teachers are using the data in their classroom lessons.

Logistics and Equipment

Originally Selker and van de Geisen set out to make a $100 weather station, which Selker admitted, “turned out to be harder than we thought.” Not only was making a widely-deployable, affordable, research-grade, no-moving-parts weather station difficult, but additional challenges presented themselves.

“The model of how we might measure the weather in Africa, the whole business model, the production model, infrastructure support, the data-base and delivery system, the agreements with the countries, agreements with potential data-buyers, that all took us a long time to sort-out.” Despite these challenges, in 2010 it started to look feasible. “That’s when we really started to figure out what the technology we were going to use was going to look like.”

After giving a lecture at Washington State University, Selker spoke with Dr. Gaylon Campbell about the project, which led to a long development-deployment-development cycle. Eventually the final product emerged as a low-maintenance, no-moving-parts, cellular-enabled, solar-powered weather station.

weather stations

An estimated 60 percent of the African population earn their income by farming.

Agricultural Benefits of Weather Stations

Crop insurance, a service that is widely used in developed countries, relies on weather data. Once historical data exists, insurance rates can be set, and farmers can purchase crop insurance to replace a crop that is lost to drought, weather, wildfire, etc. On a continent with the largest percentage of the total population subsistence farming, this empowers farmers to take larger risks. Without insurance, farmers need to conserve seed, saving enough to eat and plant again if a crop fails. With crop insurance, crop loss is not as devastating, and farmers can produce larger yields without worrying about losing everything. Hypothetically, this would lead to more food available to the global market, stabilizing food prices year over year.

Crop insurance aside, weather data provide growers with information like when to plant, when not to plant, what crops to plant, and when and if to treat for disease. For rainfed crops, this can mean the difference between a successful yield and a failure.

“Currently in most African countries, the production per acre is about one-sixth of that in the United States. That is the biggest opportunity, in my opinion, for sustainable growth without having to open up new tracts of land. The land is already under cultivation, but we can up productivity, probably by a factor of four, by giving information about when to plant,” Selker comments.  

Despite the social benefits, Selker makes it clear that the TAHMO effort is based on mutual benefit: “We are here for a reason, we want these data to advance our research on global climate processes.  This is a global win-win partnership.”

Learn how you can help TAHMO by getting active.

Next week:  Read about some of the challenges facing TAHMO

How to Get More From Your NDVI Sensor (Part 3)

In the conclusion of our three-part series on improving NDVI sensor data (see part 2), we discuss how to correct for limitations which occur in high leaf area index (LAI) conditions.

NDVI Sensor

Where there’s a large amount of vegetation, NDVI tends to saturate.

NDVI Limitations – High LAI

NDVI is useful in the midrange of LAI’s as long as you don’t have strong soil effects, but as you approach an LAI above 4, you lose sensitivity. In figure 6, loss of sensitivity is primarily due to a saturation in the red band. Measurements were taken in a wheat canopy and a maize canopy. The near infrared reflectance is sensitive across the entire spectrum of the wheat and maize canopies, but the red saturates relatively quickly. Where the red starts to saturate is where the NDVI starts to saturate.

NDVI Sensor

Figure 6: Gitelson (2004) J. Plant Phys

Note: NDVI saturates at high LAI’s, however, if your purpose is to get at the fractional interception of light, NDVI tends not to have the saturation issue. In Figure 7, Fpar or the fractional interception of light of photosynthetically radiation is nearly complete far before NDVI saturates. This is because canopies are efficient at intercepting light, and once we get to an LAI of about 4, most of the light has been intercepted or absorbed by the canopy.  Thus, incremental increases in LAI don’t significantly affect the FPar variable.

NDVI Sensor

Figure 7: Fractional interception of light is near complete at an LAI around 4. (Gamon et al. (1995) Eco. Apps)

Solution 3- WDRVI

One solution for the NDVI saturation issue is called the Wide Dynamic Range Vegetation Index (WDRVI). It’s formulation is similar to NDVI, except for a weighting coefficient that can be used to reduce the disparity between the contribution of the near infrared and red reflectance.  

NDVI Sensor

In the WDRVI, a is multiplied by the near infrared reflectance to reduce its value and bring it closer to the red reflectance value. In doing so, it balances out the red and the near infrared contribution to the vegetation index.

NDVI Sensor

Figure 8: (Gitelson (2004) J. Plant Phys)

a can range anywhere from 0 to 1. Figure 8 shows that as we use a smaller value of a, we get an increasing linear response of the wide dynamic vegetation index to LAI.

The only drawback of the WDRVI is that the selection of a is subjective. It’s something that you experiment on your own until you find a value for a that is optimal for your solution.  People tend to err on the side of a very low value simply because they’ll get closer and closer to a linear response to LAI as a decreases.

Solution 4 – Enhanced Vegetation Index

The enhanced vegetation index (EVI) was designed to enhance sensitivity in high biomass ecosystems, but it also attempts to reduce atmospheric influences.  This was a vegetation index created for the purposes of a satellite based platform. There’s a lot of atmosphere to look through from a satellite to the ground, and sometimes the aerosols in the atmosphere affect the reflectances in the red and the near infrared regions causing spurious observations.  The EVI also tries to reduce sensitivity of the index to soil. Thus the EVI is a kind of solution to both extremes.

NDVI Sensor

In the EVI equation, the two major inputs are near infrared and red reflectances.  C1 , C2, and L are all parameters that can be estimated, but the blue band is something that has to be measured. Most NDVI sensors are two band sensors, so you don’t have that information in the blue.  Plus, with satellites, the blue band is relatively noisy and doesn’t always have the best quality data, thus EVI has limited value.

Solution 6: EVI2 (Enhanced Vegetation Index 2)

Those problems led a scientist named Jiang to come up with a solution.  Jiang observed quite a bit of autocorrelation between the red band and the blue band, so he decided to try and formulate EVI without the blue band in what he called the EVI2 (Enhanced Vegetation Index 2).  if you’re interested in the mathematics, we encourage you to go read his paper, but here we give you the equation in case you’re interested in using it.

NDVI Sensor

Figure 9

When Jiang calculated his EVI2 and compared it to the traditional EVI (Figure 9), it was nearly a one to one relationship. For all intents and purposes EVI2 was equivalent to EVI.  Since this avoids blue band, it offers some exciting possibilities as it reduces to just using the two inputs of NIR and red bands to calculate NDVI.

NDVI Sensor Summary

NDVI measurements have considerable value, and though there are extremes where NDVI performs poorly, even in these cases there are several solutions.  These solutions all use the near infrared and the red bands, so you can take an NDVI sensor, obtain the raw values of NIR and red reflectances and reformulate them in one of these indices (there are several other indices available that we haven’t covered). So if you’re in a system with extremely high or low LAI, try to determine how near infrared and red bands can be used in some type of vegetation index to allow you to research your specific application.

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Get More From Your NDVI Sensor (Part 2)

Last week we discussed Normalized Difference Vegetation Index (NDVI) sampling across a range of scales both in space and in time, from satellites sampling the entire earth’s surface to handheld small sensors that measure individual plants or even leaves (see part 1).  This week, learn about NDVI applications, limitations, and how to correct for those limitations.

NDVI Sensor

Limitations of the Normalized Difference Vegetation Index tend to occur at the extremes of the spectrum.

NDVI Sensor

NDVI Applications

People use NDVI to infer things like leaf area index (LAI) or fractional light interception (FPAR) of a canopy.  Some scientists also associate NDVI with biomass or yield of a crop. People also use NDVI to get a sense of phenology (general temporal patterns of greenness), as well as where vegetation occurs or how much vegetation is in a particular location.

In Figure 4, you can see how the reflectance spectrum at a given canopy LAI changes with leaf area index, decreasing in the visible range while increasing in the near infrared.

NDVI Sensor

Figure 4

At very low LAI’s, the reflectance spectrum is relatively undifferentiated between red and NIR (black line), but when LAI is high, there’s a strong absorption of red light by chlorophyll with a strong reflectance in the NIR. If fact, as LAI increases, there’s an ever-increasing reflectance in the near infrared around 800 nm.

NDVI Limitations

Limitations of the Normalized Difference Vegetation Index tend to occur at the extremes of the spectrum. Any time there’s very low vegetation cover (majority of the scene is soil), NDVI will be sensitive to that soil. This can confound measurements.  On the other extreme, where there’s a large amount of vegetation, NDVI tends to saturate. Notice the negligible difference between spectra at an leaf area index (LAI) of 3 (purple) versus 6 (green). Indeed, in a tropical forest, NDVI will not be sensitive to small changes in the LAI because LAI is already very high.  However, several solutions exist.

Solution 1-Soil Adjusted Vegetation Index

Figure 5 shows the results of a study taking spectral measurements of different vegetation indices across a transect of bare soil.  Moving from dry clay loam to wet clay loam, we see a very strong response of NDVI due to the wetness of the soil; undesirable if we’re measuring vegetation.  We’re not interested in an index that’s sensitive to changes in soil or soil moisture. However, there are a few other indices plotted in figure 5 with much lower sensitivities to variations in the soil across the transect.

NDVI Sensor

Figure 5: Qi et al. (1994) Rem. Sens. Env.

The first one of those indices is the Soil Adjusted Vegetation Index (SAVI). The equation for SAVI is similar to NDVI. It incorporates the same two bands as the NDVI–the near infrared and the red.

NDVI Senso

Soil Adjusted Vegetation Index (Huete (1988) Rem. Sens. Env.)

The only thing that’s different, is the L parameter.  L is a soil adjustment factor with values that range anywhere from 0 to 1.  When vegetation cover is 100%, L is 0 because there’s no need for a soil background adjustment. However, when vegetation cover is very low, that L parameter will approach one. Because it is difficult to measure exactly how much vegetation cover you have without using NDVI, we can modify the NDVI so it’s not sensitive to soil by guessing beforehand what L should be. It’s common practice to set L to an intermediate value of 0.5.   You can see in Figure 5 the Soil Adjusted Vegetation Index or SAVI has a much lower sensitivity to the soil background.

Solution 2- Modified SAVI

The next vegetation index is the modified SAVI (MSAVI). The SAVI equation contains an L parameter that we have to estimate–not an accurate way of handling things.  So a scientist named Key developed a universal optimum for L. We won’t get into the math, but he was able to simplify the SAVI equation to where there’s no longer a need for the L parameter, and the only inputs required are the reflectances in the near infrared and the red.  

NDVI Sensor

Modified SAVI (Qi et al. (1994) Rem. Sens. Env.)

This was a pretty significant advance as it circumvented the need to estimate or independently measure L. When Key compared SAVI to MSAVI, there was virtually no difference between the two indices in terms of their sensitivity to the amount of vegetation and their response to the soil background.

NDVI Sensor

MSAVI compares well with SAVI in terms of dynamic range and noise level (Qi et al. (1994) Rem. Sens. Env.)

Next week:  Learn about solutions for high LAI.

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Get More From Your NDVI Sensor

Modern technology has made it possible to sample Normalized Difference Vegetation Index (NDVI) across a range of scales both in space and in time, from satellites sampling the entire earth’s surface to handheld small sensors that measure individual plants or even leaves.

NDVI

Figure 1: NDVI is sensitive to the amount of vegetation cover that is present across the earth’s surface.

NDVI – Global

The broadest way to think of NDVI is data obtained from an earth orbiting satellite. In the figure above, you can see highly vegetated areas that have high NDVI values represented by dark green colors across the globe.  Conversely, areas of low vegetation have low NDVI values, which look brown.  NDVI is sensitive to the amount of vegetation cover that is present across the earth’s surface.

NDVI – Local

How might NDVI be useful at the plot level? Figure 2 below shows a successional gradient where time zero is a bare patch of soil, or a few forbs or annual grasses. If we leave that patch of ground for enough time, the vegetation will change: shrubs may take over from grasses and eventually we might see a forest. Across a large area, we may also move from grasslands to forest. In an agricultural system, there is yearly turnover of vegetation–from bare field to plant emergence, maturity, and senescence. This cycle repeats itself every year.  Within these growth cycles NDVI helps to quantify the the canopy growth that occurs over time as well as the spatial dynamics that occur across landscapes.

NDVI

Figure 2: Seasonal growth plotted against spatiotemporal variation

Spectral Reflectance Data

So where does NDVI come from? In Figure 3, the x-axis plots wavelength of light within the electromagnetic spectrum; 450 to 950 nm covers both the visible region and a portion of the near infrared. On the y-axis is percent reflectance.  This is a typical reflectance spectrum from green vegetation.

NDVI

Figure 3: Spectral Reflectance Data. (Figure and Images: landsat.gsfc.nasa.gov)

The green hyperspectral line is what we would expect to get from a spectral radiometer.  Reflectance is typically low in the blue region, higher in the green region, and lower in the red region. It shifts dramatically as we cross from the visible to the near infrared. The two vertical bars labeled NDVI give you an idea of where a typical NDVI sensor measures within the spectrum.  One band is in the red region and the other is in the near infrared region.  

NDVI capitalizes on the large difference between the visible region and the near infrared portion of the spectrum. Healthy, growing plants reflect near infrared strongly.  The two images on the right of the figure above are of the same area.  The top image is displayed in true color, or three bands–blue, green and red. The image below is a false color infrared image.  The three bands displayed are blue, green, and in place of red, we used the near infrared. The bright red color indicates a lot of near infrared reflectance which is typical of green or healthy vegetation.

The reason NDVI is formulated with red and near infrared is because red keys in on chlorophyll absorption, and near infrared is sensitive to canopy structure and the internal cellular structure of leaves.  As we add leaves to a canopy, there’s more chlorophyll and structural complexities, thus we can expect decreasing amounts of red reflectance and higher amounts of near infrared reflectance.

How Do We Calculate the NDVI?

NDVI

The Normalized Difference Vegetation Index takes into account the amount of near infrared (NIR) reflected by plants. It is calculated by dividing the difference between the reflectances (Rho) in the near infrared and red by the sum of the two.  NDVI values typically range between negative one (surface water) and one (full, vibrant canopy). Low values (0.1 – 0.4) indicate sparse canopies, while higher values (0.7 – 0.9) suggest full, active canopies.  

The way we calculate the percent reflectance is to quantify both the upwelling radiation (the radiation that’s striking the canopy and then reflected back toward our sensor) as well as the total amount of radiation that’s downwelling (from the sky) on a canopy.  The ratio of those two give us percent reflectance in each of the bands.

Next Week: Learn about NDVI applications, limitations, and how to correct for those limitations.

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German Researchers Directly Measure Climate Change Effects Using TERENO Lysimeters

In Germany, scientists are measuring the effects of tomorrow’s climate change with a vast network of 144 large lysimeters.

lysimeters

The goal of these lysimeters is to measure energy balance, water flux and nutrition transport, emission of greenhouse gases, biodiversity, and solute leaching into the groundwater.

In 2008, the Karlsruhe Institute of Technology began to develop a climate feedback monitoring strategy at the Ammer catchment in Southern Bavaria. In 2009, the Research Centre Juelich Institute of Agrosphere, in partnership with the Helmholtz-Network TERENO (Terrestrial Environmental Observatories) began conducting experiments in an expanded approach.  

Throughout Germany, they set up a network of 144 large lysimeters with soil columns from various climatic conditions at sites where climate change may have the largest impact.  In order to directly observe the effects of simulated climate change, soil columns were taken from higher altitudes with lower temperatures to sites at a lower altitude with higher temperatures and vice versa. Extreme events such as heavy rain or intense drought were also experimentally simulated.

lysimeters

Lysimeter locations in Germany

Georg von Unold, whose company (formerly UMS, now METER) built and installed the lysimeters comments on why the project is so important. “From a scientific perspective, we accept changes for whatever reason they may happen, but it is our responsibility to carefully monitor and predict how these changes cause floods, droughts, and disease. We need to be prepared to react if and before they affect us.”

How Big Are the Lysimeters?

Georg says that each lysimeter holds approximately 3,000 kilograms of soil and has to be moved under compaction control with specialized truck techniques.  He adds,The goal of these lysimeters is to measure energy balance, water flux and nutrition transport, emission of greenhouse gases, biodiversity, and solute leaching into the groundwater. Researchers measure the conditions of water balance in the natural soil surrounding the lysimeters, and then apply those same conditions inside the lysimeters with suction ceramic cups that lay across the bottom of the lysimeter.  These cups both inject and take out water to mimic natural or artificial conditions.”

lysimeters

Researchers use water content sensors and tensiometers to monitor hydraulic conditions inside the lysimeters.

Researchers monitor the new climate situation with microenvironment monitors and count the various grass species to see which types become dominant and which might disappear. They use water content sensors and tensiometers to monitor hydraulic conditions inside the lysimeters. The systems also use a newly-designed system to inject CO2 into the atmosphere around the plants and soil to study increased carbon effects.  Georg says, “We developed, in cooperation with the HBLFA Raumberg Gumpenstein, a new, fast-responding CO2 enrichment system to study CO2 from plants and soil respiration. We analyze gases like CO2, oxygen, and methane. The chambers are rotated from one lysimeter to another, working 24 hours, 7 days a week.  Each lysimeter is exposed only for a few minutes so as not to change the natural environment.”

Next week:  Read about the intense precision required to move the soil-filled lysimeters, how problems are prevented, and how the data is used by scientists worldwide.

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Top Five Blog Posts in 2016

In case you missed them the first time around, here are the most popular Environmental Biophysics.org blog posts in 2016.

Lysimeters Determine if Human Waste Composting can be More Efficient

Top five blog posts Environmental biophysics

In Haiti, untreated human waste contaminating urban areas and water sources has led to widespread waterborne illness.  Sustainable Organic Integrated Livelihoods (SOIL) has been working to turn human waste into a resource for nutrient management by turning solid waste into compost.  Read more

Estimating Relative Humidity in Soil: How to Stop Doing it Wrong

Top five blog posts Environmental biophysics

Estimating the relative humidity in soil?  Most people do it wrong…every time.  Dr. Gaylon S. Campbell shares a lesson on how to correctly estimate soil relative humidity  from his new book, Soil Physics with Python, which he recently co-authored with Dr. Marco Bittelli.  Read more.

How Many Soil Moisture Sensors Do You Need?

Top five blog posts Environmental biophysics

“How many soil moisture sensors do I need?” is a question that we get from time to time. Fortunately, this is a topic that has received substantial attention by the research community over the past several years. So, we decided to consult the recent literature for insights. Here is what we learned.

Data loggers: To Bury, or Not To Bury

Top five blog posts Environmental biophysics

Globally, the number one reason for data loggers to fail is flooding. Yet, scientists continue to try to find ways to bury their data loggers to avoid constantly removing them for cultivation, spraying, and harvest.  Chris Chambers, head of Sales and Support at Decagon Devices always advises against it. Read more

Founders of Environmental Biophysics:  Champ Tanner

Top five blog posts Environmental biophysics

Image: http://soils.wisc.edu/people/history/champ-tanner/

We interviewed Gaylon Campbell, Ph.D. about his association with one of the founders of environmental biophysics, Champ Tanner.  Read more

And our three most popular blogs of all time:

Do the Standards for Field Capacity and Permanent Wilting Point Need to Be Reexamined?

Top five blog posts Environmental biophysics

We asked scientist, Dr. Gaylon S. Campbell, which scientific idea he thinks impedes progress.  Here’s what he had to say about the standards for field capacity and permanent wilting point.  Read more

Environmental Biophysics Lectures

Top five blog posts Environmental biophysics

During a recent semester at Washington State University a film crew recorded all of the lectures given in the Environmental Biophysics course. The videos from each Environmental Biophysics lecture are posted here for your viewing and educational pleasure.  Read more

Soil Moisture Sensors In a Tree?

Top five blog posts Environmental biophysics

Soil moisture sensors belong in the soil. Unless, of course you are feeling creative, curious, or bored. Then maybe the crazy idea strikes you that if soil moisture sensors measure water content in the soil, why couldn’t they be used to measure water content in a tree?  Read more

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How to Measure Water Potential

In the conclusion of our 3-part water potential  series (see part 1), we discuss how to measure water potential–different methods, their strengths, and their limitations.

How to measure water potential

Vapor pressure methods work in the dry range.

How to measure water potential

Essentially, there are only two primary measurement methods for water potential—tensiometers and vapor pressure methods. Tensiometers work in the wet range—special tensiometers that retard the boiling point of water (UMS) have a range from 0 to about -0.2 MPa. Vapor pressure methods work in the dry range—from about -0.1 MPa to -300 MPa (0.1 MPa is 99.93% RH; -300 MPa is 11%).

Historically, these ranges did not overlap, but recent advances in tensiometer and temperature sensing technology have changed that. Now, a skilled user with excellent methods and the best equipment can measure the full water potential range in the lab.   

There are reasons to look at secondary measurement methods, though. Vapor pressure methods are not useful in situ, and the accuracy of the tensiometer must be paid for with constant, careful maintenance (although a self-filling version of the tensiometer is available).

Here, we briefly cover the strengths and limitations of each method.

Vapor Pressure Methods:

The WP4C Dew Point Hygrometer is one of the few commercially available instruments that currently uses this technique. Like traditional thermocouple psychrometers, the dew point hygrometer equilibrates a sample in a sealed chamber.

How to Measure Water Potential

WP4C Dew Point Hygrometer

A small mirror in the chamber is chilled until dew just starts to form on it. At the dew point, the WP4C measures both mirror and sample temperatures with 0.001◦C accuracy to determine the relative humidity of the vapor above the sample.

Advantages

The most current version of this dew point hygrometer has an accuracy of ±1% from -5 to -300 MPa and is also relatively easy to use. Many sample types can be analyzed in five to ten minutes, although wet samples take longer.

Limitations

At high water potentials, the temperature differences between saturated vapor pressure and the vapor pressure inside the sample chamber become vanishingly small.

Limitations to the resolution of the temperature measurement mean that vapor pressure methods will probably never supplant tensiometers.

The dew point hygrometer has a range of -0.1 to -300 MPa, though readings can be made beyond -0.1 MPa using special techniques. Tensiometers remain the best option for readings in the 0 to-0.1 MPa range.

Secondary Methods

Water content tends to be easier to measure than water potential, and since the two values are related, it’s possible to use a water content measurement to find water potential.

A graph showing how water potential changes as water is adsorbed into and desorbed from a specific soil matrix is called a moisture characteristic or a moisture release curve.

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Example of a moisture release curve.

Every matrix that can hold water has a unique moisture characteristic, as unique and distinctive as a fingerprint. In soils, even small differences in composition and texture have a significant effect on the moisture characteristic.

Some researchers develop a moisture characteristic for a specific soil type and use that characteristic to determine water potential from water content readings. Matric potential sensors take a simpler approach by taking advantage of the second law of thermodynamics.

Matric Potential Sensors

Matric potential sensors use a porous material with known moisture characteristic. Because all energy systems tend toward equilibrium, the porous material will come to water potential equilibrium with the soil around it.

Using the moisture characteristic for the porous material, you can then measure the water content of the porous material and determine the water potential of both the porous material and the surrounding soil. Matric potential sensors use a variety of porous materials and several different methods for determining water content.

Accuracy Depends on Custom Calibration

At its best, matric potential sensors have good but not excellent accuracy. At its worst, the method can only tell you whether the soil is getting wetter or drier. A sensor’s accuracy depends on the quality of the moisture characteristic developed for the porous material and the uniformity of the material used. For good accuracy, the specific material used should be calibrated using a primary measurement method. The sensitivity of this method depends on how fast water content changes as water potential changes. Precision is determined by the quality of the moisture content measurement.

Accuracy can also be affected by temperature sensitivity. This method relies on isothermal conditions, which can be difficult to achieve. Differences in temperature between the sensor and the soil can cause significant errors.

Limited Range

All matric potential sensors are limited by hydraulic conductivity: as the soil gets drier, the porous material takes longer to equilibrate. The change in water content also becomes small and difficult to measure. On the wet end, the sensor’s range is limited by the air entry potential of the porous material being used.

Tensiometers and Traditional Methods

Read about the strengths and limitations of tensiometers and other traditional methods such as gypsum blocks, pressure plates, and filter paper at waterpotential.com

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