Integrating forest structural diversity measurement into ecological research

The measurement of forest structure has evolved steadily due to advances in technology, methodology, and theory. Such advances have greatly increased our capacity to describe key forest structural elements and resulted in a range of measurement approaches from traditional analog tools such as measurement tapes to highly derived and computationally intensive methods such as advanced remote sensing tools (e.g., lidar, radar). This assortment of measurement approaches results in structural metrics unique to each method, with the caveat that metrics may be biased or constrained by the measurement approach taken. While forest structural diversity (FSD) metrics foster novel research opportunities, understanding how they are measured or derived, limitations of the measurement approach taken, as well as their biological interpretation is crucial for proper application. We review the measurement of forest structure and structural diversity—an umbrella term that includes quantification of the distribution of functional and biotic components of forests. We consider how and where these approaches can be used, the role of technology in measuring structure, how measurement impacts extend beyond research, and current limitations and potential opportunities for future research

Monitoring tar spot disease in corn at different canopy and temporal levels using aerial multispectral imaging and machine learning

IntroductionTar spot is a high-profile disease, causing various degrees of yield losses on corn (Zea mays L.) in several countries throughout the Americas. Disease symptoms usually appear at the lower canopy in corn fields with a history of tar spot infection, making it difficult to monitor the disease with unmanned aircraft systems (UAS) because of occlusion.MethodsUAS-based multispectral imaging and machine learning were used to monitor tar spot at different canopy and temporal levels and extract epidemiological parameters from multiple treatments. Disease severity was assessed visually at three canopy levels within micro-plots, while aerial images were gathered by UASs equipped with multispectral cameras. Both disease severity and multispectral images were collected from five to eleven time points each year for two years. Image-based features, such as single-band reflectance, vegetation indices (VIs), and their statistics, were extracted from ortho-mosaic images and used as inputs for machine learning to develop disease quantification models.Results and discussionThe developed models showed encouraging performance in estimating disease severity at different canopy levels in both years (coefficient of determination up to 0.93 and Lin’s concordance correlation coefficient up to 0.97). Epidemiological parameters, including initial disease severity or y0 and area under the disease progress curve, were modeled using data derived from multispectral imaging. In addition, results illustrated that digital phenotyping technologies could be used to monitor the onset of tar spot when disease severity is relatively low (< 1%) and evaluate the efficacy of disease management tactics under micro-plot conditions. Further studies are required to apply and validate our methods to large corn fields

The Function of Heterodimeric AP-1 Comprised of c-Jun and c-Fos in Activin Mediated Spemann Organizer Gene Expression

BACKGROUND:Activator protein-1 (AP-1) is a mediator of BMP or FGF signaling during Xenopus embryogenesis. However, specific role of AP-1 in activin signaling has not been elucidated during vertebrate development. METHODOLOGY/PRINCIPAL FINDINGS:We provide new evidence showing that overexpression of heterodimeric AP-1 comprised of c-jun and c-fos (AP-1(c-Jun/c-Fos)) induces the expression of BMP-antagonizing organizer genes (noggin, chordin and goosecoid) that were normally expressed by high dose of activin. AP-1(c-Jun/c-Fos) enhanced the promoter activities of organizer genes but reduced that of PV.1, a BMP4-response gene. A loss of function study clearly demonstrated that AP-1(c-Jun/c-Fos) is required for the activin-induced organizer and neural gene expression. Moreover, physical interaction of AP-1(c-Jun/c-Fos) and Smad3 cooperatively enhanced the transcriptional activity of goosecoid via direct binding on this promoter. Interestingly, Smad3 mutants at c-Jun binding site failed in regulation of organizer genes, indicating that these physical interactions are specifically necessary for the expression of organizer genes. CONCLUSIONS/SIGNIFICANCE:AP-1(c-Jun/c-Fos) plays a specific role in organizer gene expression in downstream of activin signal during early Xenopus embryogenesis

Near-Infrared Spectroscopy of Limestone Ore for CaO Estimation under Dry and Wet Conditions

Quantitative analysis of CaO in limestone mining is mandatory, not only for ore exploration, but also for grade control. A partial least squares regression (PLSR) CaO estimation technique was developed for limestone mining. The proposed near-infrared spectroscopy (NIR)-based method uses reflectance spectra of the rock sample surface in the visible to short-wave infrared wavelength regions (350–2500 nm (4000–28,571 cm−1)) without the need to crush and pulverize the rock samples. The root mean square (RMS) error of CaO estimation using limestone ore fragment was 1.2%. The CaO content estimated by the PLSR method was used to predict average CaO content of composite samples with a sample size of 15, which resulted in an RMS error of 0.3%. The prediction accuracy with moisture on sample surfaces was also examined to find out if the NIR-based method showed a similar RMS error. Results suggest that the NIR technique can be used as a rapid assaying method in limestone workings with or without the presence of groundwater

An Unsupervised Canopy-to-Root Pathing (UCRP) Tree Segmentation Algorithm for Automatic Forest Mapping

Terrestrial laser scanners, unmanned aerial LiDAR, and unmanned aerial photogrammetry are increasingly becoming the go-to methods for forest analysis and mapping. The three-dimensionality of the point clouds generated by these technologies is ideal for capturing the structural features of trees such as trunk diameter, canopy volume, and biomass. A prerequisite for extracting these features from point clouds is tree segmentation. This paper introduces an unsupervised method for segmenting individual trees from point clouds. Our novel, canopy-to-root, least-cost routing method segments trees in a single routine, accomplishing stem location and tree segmentation simultaneously without needing prior knowledge of tree stem locations. Testing on benchmark terrestrial-laser-scanned datasets shows that we achieve state-of-the-art performances in individual tree segmentation and stem-mapping accuracy on boreal and temperate hardwood forests regardless of forest complexity. To support mapping at scale, we test on unmanned aerial photogrammetric and LiDAR point clouds and achieve similar results. The proposed algorithm’s independence from a specific data modality, along with its robust performance in simple and complex forest environments and accurate segmentation results, make it a promising step towards achieving reliable stem-mapping capabilities and, ultimately, towards building automatic forest inventory procedures

High-Resolution Canopy Height Model Generation and Validation Using USGS 3DEP LiDAR Data in Indiana, USA

Forest canopy height model (CHM) is useful for analyzing forest stocking and its spatiotemporal variations. However, high-resolution CHM with regional coverage is commonly unavailable due to the high cost of LiDAR data acquisition and computational cost associated with data processing. We present a CHM generation method using U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) LiDAR data for tree height measurement capabilities for entire state of Indiana, USA. The accuracy of height measurement was investigated in relation to LiDAR point density, inventory height, and the timing of data collection. A simple data exploratory analysis (DEA) was conducted to identify problematic input data. Our CHM model has high accuracy compared to field-based height measurement (R2 = 0.85) on plots with relatively accurate GPS locations. Our study provides an easy-to-follow workflow for 3DEP LiDAR based CHM generation in a parallel processing environment for a large geographic area. In addition, the resulting CHM can serve as critical baseline information for monitoring and management decisions, as well as the calculation of other key forest metrics such as biomass and carbon storage

A comparative study of RGB and multispectral sensor-based cotton canopy cover modelling using multi-temporal UAS data

This study presents a comparative study of multispectral and RGB (red, green, and blue) sensor-based cotton canopy cover modelling using multi-temporal unmanned aircraft systems (UAS) imagery. Additionally, a canopy cover model using an RGB sensor is proposed that combines an RGB-based vegetation index with morphological closing. The field experiment was established in 2017 and 2018, where the whole study area was divided into approximately 1 x 1 m size grids. Grid-wise percentage canopy cover was computed using both RGB and multispectral sensors over multiple flights during the growing season of the cotton crop. Initially, the normalized difference vegetation index (NDVI)-based canopy cover was estimated, and this was used as a reference for the comparison with RGB-based canopy cover estimations. To test the maximum achievable performance of RGB-based canopy cover estimation, a pixel-wise classification method was implemented. Later, four RGB-based canopy cover estimation methods were implemented using RGB images, namely Canopeo, the excessive greenness index, the modified red green vegetation index and the red green blue vegetation index. The performance of RGB-based canopy cover estimation was evaluated using NDVI-based canopy cover estimation. The multispectral sensor-based canopy cover model was considered to be a more stable and accurately estimating canopy cover model, whereas the RGB-based canopy cover model was very unstable and failed to identify canopy when cotton leaves changed color after canopy maturation. The application of a morphological closing operation after the thresholding significantly improved the RGB-based canopy cover modeling. The red green blue vegetation index turned out to be the most efficient vegetation index to extract canopy cover with very low average root mean square error (2.94% for the 2017 dataset and 2.82% for the 2018 dataset), with respect to multispectral sensor-based canopy cover estimation. The proposed canopy cover model provides an affordable alternate of the multispectral sensors which are more sensitive and expensive.This study presents a comparative study of multispectral and RGB (red, green, and blue) sensor-based cotton canopy cover modelling using multi-temporal unmanned aircraft systems (UAS) imagery. Additionally, a canopy cover model using an RGB sensor is proposed that combines an RGB-based vegetation index with morphological closing. The field experiment was established in 2017 and 2018, where the whole study area was divided into approximately 1 x 1 m size grids. Grid-wise percentage canopy cover was computed using both RGB and multispectral sensors over multiple flights during the growing season of the cotton crop. Initially, the normalized difference vegetation index (NDVI)-based canopy cover was estimated, and this was used as a reference for the comparison with RGB-based canopy cover estimations. To test the maximum achievable performance of RGB-based canopy cover estimation, a pixel-wise classification method was implemented. Later, four RGB-based canopy cover estimation methods were implemented using RGB images, namely Canopeo, the excessive greenness index, the modified red green vegetation index and the red green blue vegetation index. The performance of RGB-based canopy cover estimation was evaluated using NDVI-based canopy cover estimation. The multispectral sensor-based canopy cover model was considered to be a more stable and accurately estimating canopy cover model, whereas the RGB-based canopy cover model was very unstable and failed to identify canopy when cotton leaves changed color after canopy maturation. The application of a morphological closing operation after the thresholding significantly improved the RGB-based canopy cover modeling. The red green blue vegetation index turned out to be the most efficient vegetation index to extract canopy cover with very low average root mean square error (2.94% for the 2017 dataset and 2.82% for the 2018 dataset), with respect to multispectral sensor-based canopy cover estimation. The proposed canopy cover model provides an affordable alternate of the multispectral sensors which are more sensitive and expensive

Automated Coregistration of Multisensor Orthophotos Generated from Unmanned Aerial Vehicle Platforms

Image coregistration is a key preprocessing step to ensure the effective application of very-high-resolution (VHR) orthophotos generated from multisensor images acquired from unmanned aerial vehicle (UAV) platforms. The most accurate method to align an orthophoto is the installation of air-photo targets at a test site prior to flight image acquisition, and these targets were used as ground control points (GCPs) for georeferencing and georectification. However, there are time and cost limitations related to installing the targets and conducting field surveys on the targets during every flight. To address this problem, this paper presents an automated coregistration approach for orthophotos generated from VHR images acquired from multisensors mounted on UAV platforms. Spatial information from the orthophotos, provided by the global navigation satellite system (GNSS) at each image’s acquisition time, is used as ancillary information for phase correlation-based coregistration. A transformation function between the multisensor orthophotos is then estimated based on conjugate points (CPs), which are locally extracted over orthophotos using the phase correlation approach. Two multisensor datasets are constructed to evaluate the proposed approach. These visual and quantitative evaluations confirm the superiority of the proposed method