Investigating the influence of LiDAR ground surface errors on the utility of derived forest inventories

Light detection and ranging, or LiDAR, effectively produces products spatially characterizing both terrain and vegetation structure; however, development and use of those products has outpaced our understanding of the errors within them. LiDAR’s ability to capture three-dimensional structure has led to interest in conducting or augmenting forest inventories with LiDAR data. Prior to applying LiDAR in operational management, it is necessary to understand the errors in LiDAR-derived estimates of forest inventory metrics (i.e., tree height). Most LiDAR-based forest inventory metrics require creation of digital elevation models (DEM), and because metrics are calculated relative to the DEM surface, errors within the DEMs propagate into delivered metrics. This study combines LiDAR DEMs and 54 ground survey plots to investigate how surface morphology and vegetation structure influence DEM errors. The study further compared two LiDAR classification algorithms and found no significant difference in their performance. Vegetation structure was found to have no influence, whereas increased variability in the vertical error was observed on slopes exceeding 30°, illustrating that these algorithms are not limited by high-biomass western coniferous forests, but that slope and sensor accuracy both play important roles. The observed vertical DEM error translated into ±1%–3% error range in derived timber volumes, highlighting the potential of LiDAR-derived inventories in forest management.

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Effects of habitat edges on vegetation structure and the vulnerable golden-brown mouse lemur (Microcebus ravelobensis) in northwestern Madagascar

BMC Ecology ◽

10.1186/s12898-020-00337-z ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Bertrand Andriatsitohaina ◽

Daniel Romero-Mujalli ◽

Malcolm S. Ramsay ◽

Frederik Kiene ◽

Solofonirina Rasoloharijaona ◽

...

Keyword(s):

Body Mass ◽

Edge Effects ◽

Vegetation Structure ◽

Species Abundance ◽

Tree Height ◽

Logistic Function ◽

Study Region ◽

Large Trees ◽

Significant Difference ◽

Vegetation Parameters

Abstract Background Edge effects can influence species composition and community structure as a result of changes in microenvironment and edaphic variables. We investigated effects of habitat edges on vegetation structure, abundance and body mass of one vulnerable Microcebus species in northwestern Madagascar. We trapped mouse lemurs along four 1000-m transects (total of 2424 trap nights) that ran perpendicular to the forest edge. We installed 16 pairs of 20 m2 vegetation plots along each transect and measured nine vegetation parameters. To determine the responses of the vegetation and animals to an increasing distance to the edge, we tested the fit of four alternative mathematical functions (linear, power, logistic and unimodal) to the data and derived the depth of edge influence (DEI) for all parameters. Results Logistic and unimodal functions best explained edge responses of vegetation parameters, and the logistic function performed best for abundance and body mass of M. ravelobensis. The DEI varied between 50 m (no. of seedlings, no. of liana, dbh of large trees [dbh ≥ 10 cm]) and 460 m (tree height of large trees) for the vegetation parameters, whereas it was 340 m for M. ravelobensis abundance and 390 m for body mass, corresponding best to the DEI of small tree [dbh < 10 cm] density (360 m). Small trees were significantly taller and the density of seedlings was higher in the interior than in the edge habitat. However, there was no significant difference in M. ravelobensis abundance and body mass between interior and edge habitats, suggesting that M. ravelobensis did not show a strong edge response in the study region. Finally, regression analyses revealed three negative (species abundance and three vegetation parameters) and two positive relationships (body mass and two vegetation parameters), suggesting an impact of vegetation structure on M. ravelobensis which may be partly independent of edge effects. Conclusions A comparison of our results with previous findings reveals that edge effects are variable in space in a small nocturnal primate from Madagascar. Such an ecological plasticity could be extremely relevant for mitigating species responses to habitat loss and anthropogenic disturbances.

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Comparing Forest Structural Attributes Derived from UAV-Based Point Clouds with Conventional Forest Inventories in the Dry Chaco

Remote Sensing ◽

10.3390/rs12234005 ◽

2020 ◽

Vol 12 (23) ◽

pp. 4005

Author(s):

Beatriz Gobbi ◽

Anton Van Rompaey ◽

Dante Loto ◽

Ignacio Gasparri ◽

Veerle Vanacker

Keyword(s):

Forest Structure ◽

Forest Inventory ◽

Three Dimensional ◽

Point Clouds ◽

Tree Canopy ◽

Dry Forest ◽

Anthropogenic Activity ◽

Maximum Height ◽

Functional Changes ◽

Forest Inventories

Anthropogenic activity leading to forest structural and functional changes needs specific ecological indicators and monitoring techniques. Since decades, forest structure, composition, biomass, and functioning have been studied with ground-based forest inventories. Nowadays, satellites survey the earth, producing imagery at different spatial and temporal resolutions. However, measuring the ecological state of large extensions of forest is still challenging. To reconstruct the three-dimensional forest structure, the structure from motion (SfM) algorithm was applied to imagery taken by an unmanned aerial vehicle (UAV). Structural indicators from UAV-SfM products are then compared to forest inventory indicators of 64 circular plots of 1000 m2 in a subtropical dry forest. Our data indicate that the UAV-SfM indicators provide a valuable alternative for ground-based forest inventory’ indicators of the upper canopy structure. Based on the correlation between ground-based measures and UAV-SfM derived indicators, we can state that the UAV-SfM technique provides reliable estimates of the mean and maximum height of the upper canopy. The performance of UAV-SfM techniques to characterize the undergrowth forest structure is low, as UAV-SfM indicators derived from the point cloud in the lower forest strata are not suited to provide correct estimates of the vegetation density in the lower strata. Besides structural information, UAV-SfM derived indicators, such as canopy cover, can provide relevant ecological information as the indicators are related to structural, functional, and/or compositional aspects, such as biomass or compositional dominance. Although UAV-SfM techniques cannot replace the wealth of data collected during ground-based forest inventories, its strength lies in the three-dimensional (3D) monitoring of the tree canopy at cm-scale resolution, and the versatility of the technique to provide multi-temporal datasets of the horizontal and vertical forest structure.

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Studies of structure and specificity of some antigen-antibody complexes

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1989.0026 ◽

1989 ◽

Vol 323 (1217) ◽

pp. 487-494

Keyword(s):

Monoclonal Antibodies ◽

Three Dimensional ◽

High Specificity ◽

Single Amino Acid ◽

Dimensional Structure ◽

X Ray ◽

Homologous Antigen ◽

Significant Difference ◽

Antigen Antibody ◽

Antibody Interactions

By using X -ray diffraction and immunochemical techniques, we have exploited the use of monoclonal antibodies raised against hen egg lysozyme (HEL) to study systematically those factors responsible for the high specificity of antigen -antibody interactions. HEL was chosen for our investigations because its three-dimensional structure and immunochemistry have been well characterized and because naturally occurring sequence variants from different avian species are readily available to test the fine specificity of the antibodies. The X-ray crystal structure of a complex formed between HEL and the Fab D1.3 shows a large complementary surface with close interatomic contacts between antigen and antibody. Thus single amino acid sequence changes in heterologous antigens give antigen-antibody association constants that are several orders of magnitude smaller than that of the homologous antigen. For example, a substitution of His for Glu at position 121 in the antigen is sufficient to diminish significantly the binding between D1.3 and the variant lysozyme. The conformation of HEL when complexed to D1.3 shows no significant difference from that seen in the free molecule, and immunobinding studies with other anti-HEL antibodies suggest that this observation may be generally true for the system of monoclonal antibodies that we have studied.

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Impact of training on different observers in forest inventory

Banko Janakari ◽

10.3126/banko.v31i1.37338 ◽

2021 ◽

Vol 31 (1) ◽

pp. 12-22

Author(s):

P. Paudel ◽

P. Beckschäfer ◽

C. Kleinn

Keyword(s):

Forest Inventory ◽

Tree Height ◽

Measurement Procedure ◽

Horizontal Distance ◽

Limited Information ◽

Quality Of Data ◽

Height Measurement ◽

Forest Inventories ◽

The Mean ◽

Level Of Training

Observers with different experience levels are involved in the measurement of large number of sample plots during forest inventories, particularly in national forest inventories. However, limited information exist on the quality of data produced by different observers in forest inventory after certain levels of training. This study tries to evaluate the measurement error in forest inventory associated with observers' experience after initial and field-based training for measuring the most fundamental variables- DBH (cm), total tree height (m), and horizontal distance (m) together with bearing (azimuth) to tree from the plot-centre. On completing the second level of training, the mean of the differences in DBH measurement decreased for both the ‘experienced’ and ‘inexperienced’ groups. The mean of the differences in height measurement in the case of the experienced observers was very low as compared to the inexperienced ones. However, the mean of the differences in azimuth measurement showed that the experienced groups were overestimating by at least 1 degree. There was no trend in deviation of measurement for all four variables regardless of tree size. The decrease in the mean and error of differences in measurements after second training showed that field-based training with supervision and training on the use of instruments at laboratories were required for inexperienced surveyors whereas update in working and measurement procedure would be sufficient for the experienced ones.

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Identification and characterization of apoptosis regulator Bax involved in air-exposure stress of the mud crab, Scylla Paramamosain Estampador, 1949

Crustaceana ◽

10.1163/15685403-00003718 ◽

2017 ◽

Vol 90 (11-12) ◽

pp. 1373-1390 ◽

Cited By ~ 2

Author(s):

Wen-Bin Gu ◽

Yi-Lian Zhou ◽

Dan-Dan Tu ◽

Zhong-Kai Zhou ◽

Qi-Hui Zhu ◽

...

Keyword(s):

Cell Apoptosis ◽

Three Dimensional ◽

Expression Level ◽

Dimensional Structure ◽

Scylla Paramamosain ◽

Control Group ◽

Mud Crab ◽

Coding Region ◽

Air Exposure ◽

Significant Difference

The mud crab, Scylla paramamosain Estampador, 1949, is a widely farmed commercial species in the South-East coastal areas of China. The crabs are captured and placed in a water-free container for further transportation. The long-time air exposure makes the crabs suffer from oxidative stress, triggering cell apoptosis and leading to the crab’s death. In this study, the homologue of the apoptosis regulator BAX was firstly identified in S. paramamosain and named as SpBAX. The coding region of SpBAX yielded a polypeptide of 278 amino acids, consisting of the defining motif of the BAXs family including Bcl-2 homologous BH1, BH2, BH3 regions and a transmembrane (TM) domain. Subcellular prediction suggested that SpBAX was located in the cytoplasm. The three-dimensional structure showed that SpBAX contained 8 helical regions. Two central α-helices (α5 and α6) flanked on one side by α3 and α4, and on the other side by α1, α2 and α7, which showed the same structure as BAXs in mammals. The highest expression level of SpBAX was detected in hepatopancreas tissue. The expression level of SpBAX was up-regulated in 12 h in hepatopancreas and in 24 h in haemocytes after air exposure. Meanwhile, a flow cytometry assay revealed that the proportion of apoptotic haemocytes exceeded 65% after air exposure for 36 h, showing a significant difference with the control group. These results indicated that the cloned SpBAX might be involved in the response to air exposure stress by causing cell apoptosis. This study may thus be helpful to clarify the mechanisms of the air-exposure stress response in the mud crab.

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Human Carboxyhemoglobin at 2.2 Å Resolution: Structure and Solvent Comparisons of R-State, R2-State and T-State Hemoglobins

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444997012250 ◽

1998 ◽

Vol 54 (3) ◽

pp. 355-366 ◽

Cited By ~ 14

Author(s):

Gregory B. Vásquez ◽

Xinhua Ji ◽

Clara Fronticelli ◽

Gary L. Gilliland

Keyword(s):

Water Molecule ◽

Three Dimensional ◽

Water Structure ◽

Crystal Form ◽

Dimensional Structure ◽

Α Subunit ◽

Phosphate Ion ◽

Significant Difference ◽

Chain Conformations ◽

T State

The three-dimensional structure and associated solvent of human carboxyhemoglobin at 2.2 Å resolution are compared with other R-state and T-state human hemoglobin structures. The crystal form is isomorphous with that of the 2.7 Å structure of carboxyhemoglobin reported earlier [Baldwin (1980). J. Mol. Biol. 136, 103–128], whose coordinates were used as a starting model, and with the 2.2 Å structure described in an earlier report [Derewenda et al. (1990). J. Mol. Biol. 211, 515–519]. During the course of the refinement, a natural mutation of the α-subunit, A53S, was discovered that forms a new crystal contact through a bridging water molecule. The protein structure shows a significant difference between the α and β heme geometries, with Fe—C—O angles of 125 and 162°, respectively. The carboxyhemoglobin is compared with other fully ligated R-state human hemoglobins [Baldwin (1980). J. Mol. Biol. 136, 103–128; Shaanan (1983). J. Mol. Biol. 195, 419–422] with the R2-state hemoglobin [Silva et al. (1992). J. Biol. Chem. 267, 17248–17256] and with T-state deoxyhemoglobin [Fronticelli et al. (1994). J. Biol. Chem. 269, 23965–23969]. The structure is similar to the earlier reported R-state structures, but there are differences in many side-chain conformations, the associated water structure and the presence and the position of a phosphate ion. The quaternary changes between the R-state carboxyhemoglobin and the R2-state and T-state structures are in general consistent with those reported in the earlier structures. The location of 238 water molecules and a phosphate ion in the carboxyhemoglobin structure allows the first comparison of the solvent structures of the R-state and T-state structures. Distinctive hydration patterns for each of the quaternary structures are observed, but a number of conserved water molecule binding sites are found that are independent of the conformational state of the protein.

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Estimation of three-dimensional structure of forest and development of roots of trees using LiDAR data

Abstracts of the ICA ◽

10.5194/ica-abs-1-179-2019 ◽

2019 ◽

Vol 1 ◽

pp. 1-1

Author(s):

Mamoru Koarai ◽

Akane Narikiyo ◽

Wataru Murakami

Keyword(s):

Root System ◽

System Development ◽

Three Dimensional ◽

Tree Height ◽

Deterrent Effect ◽

Dimensional Structure ◽

Lidar Data ◽

Three Dimensional Structure ◽

Root System Development ◽

The Stability

<p><strong>Abstract.</strong> There is deterrent effect to the slope collapse for development of the root of the tree. However, it's difficult to know the development situation of the roots of the forest. On the other hand, they're becoming able to estimate the forest three-dimensional structure such as the tree height, the tree number and diameter breast height, etc. by LiDAR data. Because tree height and diameter are related to development of roots of trees, the authors try to estimate the root system development situation of the forest by LiDAR data to presume indirectly the stability of slope. The authors surveyed the diameters and root system development of about one hundred trees in the cut forest of cedar woods in the weathered granite Abukuma Mountains, Fukushima Prefecture. The three-dimensional structure of the cut forest was presumed from LiDAR data before felling. As the results of consideration, this report show that the three-dimensional structure of the forest is presumed from LiDAR data, and the development situation of the roots of the forest was estimated for slope stability analysis.</p>

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Crystal structures of 6a,6b,7,11a-tetrahydro-6H,9H-spiro[chromeno[3′,4′:3,4]pyrrolo[1,2-c]thiazole-11,3′-indoline]-2′,6-dione and 5′-methyl-6a,6b,7,11a-tetrahydro-6H,9H-spiro[chromeno[3′,4′:3,4]pyrrolo[1,2-c]thiazole-11,3′-indoline]-2′,6-dione

Acta Crystallographica Section E Crystallographic Communications ◽

10.1107/s2056989019000045 ◽

2019 ◽

Vol 75 (2) ◽

pp. 246-250

Author(s):

S. Pangajavalli ◽

R. Ranjithkumar ◽

N. Srinivasan ◽

S. Ramaswamy ◽

S. Selvanayagam

Keyword(s):

Hydrogen Bonds ◽

Three Dimensional ◽

Ring System ◽

Dimensional Structure ◽

Dihedral Angles ◽

Pyrrolidine Ring ◽

Methyl Group ◽

Significant Difference ◽

The Mean ◽

Compound Ii

The title compounds, C20H16N2O3S, (I), and C21H18N2O3S, (II), differ by the presence of a methyl group in position 5 on the 1H-indole-2-one ring of compound (II). The two compounds have a structural overlap r.m.s. deviation of 0.48 Å. There is a significant difference in the conformation of the thiazolidine ring: it has a twisted conformation on the fused N—C bond in (I), but an envelope conformation in compound (II) with the S atom as the flap. The planar pyrrolidine ring of the indole ring system is normal to the mean plane of the five-membered pyrrolidine ring of the pyrrolothiazole unit in both compounds, with dihedral angles of 88.71 (9) and 84.59 (8)°. The pyran rings in both structures have envelope conformations with the methylene C atom adjacent to the C=O group as the flap. In both compounds, there is a short intramolecular C—H...O contact present. In the crystal of (I), molecules are linked by C—H...O hydrogen bonds forming chains propagating along the b-axis direction. The chains are linked by N—H...π interactions, forming layers parallel to (10\overline{1}). In the crystal of (II), molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers which are linked by C—H...O hydrogen bonds to form a three-dimensional structure.

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Reuse of field data in ALS-assisted forest inventory

Silva Fennica ◽

10.14214/sf.10272 ◽

2020 ◽

Vol 54 (5) ◽

Author(s):

Ana de Lera Garrido ◽

Terje Gobakken ◽

Hans Ørka ◽

Erik Næsset ◽

Ole Bollandsås

Keyword(s):

Forest Inventory ◽

Laser Scanning ◽

Field Data ◽

Reference Data ◽

Growth Models ◽

Basal Area ◽

Tree Height ◽

Cost Component ◽

Forest Inventories ◽

Forest Attributes

Forest inventories assisted by wall-to-wall airborne laser scanning (ALS), have become common practice in many countries. One major cost component in these inventories is the measurement of field sample plots used for constructing models relating biophysical forest attributes to metrics derived from ALS data. In areas where ALS-assisted forest inventories are planned, and in which the previous inventories were performed with the same method, reusing previously acquired field data can potentially reduce costs, either by (1) temporally transferring previously constructed models or (2) projecting field reference data using growth models that can serve as field reference data for model construction with up-to-date ALS data. In this study, we analyzed these two approaches of reusing field data acquired 15 years prior to the current ALS acquisition to estimate six up-to-date forest attributes (dominant tree height, mean tree height, stem number, stand basal area, volume, and aboveground biomass). Both approaches were evaluated within small stands with sizes of approximately 0.37 ha, assessing differences between estimates and ground reference values. The estimates were also compared to results from an up-to-date forest inventory relying on concurrent field- and ALS data. The results showed that even though the reuse of historical information has some potential and could be beneficial for forest inventories, systematic errors may appear prominent and need to be overcome to use it operationally. Our study showed systematic trends towards the overestimation of lower-range ground references and underestimation of the upper-range ground references.

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Laser scanning as a tool for the analysis of the greenery on the example of Poremba district in Lublin

Ecology and Noospherology ◽

10.15421/031527 ◽

2015 ◽

Vol 26 (3-4) ◽

pp. 132-140

Author(s):

P. G. Kotsyuba ◽

I. D. Semko ◽

I. I. Kozak ◽

T. V. Parpan ◽

G. G. Kozak ◽

...

Keyword(s):

Laser Scanning ◽

Green Space ◽

Three Dimensional ◽

Tree Height ◽

Field Measurements ◽

Airborne Lidar ◽

Dimensional Structure ◽

Lidar Data ◽

Definition Of ◽

Airborne Lidar Data

World experience shows that the survey of green spaces by traditional methods is very time consuming, costly and does not always get all the information you need to make of adequate management decisions by municipal authorities. The aim of this article was to show the main stages of analysis and prospects of urban green space using aerial lidar data and submit the effect of three-dimensional visualization of the study area. There were presented the possibilities and perspectives of using the data obtained from airborne laser scanning (ALS) for the analysis of greenery on the example of Poremba district in Lublin (Poland). Research conducted in Poremba district in the Polish city of Lublin (district was built from 1988 to 2005 and is located in the western part of the city). Analysis of green space conducted using quantitative analytical methods. By detailed analysis of the study area were used aerial lidar data from the year 2015. To classify aerial lidar data such software were used: LP360, ArcMap 10.3, Toolbox LAStools. The process of analysis begins with the definition of points, belonging to ground (Ground - GR), and the classification was realized using «lasground» with tools LAStools. The article is dedicated to development the method of estimation the tree height based on airborne LiDAR data. Method applies more information about the three-dimensional structure of natural objects derived from the processing of airborne LiDAR data compared with known methods. Furthermore, the method is adapted to determine and calculate characteristics of stand which using for tree inventory in cities. Methodological and algorithmic instructions to determine the tree parameters in city were proposed. These instructions allow automatically calculating the characteristics of the tree parameters, such as the allocation of each tree and tree height. The study area was analyzed in terms of the distribution of vegetation (separately individual growing trees and groups of trees). For that purpose there was applied an available ALS data. Based on the ALS data there were separated the tops of the trees and their height. In order to verify the ALS data there were used the results of field measurements (coordinates for the tree trunks, the diameter at breast height of trees, their height, crown projection). The analysis of the greenery within the Poremba district using the ALS data after verification with the field measurements proved to be an effective tool for the characterization of the greenery areas in particular city. This research may be important in terms of planning the planting of greenery areas and spatial development of the Lublin.

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