Indirect Optical Methods Research Articles

Correcting for the clumping effect in leaf area index calculations using one-dimensional fractal dimension

The clumping effect is the main issue causing the heterogeneity in vegetation canopies and the underestimation of leaf area index (LAI) obtained using indirect measurement methods. Significant efforts have been exerted to correct for the clumping effect and derive the true LAI. Recent research has shown that the fractal dimension (FD) is directly related to the clumping effect of foliage, yet practical methods are needed to calculate field estimates. Considering that widely used LAI applications such as digital hemispherical photography (DHP), tracing radiation and architecture of canopies (TRAC), and digital cover photography (DCP) estimate LAI with one-dimensional (1D) gap probability and gap size data, we propose a method to correct for the clumping effect using 1D FD. Resulting formulae describing the relationship between LAI, CI, and 1D FD were based on the box-counting method (BCM) and a binomial distribution model. Sixty-four simulated scenes including four RAdiation transfer Model Intercomparison (RAMI) actual canopies and field measurements from nine plots (four orchard plots and five coniferous forest plots) were used to validate the novel method. Results showed good agreement with reference LAI values for simulated scenes (R2 = 0.96 and RMSE = 0.35). The 1DFD method generated higher LAI estimates compared with the LAI measured using TRAC at the four orchard plots especially at high canopy closure, while its results were more consistent with LAI obtained by litter collection than those of comparable methods at coniferous forest plots (bias from −13.5% to 9.9% for DCP images, from −3.0% to 19.7% for DHP images, and from −3.8% to 17.0% for TRAC transects). Our validation efforts indicate that the method proposed herein corrects for the clumping effect of vegetated canopies more effectively with DCP images, DHP images, and TRAC measurement when compared with traditional indirect optical methods. The 1DFD method is expected to improve indirect measurement accuracy of LAI.

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.

Canopy clumping index (CI): A review of methods, characteristics, and applications

Canopy clumping index (CI) characterizes the spatial distribution of leaves or needles within a vegetation canopy. CI is critical in determining the canopy radiation transfer, photosynthesis, and hydrological processes. This paper reviews the field measurement and remote sensing estimation methods, characteristics, and applications of CI. CI is generally estimated in the field using direct, indirect optical, and allometric methods. The basis for the indirect optical approach is the gap-fraction based method. Remote sensing of CI is carried out using passive optical and active LiDAR technology. Current CI products are mainly derived from an empirical relationship with the normalized difference hotspot and darkspot (NDHD) index. Further CI product validation studies should be conducted using enhanced field measurements. CI typically shows vertical, scale, directional, and temporal variations. The overall CI is calculated as the integration of the directional CI values. CI is a key parameter in leaf area index (LAI) estimation, and canopy reflectance and land surface modeling studies. Future studies should focus on the adoption of automated and wireless measurement methods, development of new remote sensing estimation methods, improving our understanding of the CI characteristics, and accounting for CI in land surface models.

Influence of image pixel resolution on canopy cover estimation in poplar plantations from field, aerial and satellite optical imagery

Accurate estimates of canopy cover (CC) are central for a wide range of forestry studies. As direct measurements are impractical, indirect optical methods have often been used to estimate CC from the complement of gap fraction measurements obtained with restricted-view sensors. In this short note we evaluated the influence of the image pixel resolution (ground sampling distance; GSD) on CC estimation in poplar plantations obtained from field (cover photography; GSD < 1 cm), unmanned aerial (UAV; GSD <10 cm) and satellite (Sentinel-2; GSD = 10 m) imagery. The trial was conducted in poplar tree plantations in Northern Italy, with varying age and canopy cover. Results indicated that the coarser resolution available from satellite data is suitable to obtain estimates of canopy cover, as compared with field measurements obtained from cover photography; therefore, S2 isrecommended for larger scale monitoring and routine assessment of canopy cover in poplar plantations. The higher resolution of UAV compared with Sentinel-2 allows finer assessment of canopy structure, which could also be used for calibrating metrics obtained from coarser-scale remote sensing products, avoiding the need of ground measurements.

Comparison of Direct and Indirect Determination of Leaf Area Index in Permanent Grassland

Indirect, non-destructive methods to derive biophysical parameters, such as leaf area index (LAI), are of major importance for optimal grassland growth modelling and management. In this study, we compared different methods for the estimation of LAI in permanent grassland including (i) two direct methods, (ii) two indirect optical methods (AccuPAR and LAI-2200C), (iii) a proximal (field spectrometer) and a satellite remote sensing approach using Sentinel-2 (S-2) data, both based on radiative transfer modelling (RTM) of vegetation. To consider the seasonal variability of LAI sufficiently, we performed in situ measurements weekly during the entire growing season of 2018 and 2019. The RTM-based methods showed the lowest root-mean-square error (RMSE) when compared with direct green LAI measurements, which ranged from 1.68 to 7.85. The indirect optical methods resulted in higher RMSE values but in similar high correlation coefficients (r). The comparison between the indirect optical methods showed that the AccuPAR and the LAI-2200C highly correlate with a systematic underestimation of the AccuPAR in the upper range of LAI values. As expected, S-2 and the field spectrometer showed the highest correlation (RMSE: 0.40 and r: 0.95). Generally, we observed a significant influence of the seasonal changes of the canopy structure and morphology on the estimation accuracy.

Single particles electrochemistry for batteries

Ion migration is the most fundamental process in the field of energy storage and conversion. During the charge-discharge cycle, the (de)intercalation of guest ions in solid host particles as electrode materials change the distribution of element, phase and stress in the particle and give rise to crushing and degradation, which will influence the electrochemical behavior of the particles. New methods are constantly being proposed to probe the electrochemical reactions on individual particle for understanding the mechanism of the process. In this short review, we highlight some pioneer works from two different perspectives, namely direct electrochemical detection methods, such as nano-impact method, nanoprobe detection and flowing particle analysis, and indirect optical analysis methods utilizing X-ray imaging, infrared near-field nanoscopy, Raman microscopy and surface plasmon resonance microscopy.

Development of an effective way to increase the biological activity of nicotinamide – a new strategy to protect against photoageing and skin neoplasia

The objective of this work is to demonstrate changes in properties and increase of biological activity of nicotinamide (NAM) substance for skin protectants activated by mechanical activation (MA). To assess the physical, chemical and biological properties of NAM were used biotesting by the Spirotox-method, direct and indirect optical methods (microscopy, laser diffraction), infrared spectroscopy, pH-metry. The results of the study showed an increase in biological activity, expressed in changes in the energy of activation of cell transition to the “dead cell” state on the example of biosensor Spirostomum ambiguum. Also we indicated an increase in the rate of the chemical process of dissolution of mechanoactivated molecular crystals of nicotinamide (NAM) expressed in the values of the first order rate constant. Mechanical activation at a high rate of NAM substance powder deformation has led to changes in physical, chemical and biological properties of the drug, which can be used in medicine to increase efficiency and reduce doses of pharmacotherapy.

An intensity, image-based method to estimate gap fraction, canopy openness and effective leaf area index from phase-shift terrestrial laser scanning

Accurate in situ estimates of leaf area index (LAI) are essential for a wide range of ecological studies and applications. Due to the destructiveness and impracticality of direct measurements, indirect optical methods have mostly been used in the field to derive estimates of LAI from gap fraction measurements. Terrestrial laser scanning (TLS) is strongly supporting use of this active technology, which possesses several advantages compared to passive sensors. However, edge effects and partial beam interceptions are significantly challenges for the accurate retrieval of gap fraction from 3D point cloud data available from TLS, particularly in phase-shift instruments, which in turns require point cloud filtering to correct erroneous point measurements.As the limitations above influences the point cloud, we proposed a new method which is based only on the laser return intensity (LRI) information derived from raw TLS data, which are used to generate 2D intensity images. The intensity image contains all the unfiltered LRI information captured by TLS, which is used to separate gap from non-gap pixels, using a procedure comparable to the standard image analysis processing of digital hemispherical images. This allows a theoretically consistent comparison between active and passive optical measurements of gap fraction across all the zenith angle range.The method was tested in real and simulated forests. Gap fraction, canopy openness and effective leaf area index derived from real and simulated intensity TLS images were compared with those obtained using digital hemispherical photography (DHP). Results indicated that the intensity, image-based method outperformed DHP, as the higher pixel resolution of the intensity images and the larger distance covered by TLS allowed detection of many small canopy elements, particularly at higher zenith angles (longer optical distance), which are not detected in DHP. The main findings support the reliability of the intensity, image-based method to standardize protocols for TLS phase-shift scan data processing and use of the produced canopy estimates as a benchmark for passive optical measurements.

Dynamic nuclear polarization

Abstract Dynamic nuclear polarization, or DNP, refers to the increase of the polarization of nuclear spins in condensed matter, liquid or solid, coupled with electronic spins at low relative concentration, by inducing radio or microwave transitions at frequencies close to the electronic resonance frequency in the external magnetic field. Another described method relies on indirect optical pumping methods at temperatures close to room temperature for the nuclear polarization of rare gases. The various mechanisms of DNP are described in physical terms. This is followed by a succinct description of its main applications in various domains of physics, in chemistry and in medicine.

Molecular methods for assessment of non-covalent metallodrug-DNA interactions.

The binding of small molecule metallodrugs to discrete regions of nucleic acids is an important branch of medicinal chemistry and the nature of these interactions, allied with sequence selectivity, forms part of the backbone of modern medicinal inorganic chemistry research. In this tutorial review we describe a range of molecular methods currently employed within our laboratories to explore novel metallodrug-DNA interactions. At the outset, an introduction to DNA from a structural perspective is provided along with descriptions of non-covalent DNA recognition focusing on intercalation, insertion, and phosphate binding. Molecular methods, described from a non-expert perspective, to identify non-covalent and pre-associative nucleic acid recognition are then demonstrated using a variety of techniques including direct (non-optical) and indirect (optical) methods. Direct methods include: X-ray crystallography; NMR spectroscopy; mass spectrometry; and viscosity while indirect approaches detail: competitive inhibition experiments; fluorescence and absorbance spectroscopy; circular dichroism; and electrophoresis-based techniques. For each method described we provide an overview of the technique, a detailed examination of results obtained and relevant follow-on of advanced biophysical/analytical techniques. To achieve this, a selection of relevant copper(ii) and platinum(ii) complexes developed within our laboratories are discussed and are compared, where possible, to classical DNA binding agents. Applying these molecular methods enables us to determine structure-activity factors important to rational metallodrug design. In many cases, combinations of molecular methods are required to comprehensively elucidate new metallodrug-DNA interactions and, from a drug discovery perspective, coupling this data with cellular responses helps to inform understanding of how metallodrug-DNA binding interactions manifest cytotoxic action.

LaiPen LP 100 - a new device for estimating forest ecosystem leaf area index compared to the etalon: A methodologic case study

Fast and precise leaf area index (LAI) estimation of a forest stand is frequently needed for a wide range of ecological studies. In the presented study, we compared side-by-side two instruments for performing LAI estimation (i.e. LaiPen LP 100 as a “newly developed device” and LAI-2200 PCA as the “world standard”), both based on indirect optical methods for performing LAI estimation in pure Norway spruce (Picea abies (Linnaeus) H. Karsten) stands under different thinning treatments. LAI values estimated by LaiPen LP 100 were approximate 5.8% lower compared to those measured by LAI-2200 PCA when averaging all collected data regardless of the thinning type. Nevertheless, when we considered the differences among LAI values at each measurement point within a regular grid, LaiPen LP 100 overestimated LAI values compared to those from LAI-2200 PCA on average by 1.4%. Therefore, both instruments are comparable. Similar LAI values between thinning from above (A) and thinning from below (B) approaches were indirectly detected by both instruments. The highest values of canopy production index and leaf area efficiency were observed within the stand thinned from above (plot A).

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Importance of woody materials for seasonal variation in leaf area index from optical methods in a deciduous needleleaf forest

ABSTRACTWoody materials (woody area index, WAI) is a key error source in estimating leaf area index (LAI) by optical methods, but how to correct the error caused by WAI during different seasons has not reached consensus. In this study, effective plant area index (PAIe) was first estimated using two indirect optical methods (digital hemispherical photography, DHP, and LAI-2000) in a deciduous needleleaf forest, and then four different schemes for correcting the contribution of WAI to PAIe were tested here. We also directly estimated the seasonality of LAI by a litter collection method and an allometric method. Directly subtracting WAI from PAI resulted in a greater degree of uncertainty in correcting seasonal changes of PAIe from both DHP and LAI-2000. Therefore, we introduced a new correction factor, the stem-to-total area ratio, which was reasonable and useful for quantifying seasonal changes in the contribution of WAI to PAIe. We finally recommend a practical scheme for correcting PAIe from both DHP and LAI-2000, with accuracies as high as 88% and 87% during most growing seasons, respectively. Additionally, LAI values estimated from allometry were concordant with those estimated from litter collection, indicating that the allometry method is useful for tracking seasonal changes in LAI.

Sediment transport induced by tidal bores. An estimation from suspended matter measurements in the Sée River (Mont-Saint-Michel Bay, northwestern France)

Tidal bores are believed to induce significant sediment transport in macrotidal estuaries. However, due to high turbulence and very large suspended sediment concentration (SSC), the measurement of sediment transport induced by a tidal bore is actually a technical challenge. Consequently, very few quantitative data have been published so far. This paper presents SSC measurements performed in the Sée River estuary (Mont-Saint-Michel Bay, northwestern France) during the tidal bore passage with direct and indirect (optical) methods. Both methods are calibrated in laboratory in order to verify the consistency of measurements, to calculate the uncertainties, and to correct the raw data. The SSC measurements coupled with ADCP velocity data are used to calculate the instantaneous sediment transport (qs) associated with the tidal bore passage (up to 40kg/m2/s).

Long-term response to thinning in a beech (&lt;i&gt;Fagus sylvatica&lt;/i&gt; L.) coppice stand under conversion to high forest in Central Italy

European beech (L.) forests have a long history of coppicing, but the majority of formerly managed coppices are currently under conversion to high forest. The long time required to achieve conversion requires a long-term perspective to fully understand the implication of the applied conversion practices. In this study, we showed results from a long-term (1992–2014) case-study comparing two management options (natural evolution andperiodic thinning) in a beech coppice in conversion to high forest. Leaf area index, litter production, radiation transmittance and growth efficiency taken as relevant stand descriptors, were estimated using both direct and indirect optical methods. Overall, results indicated that beech coppice showed positive and prompt responses to active conversion practices based on periodic medium-heavy thinning. A growth efficiency index showed that tree growth increased as the cutting intensity increased. Results from the case study supported the effectiveness of active conversion management from an economic (timber harvesting) and ecological (higher growth efficiency) point of view.Fagus sylvatica

A note on estimating canopy cover from digital cover and hemispherical photography

Fast and accurate estimates of canopy cover are central for a wide range of forestry studies. As direct measurements are impractical, indirect optical methods have often been used in forestry to estimate canopy cover. In this paper the accuracy of canopy cover estimates from two widely used canopy photographic methods, hemispherical photography (DHP) and cover photography (DCP) was evaluated. Canopy cover was approximated in DHP as the complement of gap fraction data at narrow viewing zenith angle range (0°–15°), which was comparable with that of DCP. The methodology was tested using artificial images with known canopy cover; this allowed exploring the influence of actual canopy cover and mean gap size on canopy cover estimation from photography. DCP provided robust estimates of canopy cover, whose accuracy was not influenced by variation in actual canopy cover and mean gap size, based on comparison with artificial images; by contrast, the accuracy of cover estimates from DHP was influenced by both actual canopy cover and mean gap size, because of the lower ability of DHP to detect small gaps within crown. The results were replicated in both DHP and DCP images collected in real forest canopies. Finally, the influence of canopy cover on foliage clumping index and leaf area index was evaluated using a theoretical gap fraction model. The main findings indicate that DCP can overcome the limits of indirect techniques for obtaining unbiased and precise estimates of canopy cover, which are comparable to those obtainable from direct, more labour-intensive techniques, being therefore highly suitable for routine monitoring and inventory purposes.

Seasonal variation of leaf area index (LAI) over paddy rice fields in NE China: Intercomparison of destructive sampling, LAI-2200, digital hemispherical photography (DHP), and AccuPAR methods

Continuous field leaf area index (LAI) measurement has become increasingly important for the validation of remote sensing LAI products. A seasonal field campaign was carried out to take continuous LAI measurements over paddy rice fields in NE China in 2012. Three indirect optical methods, LAI-2200, digital hemispherical photography (DHP), and AccuPAR, were compared with a destructive sampling method conducted concurrently. Corrections for the clumping effect were applied to the effective plant area indices (PAIeff) estimated from the indirect optical measurements.Both LAI-2200 and DHP produce consistent PAIeff estimates over the season (R2=0.76, RMSE=0.97). The clumping index (CI) values obtained from DHP generally decrease with plant growth and range between 0.63 and 0.74 during the peak growing period from day of year (DOY) 191−230. The CI values retrieved from DHP photos generally decrease with increasing view angles. The optical PAI and LAI values estimated from LAI-2200 and DHP correspond very well with the destructive values before DOY 230 (R2=0.75, RMSE=1.15 for PAI and R2=0.78, RMSE=0.74 for LAI), and the relative errors are less than 10% and 5%, respectively, for the two instruments. Omitting ring 5 for LAI-2200 generates very accurate PAI and LAI estimations during the peak season. Nevertheless, AccuPAR underestimates the PAIeff, PAI, and LAI values obtained from other methods (up to 30%). After DOY 231, the capability to detect PAI decreases significantly for both destructive and optical methods due to the leaf senescence and the DHP classification difficulty. In general, rice PAI could be accurately estimated with LAI-2200 and DHP before senescence if the clumping effect could be properly taken into account. The seasonal continuous LAI measurements obtained from this study are valuable for the validation of remote sensing LAI products.

Evaluating optical measurements of leaf area index against litter collection in a mixed broadleaved-Korean pine forest in China

We evaluated the error caused by optical measurements of leaf area index using a direct method in a mixed broadleaf-coniferous forest in China. Indirect optical methods to measure leaf area index (LAI) have been previously developed, but it is difficult to evaluate the accuracy of these methods in a mixed broadleaf-coniferous forest. In this study, the LAI in a mixed broadleaved-Korean pine (Pinus koraiensis) forest in China was estimated directly by litter collection (LAIlit) for the purpose of evaluating optical LAI measurements using digital hemispherical photography (DHP) and LAI-2000. With the DHP method, we corrected a systematic error due to incorrect automatic photographic exposure. With both DHP and LAI-2000 methods, we studied the influences of zenith angle selection schemes (0°–45°, 30°–60°, 45°–60° and 0°–75°) on the effective LAI (L e) measurement. In addition to optical L e, we also investigated other major factors influencing the determination of LAI, including woody-to-total area ratio (α), element clumping index (Ω E) and needle-to-shoot area ratio (γ E). A significant correlation (P < 0.01) was observed between optical (DHP and LAI-2000) and litter collection methods, but DHP L e underestimated LAIlit by 61 % on average based on different zenith angle ranges, and L e at 45°–60° agrees better with LAIlit (R 2 = 0.75, P < 0.01 and RMSE = 4.5), and the accuracy was enhanced by 21 % on average after considering α, Ω E and γ E and was further improved by 36 % after correcting for the error due to exposure. In contrast, LAI-2000 L e underestimated LAIlit by 32 % on average based on different zenith angle ranges, and L e in rings 1–3 is closer to LAIlit (R 2 = 0.80, P < 0.01 and RMSE = 2.1) than those in other rings (e.g., 3–4, 4 and 1–5), and after correcting for α, Ω E and γ E, the difference between LAI-2000 LAI and LAIlit was less than 6 %. Although DHP L e underestimated LAI-2000 L e by an average of 43 % at different zenith angle ranges, significant correlations between them were found (minimum r = 0.787, P < 0.01). We confirm the accuracy of the best estimates of LAI using DHP and LAI-2000 methods are to be over 94 % after considering woody materials and foliage clumping within shoots and the canopy. Meanwhile, the litter collection method is useful for estimating LAI in a mixed broadleaf-coniferous forest, if the specific leaf area for all major species and the average leaf age for evergreen coniferous species are known.

Constraining black hole masses in low-accreting active galactic nuclei using X-ray spectra

In a recent work we demonstrated that a novel X-ray scaling method, originally introduced for Galactic black holes (GBHs), can be reliably extended to estimate the mass of supermassive black holes accreting at a moderate to high level. Here we investigate the limits of applicability of this method to low-accreting active galactic nuclei, using a control sample with good-quality X-ray data and dynamically measured mass. For low-accreting AGNs, because the basic assumption that the photon index positively correlates with the accretion rate no longer holds the X-ray scaling method cannot be used. Nevertheless, the inverse correlation in the Gamma-Lx/LEdd diagram, found in several low-accreting black holes and confirmed by this sample, can be used to constrain black hole mass within a factor of ~10 from the dynamically determined values. We provide a simple recipe to determine black hole mass using solely X-ray spectral data, which can be used as a sanity check for black hole mass determination based on indirect optical methods.

Estimation of Leaf Area Index and Foliage Area Index of Rice using an Indirect Gravimetric Method

The aim of this study was to present a gravimetric method for the estimation of leaf area index (LAI) and foliage area index (FAI) of rice. The method estimates indirectly the LAI-FAI variation during the growing season using simple measurements during harvest, based on a module of predetermined relations among agronomic parameters. The method confronts the limitations of other methods under specific conditions, such as (a) high plant densities and high LAI-FAI values, where indirect optical methods are restricted and (b) experiments related to crop modeling applications where direct destructive methods are not allowed because they alter the initial design of the experimental setup. The method was applied for the high-yield cultivar (Oryza sativa L. ssp. indica, cv. Thaibonnet) during 2-year evapotranspiration experiments in lysimeters. The method identified the differences between the replicate lysimeters, and LAI-FAI estimations were significantly correlated with the final grain yields and the crop factors obtained from evapotranspiration measurements.