Name: field measurement of effective leaf area index using optical device in vegetation canopy
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Description: Watch this Scientific Journal Video about Field Measurement of Effective Leaf Area Index using Optical Device in Vegetation Canopy at JoVE.com

The authors are indebted to the Journal of Forest Science editorial board for encouraging and authorizing us to use the representative results in this protocol from the article published there.
The research was financially supported by the Ministry of Agriculture of the Czech Republic, institutional support MZE-RO0118, National Agency of Agricultural Research (Project No. QK21020307), and the European Union&#39;s Horizon 2020 research and innovation program (grant agreement No. 952314).
The authors also kindly thank three anonymous reviewers for their constructive criticism, which improved the manuscript. In addition, thanks go to Dusan Bartos, Alena Hvezdova, and Tomas Petr for helping with field measurements and Photon Systems Instruments Ltd. company for their collaboration and providing device photos.

NOTE: Before beginning to take planned field measurements, sufficiently charge the battery of the LP 110 device. Connect the instrument (USB connector, see Figure 1) and the computer through the attached cable. Battery status is shown in the left-upper corner of the device display.
1. Calibration before measurement
NOTE: For the LP 110, perform a dark calibration of the LAI sensor and in-built inclinometer calibrations before beginning ea...

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What are the differences between the LP 110 as a newly presented device for estimating LAI (or taking PAR intensity measurements) and the LAI-2200 PCA as an improved version of the previous standard LAI-2000 PCA for estimating LAI via an indirect method? Beyond the price being about fourfold higher for the Plant Canopy Analyzer compared to the LP 110, the number of output parameters, measurement conditions, methodological approaches, and possibilities of estimating LAI for different canopies, accuracy of results, etc., c...

Canopies are loci of numerous biological, physical, chemical, and ecological processes. Most of them are affected by canopy structures1. Therefore, accurate, rapid, non-destructive, and reliable in situ&#160;vegetation canopy quantification is crucial for a wide range of studies involving hydrology, carbon and nutrient cycling, and global climate change2,3. Since leaves or needles represent an active interface between the atmosphere and vegetation4, one of the critical canopy structural characteristics is leaf area index (LAI)5, defined as one-half of the total green leaf surface area per unit of horizontal ground surface area or crown projection for individuals, expressed in m2 per m2 as a dimensionless variable6,7.
Various instruments and methodological approaches for estimating terrestrial LAI and their pros and cons in diverse ecosystems have already been presented8,9,10,11,12,13,14,15. There are two main categories of LAI estimation methods: direct and indirect (see comprehensive reviews8,9,10,11,12 for more details). Mainly used in forest stands, ground-based&#160;LAI estimates are routinely obtained using indirect optical methods due to the lack of direct LAI determination, but they usually represented a time-consuming, labor-intensive, and destructive method9,10,12,16. Moreover, indirect optical methods derive LAI from more easily measure related parameters (from the viewpoint of its time-demanding and labor-intense nature)17, such as the ratio between incident irradiation above and below the canopy and the quantification of canopy gaps14. It is evident that Plant Canopy Analyzers have also been widely used to validate satellite LAI retrievals18; therefore, it has been considered a standard for LP 110 comparison (see Table of Materials for more details about employed instruments).
The LP 110, as an updated version of initially self-made simple instrument ALAI-02D19 and later LP 10020, was developed as a close competitor for Plant Canopy Analyzers. As a representative of indirect optical methods, the device is hand-held, lightweight, battery-powered, without any need for a cable connection between the sensor and data-logger that uses a digital inclinometer instead of a bubble level and enables faster and more accurate positioning and value reading. In addition, the device was designed to note immediate readouts. Thus, the time estimate needed for collecting data in the field is shorter for the LP 110 than Plant Canopy Analyzer by approximately &#8531;. After the export of readouts to a computer, the data are available for subsequent processing. The device records irradiance within the blue light wavelengths (i.e., 380-490 nm)21,22 using an LAI sensor for making an LAI calculation. The LAI sensor is masked by an opaque restriction cap with 16&#176; (Z-axis) and 112&#176; (X-axis) fields of view (Figure 1). Thus, light transmittance can be noted using the device held either perpendicularly to the ground surface (i.e., zenith angle 0&#176;), or at five different angles of 0&#176;, 16&#176;, 32&#176;, 48&#176;, and 64&#176; to be able also to deduce canopy elements&#39; inclination.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/62802/62802fig01.jpg" /> 
Figure 1: Physical features of the LP 110. The MENU key enables the user shift up and down throughout the display, and the SET button serves as the Enter key (A).The zenith view under different inclination angles (&#177;8 due to the side view) and the horizontal view is fixed for LP 110 to 112&#176; (B) similarly to the Plant Canopy Analyzer&#160;(modified by restrictors). <a href="https://www.jove.com/files/ftp_upload/62802/62802fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Due to the higher sensitivity of the LAI sensor, its restricted field of view, in-built digital inclinometer, automatic logging of reading values at the correct position indicated by sound without a button press, the new instrument is also suitable for above-canopy readings at narrow valleys or even on broader forest roads to measure a wide range of sky conditions. Besides that, it enables quantification of mature stand canopies above the relatively high regeneration, and it attains higher accuracy of irradiance values than Plant Canopy Analyzer. Moreover, the price of LP 110 equals about &#188; of the Plant Canopy Analyzer. Contrariwise, the utilization of LP 110 in dense (i.e.,&#160;LAIe at stand level over 7.88)23 or very low canopies as grassland is limited.
The LP 110 can work within two operating modes: (i) a single sensor mode taking both below-canopy and reference readings (above the studied canopy or in a sufficiently widespread clearing located within the vicinity of the analyzed vegetation) performed before, after, or during below-canopy measurements taken with the same instrument and (ii) a dual sensor mode using the first instrument for taking below-canopy readings, whereas the second one is employed for automatically logging reference readings within a regular predefined time interval (from 10 up to 600 s). The LP 110 can be matched with a compatible GPS device (see Table of Materials) to record each below-canopy measurement point&#39;s coordinates for both the modes mentioned above.
The effective leaf area index (LAIe)24 incorporates the clumping index effect and can be derived from measurements of solar beam irradiance taken above and below the studied vegetation canopy25. Thus, for the following LAIe calculation, transmittance (t) must be calculated from irradiation both transmitted below the canopy (I) and incident above the vegetation (Io) measured by the LP 110 device.
t = I / I0 (1)
Since the irradiation intensity exponentially decreases as it passes through a vegetation canopy, LAIe can be calculated according to the Beer-Lambert extinction law modified by Monsi and Saeki9,26
LAIe = - ln (I / I0) x k-1 (2),
Where, k is the extinction coefficient. The extinction coefficient reflects each element&#39;s shape, orientation, and position in the vegetation canopy with the known canopy element inclination and view direction9,12. The k coefficient (see equation 2) depends on the absorption of irradiance by foliage, and it differs among plant species based on the morphological parameters of canopy elements, their spatial arrangement, and optical properties. Since the extinction coefficient usually fluctuates around 0.59,27, equation 2 can be simplified as presented by Lang et al.28 in a slightly different way for heterogeneous and homogenous canopies:
In a heterogeneous canopy
LAIe = 2 x |<img alt="Equation 1" src="/files/ftp_upload/62802/62802eq01.jpg" />ln t| (3),
or
In a homogeneous canopy
LAIe = 2 x |ln T| (4),
Where, t: is transmittance at each below-canopy measurement point, and T: is the average transmittance of all t values per measured transect or stand.
In forest stands, LAIe must be further corrected due to a clumping effect of the assimilation apparatus within the shoots29,30,31,32,33,34 to obtain the actual LAI value.
The protocol is devoted to the practical utilization of the LP 110 optical device for estimating LAIe in a selected example of Central European conifer forest stands (see Table 2 and Table 3 for the site, structural, and dendrometric characteristics). LAIe estimation in a vegetation canopy using this device is based on a widely used optical method related to the transmittance of photosynthetically active radiation and canopy gap fraction. The paper aims to provide a comprehensive protocol for performing LAIe estimation using the new LP 110 optical device.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>AccuPAR</td>
			<td>METER Group, Inc., Pullman, WA, USA</td>
			<td>AccuPaR LP-80</td>
			<td>https://www.metergroup.com/environment/products/accupar-lp-80-leaf-area-index/</td>
		</tr>
		<tr>
			<td>DEMON</td>
			<td>CSIRO, Canberra, Australia</td>
			<td>DEMON</td>
			<td></td>
		</tr>
		<tr>
			<td>File Viewer</td>
			<td>LI-COR Biosciences Inc., NE, USA</td>
			<td>FV2200C Software</td>
			<td>https://www.licor.com/env/products/leaf_area/LAI-2200C/software.html</td>
		</tr>
		<tr>
			<td>FluorPen</td>
			<td>Photon System Instruments Ltd. (PSI), Czech Republic</td>
			<td>FluorPen 1.1.2.3 Sofware</td>
			<td>https://handheld.psi.cz/products/laipen/#download</td>
		</tr>
		<tr>
			<td>Hand-held GPS device</td>
			<td>Garmin Ltd., Czech Republic</td>
			<td>Garmin eTrex 32x Europe46</td>
			<td>https://www.garmin.cz/garmin-etrex-32x-europe46/80117</td>
		</tr>
		<tr>
			<td>Hand-held device for leaf area index estimation(LP 110)</td>
			<td>Photon System Instruments Ltd. (PSI) Czech Republic</td>
			<td>LaiPen LP 110</td>
			<td>https://handheld.psi.cz/products/laipen/#info</td>
		</tr>
		<tr>
			<td>Plant Canopy Analyser</td>
			<td>LI-COR Biosciences Inc., NE, USA</td>
			<td>LAI-2000 PCA</td>
			<td>LAI-2200 PCA or LAI-2200C as improved versions of LAI-2000 PCA can be used, see: https://www.licor.com/env/products/leaf_area/LAI-2200C/</td>
		</tr>
		<tr>
			<td>Statistical software</td>
			<td>Systat Software Inc., CA, USA</td>
			<td>SigmaPlot 13.0</td>
			<td>https://systatsoftware.com/products/sigmaplot/sigmaplot-version-13/?gclid=Cj0KCQjwzYGGBhCTARIs 
			AHdMTQzgfb42vv0mWmcbVcflNO 
			UvrLl802Lrhkfh23Qie2mIZfw4O8kp 
			7p0aAsoiEALw_wcB</td>
		</tr>
		<tr>
			<td>Statistical software</td>
			<td>StatSoft Inc., OK, USA</td>
			<td>STATISTICA 10.0</td>
			<td>For LAI visualization, wafer-plots in STATISTICA 10.0 were employed.</td>
		</tr>
		<tr>
			<td>SunScan</td>
			<td>Delta-T Devices, Ltd., Cambridge, UK</td>
			<td>SS1 SunScan</td>
			<td>https://www.delta-t.co.uk/product/sunscan</td>
		</tr>
		<tr>
			<td>TRAC</td>
			<td>3rd Wave Engineering, Ontarion Canada</td>
			<td>Tracing Radiation and Architecture of Canopies</td>
			<td>http://faculty.geog.utoronto.ca/Chen/Chen&#39;s%20homepage/res_trac.htm</td>
		</tr>
		<tr>
			<td>Tripod</td>
			<td>Any</td>
			<td>NA</td>
			<td>Tripod with standard nut</td>
		</tr>
		<tr>
			<td>Water level</td>
			<td>Any</td>
			<td>NA</td>
			<td></td>
		</tr>
	</tbody>
</table>

field measurement of effective leaf area index using optical device in vegetation canopy

Leaf area index (LAI) is an essential canopy variable describing the amount of foliage in an ecosystem. The parameter serves as the interface between green components of plants and the atmosphere, and many physiological processes occur there, primarily photosynthetic uptake, respiration, and transpiration. LAI is also an input parameter for many models involving carbon, water, and the energy cycle. Moreover, ground-based in situ measurements serve as the calibration method for LAI obtained from remote sensing products. Therefore, straightforward indirect optical methods are necessary for making precise and rapid LAI estimates. The methodological approach, advantages, controversies, and future perspectives of the newly developed LP 110 optical device based on the relation between radiation transmitted through the vegetation canopy and canopy gaps were discussed in the protocol. Furthermore, the instrument was compared to the world standard LAI-2200 Plant Canopy Analyzer. The LP 110 enables more rapid and more straightforward processing of data acquired in the field, and it is more affordable than the Plant Canopy Analyzer. The new instrument is characterized by its ease of use for both above- and below-canopy readings due to its greater sensor sensitivity, in-built digital inclinometer, and automatic logging of readings at the correct position. Therefore, the hand-held LP 110 device is a suitable gadget for performing LAI estimation in forestry, ecology, horticulture, and agriculture based on the representative results. Moreover, the same device also enables the user to take accurate measurements of incident photosynthetically active radiation (PAR) intensity.

The spatial structure obtained from both tested devices obviously differed in all studied plots, i.e., thinned from above (A), thinned from below (B) and a control without any silvicultural intervention (C; see Table 2 for more details). At the stand level, similar differences in LAI values obtained from the LP 110 and the Plant Canopy Analyzer were confirmed between thinned plots with various densities (A vs. B) using ANOVA and Tukey&#39;s test. For the Plant Canopy Analyzer, significantly higher LAI va...

Watch this Scientific Journal Video about Field Measurement of Effective Leaf Area Index using Optical Device in Vegetation Canopy at JoVE.com

Field Measurement of Effective Leaf Area Index using Optical Device in Vegetation Canopy

Fast and precise leaf area index (LAI) estimation in terrestrial ecosystems is crucial for a wide range of ecological studies and calibrating remote sensing products. Presented here is the protocol for using the new LP 110 optical device for taking ground-based in situ LAI measurements.

Leaf area index (LAI) is an essential canopy variable describing the amount of foliage in an ecosystem. The parameter serves as the interface between ...

This protocol introduces the recently developed device LaiPen LP 110 for leaf area index estimation by indirect optical method, and compares it with the standard LAI-2200 Plant Canopy Analyzer. The new device takes both above and below canopy readings easily, due to its greater sense of sensitivity, in-built digital inclinometer, and automatic logging of readings at the correct position. Also operating control is intuitive.The manual is necessary. For measurement design preparation, a brief planned canopy structure survey before its measurement is recommended to the operator. Begin by turning on both the instruments by holding the Set key for at least one second.Find Settings in the main menu by repeatedly pressing the Menu button and set the current date and time of both instruments by pressing Set, Time, Set. Then, choose Return and hold the Set key to return to the main menu. Then, set both the instruments at a single angle measurement mode.Select Settings holding the Set key, and press Angles, Set, Single, and confirm with the Menu key. Choose Return and hold the Set key to return to the main menu. After calibrating both the LAI sensor and the inbuilt inclinometer, calibrate both LP 110 devices, instrument one and instrument two with each other.Select Settings in the main menu by pressing the Set key, choose LAI calibration, and press the Set button. Next, hold both the devices in a horizontal plane in the vertical position, and adjust the constant value marked as C on the display by repeatedly pressing the Set key on instrument one, to achieve the same values as depicted on the device's screen on instrument two. Then, press the Menu button and return to the main menu.Attach instrument one vertically to a tripod placed in an open area or above the studied canopy. Obtain both above and below canopy readings under constant light conditions with standard overcast before sunrise or after sunset, to avoid obtaining incorrect irradiance values. First, select Settings in the main menu, and then choose Auto Interval pressing the Set key.Next, repeatedly pressed the Set key and then hold the Menu button to select the required interval for automatically logging reference values from 10 up to 600 seconds. Set a shorter time interval if light conditions change rapidly. Press the Menu key, select Return, and hold the Set button to return to the main menu.Subsequently press the Menu button repeatedly, holding the Set key to reselect measurement in the main menu. Then, choose Auto LAI Ref pressing the Set key to search for the correct LAI sensor position. Check the display, tilt the instrument both to the left and to the right, and forward and backward.After reaching the zenith angle defined by X and Z axes with zero or less than the value of five, fix the device firmly at the required position mentioned above, and then press the Set key. To start measuring the transmitted irradiance below the vegetation canopy using instrument two, choose Measurement in the main menu. Press the Set key and select LAI.Keep the orientation of the instrument two as that of instrument one. Press the Set key to activate the mode for our transmitted irradiance measurement below the canopy. Press the Set key again to obtain the value of transmitted irradiance below the canopy, and trigger both the inbuilt inclinometer and sound indicator serving to find the correct LAI sensor position.Then, keep the device perpendicularly to the ground service to be the LAI sensor pointed up to the zenith. Check the display, tilt the instrument both to the left and to the right, and forward and backward. All below canopy readings are automatically acquired and stored immediately once the zenith angle defined by both the X and Z axes reach zero or less than five.The beeping tone stops. Proceed with taking further measurements of transmitted irradiance that is below canopy readings, following steps for previous below canopy readings mentioned above. After taking the below canopy measurements using instrument two, press the Menu button and the Menu key repeatedly until Return is selected to return to the main menu, and then press the Set button.The data is saved in the instrument's memory after each reading. Hold the Menu button for at least one second to turn off the device safely without erasing any data. For the Plant Canopy Analyzer, significantly higher LAI values were observed in the control plot, with no silvicultural intervention in the thin ones.For the LP 110, the leaf area index did not significantly differ in the C and B treatments. For LP 110, a significant difference in leaf area index values between the C and A plots was found. Generally, the leaf area index significantly decreased after applied thinning treatments in the studied stance.The leaf area index values recording using LP 110 and Plant Canopy Analyzer for each thinning treatment in pure Norway spruce pole stands exhibited spatial variability. Linear regression was performed for all leaf area index data measured at a particular point level using the LP 110 and the Plant Canopy Analyzer. Ensure measuring under suitable synoptic conditions, use sufficiently sizeable open area for a reference readings, and reflect stand heterogeneity and measurement design for below canopy readings.Since transmitters can be recorded in different sensor view inclination angles, canopy elements angle orientation can be calculated. If canopy layer width is known, then the leaf area density can be deduced as well.

field-measurement-effective-leaf-area-index-using-optical-device

Research

JoVE Journal

Environment

Integrated Field Lysimetry and Porewater Sampling for Evaluation of Chemical Mobility in Soils and Established Vegetation

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals is often not well understood. Here we demonstrate an integrated field lysimetry and porewater sampling method for evaluating the mobility of chemicals applied to soils and established vegetation. Lysimeters, open columns made of metal or plastic, are driven into bareground or vegetated soils. Porewater samplers, which are commercially available and use vacuum to collect percolating soil water, are installed at predetermined depths within the lysimeters. At prearranged times following chemical application to experimental plots, porewater is collected, and lysimeters, containing soil and vegetation, are exhumed. By analyzing chemical concentrations in the lysimeter soil, vegetation, and porewater, downward leaching rates, soil retention capacities, and plant uptake for the chemical of interest may be quantified. Because field lysimetry and porewater sampling are conducted under natural environmental conditions and with minimal soil disturbance, derived results project real-case scenarios and provide valuable information for chemical management. As chemicals are increasingly applied to land worldwide, the described techniques may be utilized to determine whether applied chemicals pose adverse effects to human health or the environment.

Field lysimetry and porewater sampling allow researchers to evaluate the fate of chemicals applied to soils and established vegetation. The goal of this protocol is to demonstrate how to install required instrumentation and collect samples for chemical analysis during integrated field lysimetry and porewater sampling experiments.

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals ...

Modifying the Bank Erosion Hazard Index (BEHI) Protocol for Rapid Assessment of Streambank Erosion in Northeastern Ohio

Understanding the source of pollution in a stream is vital to preserving, restoring, and maintaining the stream&#8217;s function and habitat it provides. Sediments from highly eroding streambanks are a major source of pollution in a stream system and have the potential to jeopardize habitat, infrastructure, and stream function. Watershed management practices throughout the Cleveland Metroparks attempt to locate and inventory the source and rate the risk of potential streambank erosion to assist in formulating effect stream, riparian, and habitat management recommendations. The Bank Erosion Hazard Index (BEHI), developed by David Rosgen of Wildland Hydrology is a fluvial geomorphic assessment procedure used to evaluate the susceptibility of potential streambank erosion based on a combination of several variables that are sensitive to various processes of erosion. This protocol can be time consuming, difficult for non-professionals, and confined to specific geomorphic regions. To address these constraints and assist in maintaining consistency and reducing user bias, modifications to this protocol include a &#8220;Pre-Screening Questionnaire&#8221;, elimination of the Study Bank-Height Ratio metric including the bankfull determination, and an adjusted scoring system. This modified protocol was used to assess several high priority streams within the Cleveland Metroparks. The original BEHI protocol was also used to confirm the results of the modified BEHI protocol. After using the modified assessment in the field, and comparing it to the original BEHI method, the two were found to produce comparable BEHI ratings of the streambanks, while significantly reducing the amount of time and resources needed to complete the modified protocol.

Modifying the Bank Erosion Hazard Index BEHI Protocol for Rapid Assessment of Streambank Erosion in Northeastern Ohio

Streambank erosion potential can be evaluated and ranked using David Rosgen&#8217;s Bank Erosion Hazard Index (BEHI), however this protocol has significant limitations. Here we present protocol modifications to address time constraints, allow nonprofessionals to complete accurate assessments, and account for non-alluvial stream conditions in Northeast Ohio.

Understanding the source of pollution in a stream is vital to preserving, restoring, and maintaining the stream&#8217;s function and habitat it provides. ...

Modification and Application of a Leaf Blower-vac for Field Sampling of Arthropods

Rice fields host a large diversity of arthropods, but investigating their population dynamics and interactions is challenging. Here we describe the modification and application of a leaf blower-vac for suction sampling of arthropod populations in rice. When used in combination with an enclosure, application of this sampling device provides absolute estimates of the populations of arthropods as numbers per standardized sampling area. The sampling efficiency depends critically on the sampling duration. In a mature rice crop, a two-minute sampling in an enclosure of 0.13 m2 yields more than 90% of the arthropod population. The device also allows sampling of arthropods dwelling on the water surface or the soil in rice paddies, but it is not suitable for sampling fast flying insects, such as predatory Odonata or larger hymenopterous parasitoids. The modified blower-vac is simple to construct, and cheaper and easier to handle than traditional suction sampling devices, such as D-vac. The low cost makes the modified blower-vac also accessible to researchers in developing countries.

Assessment of arthropod abundance in crops is critical for investigating population dynamics and species interactions. Here we describe the modification and application of a leaf blower-vac for suction sampling of arthropods in rice.

Rice fields host a large diversity of arthropods, but investigating their population dynamics and interactions is challenging. Here we describe the ...

Cereal Crop Ear Counting in Field Conditions Using Zenithal RGB Images

Ear density, or the number of ears per square meter (ears/m2), is a central focus in many cereal crop breeding programs, such as wheat and barley, representing an important agronomic yield component for estimating grain yield. Therefore, a quick, efficient, and standardized technique for assessing ear density would aid in improving agricultural management, providing improvements in preharvest yield predictions, or could even be used as a tool for crop breeding when it has been defined as a trait of importance. Not only are the current techniques for manual ear density assessments laborious and time-consuming, but they are also without any official standardized protocol, whether by linear meter, area quadrant, or an extrapolation based on plant ear density and plant counts postharvest. An automatic ear counting algorithm is presented in detail for estimating ear density with only sunlight illumination in field conditions based on zenithal (nadir) natural color (red, green, and blue [RGB]) digital images, allowing for high-throughput standardized measurements. Different field trials of durum wheat and barley distributed geographically across Spain during the 2014/2015 and 2015/2016 crop seasons in irrigated and rainfed trials were used to provide representative results. The three-phase protocol includes crop growth stage and field condition planning, image capture guidelines, and a computer algorithm of three steps: (i) a Laplacian frequency filter to remove low- and high-frequency artifacts, (ii) a median filter to reduce high noise, and (iii) segmentation and counting using local maxima peaks for the final count. Minor adjustments to the algorithm code must be made corresponding to the camera resolution, focal length, and distance between the camera and the crop canopy. The results demonstrate a high success rate (higher than 90%) and R2 values (of 0.62-0.75) between the algorithm counts and the manual image-based ear counts for both durum wheat and barley.

We present a protocol for counting durum wheat and barley ears, using natural color (RGB) digital photographs taken in natural sunlight under field conditions. With minimal adjustments for camera parameters and some environmental condition limitations, the technique provides precise and consistent results across a range of growth stages.

Ear density, or the number of ears per square meter (ears/m2), is a central focus in many cereal crop breeding programs, such as wheat and barley, ...

Measurement of Aerosols Optical Thickness of the Atmosphere using the GLOBE Handheld Sun Photometer

Here, we describe the measurement of aerosol optical thickness using the GLOBE handheld sun photometer. Aerosol optical thickness (AOT) was measured at Xavier University of Louisiana (XULA, 29.96&#176; N, 90.11&#176; W and 3 m above sea level). The measurements were done at two different wavelengths, 505 nm and 625 nm. AOT measurements were done 6 times a day (7 AM, 9 AM, 11 AM, solar noon, 3 PM and 5 PM). The data shown in this paper are the monthly average AOT values taken at solar noon. During each measurement time; at least five values of the sunlight voltage V and the dark voltage Vdark are taken for each channel. The mean for these five measurements is taken as the average for that measurement time. Other meteorological data such as temperature, surface pressure, rainfall and relative humidity are also measured at the same time. The whole protocol is completed within a time span of 10&#8211;15 min. The measured AOT values at 505 nm and 625 nm are then used to extrapolate the AOT values for wavelengths 667 nm, 551 nm, 532 nm and 490 nm. The measured and extrapolated AOT values were then compared with values from the nearest AERONET station at Wave CIS site 6 (AERONET, 28.87&#176; N, 90.48&#176; W and 33 m above sea level), which is about 96 km south of XULA. In this study we tracked the annual and daily variations of AOT for a 12 month period from September 2017 to August 2018. We also compared AOT data from two independently calibrated GLOBE handheld sun photometers at the XULA site. The data show that the two instruments are in excellent agreement.

The goal of the methods presented here is to measure aerosol optical thickness of the atmosphere. The sun photometer is pointed at the sun and the largest voltage reading obtained on an in-built digital voltmeter is recorded. Atmospheric measurements such as barometric pressure and relative humidity are also performed.

Here, we describe the measurement of aerosol optical thickness using the GLOBE handheld sun photometer. Aerosol optical thickness (AOT) was measured at ...

Leaf Area Index Estimation Using Three Distinct Methods in Pure Deciduous Stands

Accurate estimations of leaf area index (LAI), defined as half of the total leaf surface area per unit of horizontal ground surface area, are crucial for describing the vegetation structure in the fields of ecology, forestry, and agriculture. Therefore, procedures of three commercially used methods (litter traps, needle technique, and a plant canopy analyzer) for performing LAI estimation were presented step-by-step. Specific methodological approaches were compared, and their current advantages, controversies, challenges, and future perspectives were discussed in this protocol. Litter traps are usually deemed as the reference level. Both the needle technique and the plant canopy analyzer (e.g., LAI-2000) frequently underestimate LAI values in comparison with the reference. The needle technique is easy to use in deciduous stands where the litter completely decomposes each year (e.g., oak and beech stands). However, calibration based on litter traps or direct destructive methods is necessary. The plant canopy analyzer is a commonly used device for performing LAI estimation in ecology, forestry, and agriculture, but is subject to potential error due to foliage clumping and the contribution of woody elements in the field of view (FOV) of the sensor. Eliminating these potential error sources was discussed. The plant canopy analyzer is a very suitable device for performing LAI estimations at the high spatial level, observing a seasonal LAI dynamic, and for long-term monitoring of LAI.

An accurate estimation of leaf area index (LAI) is crucial for many models of material and energy fluxes within plant ecosystems and between an ecosystem and the atmospheric boundary layer. Therefore, three methods (litter traps, needle technique, and PCA) for taking precise LAI measurements were in the presented protocol.

Accurate estimations of leaf area index (LAI), defined as half of the total leaf surface area per unit of horizontal ground surface area, are crucial for ...

Using Changes in Leaf Transmission to Investigate Chloroplast Movement in Arabidopsis thaliana

Chloroplast movement in leaves has been shown to help minimize photoinhibition and increase growth under certain conditions. Much can be learned about chloroplast movement by studying the chloroplast positioning in leaves using e.g., confocal fluorescence microscopy, but access to this type of microscopy is limited. This protocol describes a method that uses the changes in leaf transmission as a proxy for chloroplast movement. If chloroplasts are spread out in order to maximize light interception, the transmission will be low. If chloroplasts move towards the anticlinal cell walls to avoid light, the transmission will be higher. This protocol describes how to use a straightforward, home-built instrument to expose leaves to different blue light intensities and quantify the dynamic changes in leaf transmission. This approach allows researchers to quantitatively describe chloroplast movement in different species and mutants, study the effects of chemicals and environmental factors on it, or screen for novel mutants e.g., to identify missing components in the process that leads from light perception to the movement of chloroplasts.

Using Changes in Leaf Transmission to Investigate Chloroplast Movement in Arabidopsis thaliana

Many plant species change the positioning of chloroplasts to optimize light absorption. This protocol describes how to use a straightforward, home-built instrument to investigate chloroplast movement in Arabidopsis thaliana leaves using changes in the transmission of light through a leaf as a proxy.

Chloroplast movement in leaves has been shown to help minimize photoinhibition and increase growth under certain conditions. Much can be learned about ...

Rapid and Non-Destructive Characterization of Biofilm Elastic Properties

Quantifying Elastic Properties of Environmental Biofilms using Optical Coherence Elastography

Biofilms are complex biomaterials comprising a well-organized network of microbial cells encased in self-produced extracellular polymeric substances (EPS). This paper presents a detailed account of the implementation of optical coherence elastography (OCE) measurements tailored for the elastic characterization of biofilms. OCE is a non-destructive optical technique that enables the local mapping of the microstructure, morphology, and viscoelastic properties of partially transparent soft materials with high spatial and temporal resolution. We provide a comprehensive guide detailing the essential procedures for the correct implementation of this technique, along with a methodology to estimate the bulk Young's modulus of granular biofilms from the collected measurements. These consist of the system setup, data acquisition, and postprocessing. In the discussion, we delve into the underlying physics of the sensors used in OCE and explore the fundamental limitations regarding the spatial and temporal scales of OCE measurements. We conclude with potential future directions for advancing the OCE technique to facilitate elastic measurements of environmental biofilms.

Author Spotlight: Characterizing Environmental Biofilm Mechanics Using Optical Coherence Elastography and its Applications in Wastewater Treatment

This paper highlights the optical coherence elastography (OCE) technique's efficacy in rapidly and non-destructively characterizing biofilm elastic properties. We elucidate critical OCE implementation procedures for accurate measurements and present Young's modulus values for two granular biofilms.

Biofilms are complex biomaterials comprising a well-organized network of microbial cells encased in self-produced extracellular polymeric substances ...

Optical Coherence Tomography and Optical Coherence Elastography System Setup and Imaging Granular Biofilms for Elastic Wave Field Analysis

Field Collection and Laboratory Maintenance of Canopy-Forming Giant Kelp to Facilitate Restoration

Canopy-forming kelps are essential foundation species, supporting biodiversity and providing ecosystem services valued at more than USD$500 billion annually. The global decline of giant kelp forests due to climate-driven ecological stressors underscores the need for innovative restoration strategies. An emerging restoration technique known as &#39;green gravel&#39; aims to seed young kelps over large areas without extensive underwater labor and represents a promising restoration tool due to cost-effectiveness and scalability. This video article illustrates a protocol and tools for culturing giant kelp, Macrocystis pyrifera. It also provides a resource for further studies to address the successes and limitations of this method in field settings. We outline field and laboratory-based methods for collecting reproductive tissue, sporulating, inoculating, rearing, maintaining, and monitoring substrates seeded with early life stages using the &#39;green gravel&#39;&#160;technique. The protocol simplifies and centralizes current restoration practices in this field to support researchers, managers, and stakeholders in meeting kelp conservation objectives.

This protocol describes the field collection and regular laboratory maintenance of substrates seeded with canopy-forming giant kelp for use in restoration trials to address the success and limitations of the 'green gravel' technique in field settings.

Canopy-forming kelps are essential foundation species, supporting biodiversity and providing ecosystem services valued at more than USD$500 billion ...