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  1. Article: A Particle Swarm Optimization Based Approach to Pre-tune Programmable Hyperspectral Sensors

    Banerjee, Bikram Pratap / Raval, Simit

    Remote Sensing. 2021 Aug. 20, v. 13, no. 16

    2021  

    Abstract: Identification of optimal spectral bands often involves collecting in-field spectral signatures followed by thorough analysis. Such rigorous field sampling exercises are tedious, cumbersome, and often impractical on challenging terrain, which is a ... ...

    Abstract Identification of optimal spectral bands often involves collecting in-field spectral signatures followed by thorough analysis. Such rigorous field sampling exercises are tedious, cumbersome, and often impractical on challenging terrain, which is a limiting factor for programmable hyperspectral sensors mounted on unmanned aerial vehicles (UAV-hyperspectral systems), requiring a pre-selection of optimal bands when mapping new environments with new target classes with unknown spectra. An innovative workflow has been designed and implemented to simplify the process of in-field spectral sampling and its realtime analysis for the identification of optimal spectral wavelengths. The band selection optimization workflow involves particle swarm optimization with minimum estimated abundance covariance (PSO-MEAC) for the identification of a set of bands most appropriate for UAV-hyperspectral imaging, in a given environment. The criterion function, MEAC, greatly simplifies the in-field spectral data acquisition process by requiring a few target class signatures and not requiring extensive training samples for each class. The metaheuristic method was tested on an experimental site with diversity in vegetation species and communities. The optimal set of bands were found to suitably capture the spectral variations between target vegetation species and communities. The approach streamlines the pre-tuning of wavelengths in programmable hyperspectral sensors in mapping applications. This will additionally reduce the total flight time in UAV-hyperspectral imaging, as obtaining information for an optimal subset of wavelengths is more efficient, and requires less data storage and computational resources for post-processing the data.
    Keywords algorithms ; covariance ; data collection ; flight ; information storage ; landscapes ; spectral analysis ; vegetation
    Language English
    Dates of publication 2021-0820
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2513863-7
    ISSN 2072-4292
    ISSN 2072-4292
    DOI 10.3390/rs13163295
    Database NAL-Catalogue (AGRICOLA)

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  2. Article: An Open-Source Package for Thermal and Multispectral Image Analysis for Plants in Glasshouse.

    Sharma, Neelesh / Banerjee, Bikram Pratap / Hayden, Matthew / Kant, Surya

    Plants (Basel, Switzerland)

    2023  Volume 12, Issue 2

    Abstract: Advanced plant phenotyping techniques to measure biophysical traits of crops are helping to deliver improved crop varieties faster. Phenotyping of plants using different sensors for image acquisition and its analysis with novel computational algorithms ... ...

    Abstract Advanced plant phenotyping techniques to measure biophysical traits of crops are helping to deliver improved crop varieties faster. Phenotyping of plants using different sensors for image acquisition and its analysis with novel computational algorithms are increasingly being adapted to measure plant traits. Thermal and multispectral imagery provides novel opportunities to reliably phenotype crop genotypes tested for biotic and abiotic stresses under glasshouse conditions. However, optimization for image acquisition, pre-processing, and analysis is required to correct for optical distortion, image co-registration, radiometric rescaling, and illumination correction. This study provides a computational pipeline that optimizes these issues and synchronizes image acquisition from thermal and multispectral sensors. The image processing pipeline provides a processed stacked image comprising RGB, green, red, NIR, red edge, and thermal, containing only the pixels present in the object of interest, e.g., plant canopy. These multimodal outputs in thermal and multispectral imageries of the plants can be compared and analysed mutually to provide complementary insights and develop vegetative indices effectively. This study offers digital platform and analytics to monitor early symptoms of biotic and abiotic stresses and to screen a large number of genotypes for improved growth and productivity. The pipeline is packaged as open source and is hosted online so that it can be utilized by researchers working with similar sensors for crop phenotyping.
    Language English
    Publishing date 2023-01-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants12020317
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Comparative Evaluation of Traditional and Deep Learning-Based Segmentation Methods for Spoil Pile Delineation Using UAV Images

    Thiruchittampalam, Sureka / Banerjee, Bikram P. / Glenn, Nancy F. / Raval, Simit

    2024  

    Abstract: The stability of mine dumps is contingent upon the precise arrangement of spoil piles, taking into account their geological and geotechnical attributes. Yet, on-site characterisation of individual piles poses a formidable challenge. The utilisation of ... ...

    Abstract The stability of mine dumps is contingent upon the precise arrangement of spoil piles, taking into account their geological and geotechnical attributes. Yet, on-site characterisation of individual piles poses a formidable challenge. The utilisation of image-based techniques for spoil pile characterisation, employing remotely acquired data through unmanned aerial systems, is a promising complementary solution. Image processing, such as object-based classification and feature extraction, are dependent upon effective segmentation. This study refines and juxtaposes various segmentation approaches, specifically colour-based and morphology-based techniques. The objective is to enhance and evaluate avenues for object-based analysis for spoil characterisation within the context of mining environments. Furthermore, a comparative analysis is conducted between conventional segmentation approaches and those rooted in deep learning methodologies. Among the diverse segmentation approaches evaluated, the morphology-based deep learning segmentation approach, Segment Anything Model (SAM), exhibited superior performance in comparison to other approaches. This outcome underscores the efficacy of incorporating advanced morphological and deep learning techniques for accurate and efficient spoil pile characterisation. The findings of this study contribute valuable insights to the optimisation of segmentation strategies, thereby advancing the application of image-based techniques for the characterisation of spoil piles in mining environments.
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Statistics - Applications
    Subject code 004
    Publishing date 2024-01-31
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: CBM: An IoT Enabled LiDAR Sensor for In-Field Crop Height and Biomass Measurements.

    Banerjee, Bikram Pratap / Spangenberg, German / Kant, Surya

    Biosensors

    2021  Volume 12, Issue 1

    Abstract: The phenotypic characterization of crop genotypes is an essential, yet challenging, aspect of crop management and agriculture research. Digital sensing technologies are rapidly advancing plant phenotyping and speeding-up crop breeding outcomes. However, ... ...

    Abstract The phenotypic characterization of crop genotypes is an essential, yet challenging, aspect of crop management and agriculture research. Digital sensing technologies are rapidly advancing plant phenotyping and speeding-up crop breeding outcomes. However, off-the-shelf sensors might not be fully applicable and suitable for agricultural research due to the diversity in crop species and specific needs during plant breeding selections. Customized sensing systems with specialized sensor hardware and software architecture provide a powerful and low-cost solution. This study designed and developed a fully integrated Raspberry Pi-based LiDAR sensor named CropBioMass (CBM), enabled by internet of things to provide a complete end-to-end pipeline. The CBM is a low-cost sensor, provides high-throughput seamless data collection in field, small data footprint, injection of data onto the remote server, and automated data processing. The phenotypic traits of crop fresh biomass, dry biomass, and plant height that were estimated by CBM data had high correlation with ground truth manual measurements in a wheat field trial. The CBM is readily applicable for high-throughput plant phenotyping, crop monitoring, and management for precision agricultural applications.
    MeSH term(s) Agriculture ; Biomass ; Phenotype ; Software ; Triticum
    Language English
    Publishing date 2021-12-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662125-3
    ISSN 2079-6374 ; 2079-6374
    ISSN (online) 2079-6374
    ISSN 2079-6374
    DOI 10.3390/bios12010016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Roots' Drought Adaptive Traits in Crop Improvement.

    Shoaib, Mirza / Banerjee, Bikram P / Hayden, Matthew / Kant, Surya

    Plants (Basel, Switzerland)

    2022  Volume 11, Issue 17

    Abstract: Drought is one of the biggest concerns in agriculture due to the projected reduction of global freshwater supply with a concurrent increase in global food demand. Roots can significantly contribute to improving drought adaptation and productivity. Plants ...

    Abstract Drought is one of the biggest concerns in agriculture due to the projected reduction of global freshwater supply with a concurrent increase in global food demand. Roots can significantly contribute to improving drought adaptation and productivity. Plants increase water uptake by adjusting root architecture and cooperating with symbiotic soil microbes. Thus, emphasis has been given to root architectural responses and root-microbe relationships in drought-resilient crop development. However, root responses to drought adaptation are continuous and complex processes and involve additional root traits and interactions among themselves. This review comprehensively compiles and discusses several of these root traits such as structural, physiological, molecular, hydraulic, anatomical, and plasticity, which are important to consider together, with architectural changes, when developing drought resilient crop varieties. In addition, it describes the significance of root contribution in improving soil structure and water holding capacity and its implication on long-term resilience to drought. In addition, various drought adaptive root ideotypes of monocot and dicot crops are compared and proposed for given agroclimatic conditions. Overall, this review provides a broader perspective of understanding root structural, physiological, and molecular regulators, and describes the considerations for simultaneously integrating multiple traits for drought tolerance and crop improvement, under specific growing environments.
    Language English
    Publishing date 2022-08-30
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants11172256
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Automated hyperspectral vegetation index derivation using a hyperparameter optimisation framework for high-throughput plant phenotyping.

    Koh, Joshua C O / Banerjee, Bikram P / Spangenberg, German / Kant, Surya

    The New phytologist

    2022  Volume 233, Issue 6, Page(s) 2659–2670

    Abstract: Hyperspectral vegetation indices (VIs) are widely deployed in agriculture remote sensing and plant phenotyping to estimate plant biophysical and biochemical traits. However, existing VIs consist mainly of simple two-band indices that limit the net ... ...

    Abstract Hyperspectral vegetation indices (VIs) are widely deployed in agriculture remote sensing and plant phenotyping to estimate plant biophysical and biochemical traits. However, existing VIs consist mainly of simple two-band indices that limit the net performance and often do not generalise well for traits other than those for which they were originally designed. We present an automated hyperspectral vegetation index (AutoVI) system for the rapid generation of novel two- to six-band trait-specific indices in a streamlined process covering model selection, optimisation and evaluation, driven by the tree parzen estimator algorithm. Its performance was tested in generating novel indices to estimate chlorophyll and sugar contents in wheat. Results showed that AutoVI can rapidly generate complex novel VIs (at least a four-band index) that correlated strongly (R
    MeSH term(s) Chlorophyll/analysis ; Least-Squares Analysis ; Phenotype ; Plant Leaves/chemistry ; Triticum
    Chemical Substances Chlorophyll (1406-65-1)
    Language English
    Publishing date 2022-01-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.17947
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Three-Dimensional Unique-Identifier-Based Automated Georeferencing and Coregistration of Point Clouds in Underground Mines

    Singh, Sarvesh Kumar / Banerjee, Bikram Pratap / Raval, Simit

    Remote Sensing. 2021 Aug. 09, v. 13, no. 16

    2021  

    Abstract: Spatially referenced and geometrically accurate laser scans are essential for mapping and monitoring applications in underground mines to ensure safe and smooth operation. However, obtaining an absolute 3D map in an underground mine environment is ... ...

    Abstract Spatially referenced and geometrically accurate laser scans are essential for mapping and monitoring applications in underground mines to ensure safe and smooth operation. However, obtaining an absolute 3D map in an underground mine environment is challenging using laser scanning due to the unavailability of global navigation satellite system (GNSS) signals. Consequently, applications that require georeferenced point cloud or coregistered multitemporal point clouds such as detecting changes, monitoring deformations, tracking mine logistics, measuring roadway convergence rate and evaluating construction performance become challenging. Current mapping practices largely include a manual selection of discernable reference points in laser scans for georeferencing and coregistration which is often time-consuming, arduous and error-prone. Moreover, challenges in obtaining a sensor positioning framework, the presence of structurally symmetric layouts and highly repetitive features (such as roof bolts) makes the multitemporal scans difficult to georeference and coregister. This study aims at overcoming these practical challenges through development of three-dimensional unique identifiers (3DUIDs) and a 3D registration (3DReG) workflow. Field testing of the developed approach in an underground coal mine has been found effective with an accuracy of 1.76 m in georeferencing and 0.16 m in coregistration for a scan length of 850 m. Additionally, automatic extraction of mine roadway profile has been demonstrated using 3DUID which is often a compliant and operational requirement for mitigating roadway related hazards that includes roadway convergence rate, roof/rock falls, floor heaves and vehicle clearance for collision avoidance. Potential applications of 3DUID include roadway profile extraction, guided automation, sensor calibration, reference targets for a routine survey and deformation monitoring.
    Keywords automation ; calibration ; coal ; data collection ; deformation ; digital images ; georeferencing ; global positioning systems ; roads ; surveys
    Language English
    Dates of publication 2021-0809
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2513863-7
    ISSN 2072-4292
    ISSN 2072-4292
    DOI 10.3390/rs13163145
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: Automated structural discontinuity mapping in a rock face occluded by vegetation using mobile laser scanning

    Singh, Sarvesh Kumar / Raval, Simit / Banerjee, Bikram Pratap

    Elsevier B.V. Engineering geology. 2021 May, v. 285

    2021  

    Abstract: Mapping of structures, such as discontinuities, in an exposed rock mass is fundamental for slope stability analysis. This study investigates mobile laser scanning technology to identify structural discontinuity in a complex environment where the exposed ... ...

    Abstract Mapping of structures, such as discontinuities, in an exposed rock mass is fundamental for slope stability analysis. This study investigates mobile laser scanning technology to identify structural discontinuity in a complex environment where the exposed rock face is partially covered with vegetation. The conventional terrestrial laser scanning and photogrammetry based approaches for structure identification rely solely on coplanarity criteria or point normal vectors and often miss several prominent discontinuity planes in a complex environment with inherent noise. To enhance structural mapping in such environments, this study tests a mobile scanner which has multi-view data collection to reduce blind spots. A new automated and robust algorithm termed clustering on local point descriptors (CLPD) is developed for more accurate discontinuity identification. The algorithm involves a rigorous pre-processing step to remove erroneous and irrelevant points followed by computation of local point descriptors. Five descriptors (i.e. eigenvalue descriptor (EVD), radial surface descriptor (RSD), fast point feature histogram (FPFH), normal and curvature) were generated for each point to capture spatial distribution, geometrical relationships and local surface variations in the point cloud. Finally, a K-Medoids clustering was performed on the computed descriptors using a histogram of normals to identify discontinuity planes. Results indicate that the proposed CLPD algorithm outperforms existing approaches in terms of accuracy in discontinuity orientation estimate (3.50° in dip angle and 4.32° in dip direction) for the study site. The stereonet comparison also validated that the poles distribution from CLPD is on par with the ground truth as well as results from commercially available software. The study presents a comparative evaluation of various approaches for kinematic feasibility of planar, wedge and sliding failures.
    Keywords algorithms ; automation ; computer software ; data collection ; photogrammetry ; rocks ; scanners ; vegetation
    Language English
    Dates of publication 2021-05
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ISSN 0013-7952
    DOI 10.1016/j.enggeo.2021.106040
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Dissecting Physiological and Agronomic Diversity in Safflower Populations Using Proximal Phenotyping

    Thoday-Kennedy, Emily / Banerjee, Bikram / Panozzo, Joe / Maharjan, Pankaj / Hudson, David / Spangenberg, German / Hayden, Matthew / Surya Kant

    Agriculture. 2023 Mar. 04, v. 13, no. 3

    2023  

    Abstract: Safflower (Carthamus tinctorius L.) is a highly adaptable but underutilized oilseed crop capable of growing in marginal environments, with crucial agronomical, commercial, and industrial uses. Considerable research is still needed to develop commercially ...

    Abstract Safflower (Carthamus tinctorius L.) is a highly adaptable but underutilized oilseed crop capable of growing in marginal environments, with crucial agronomical, commercial, and industrial uses. Considerable research is still needed to develop commercially relevant varieties, requiring effective, high-throughput digital phenotyping to identify key selection traits. In this study, field trials comprising a globally diverse collection of 350 safflower genotypes were conducted during 2017–2019. Crop traits assessed included phenology, grain yield, and oil quality, as well as unmanned aerial vehicle (UAV) multispectral data for estimating vegetation indices. Phenotypic traits and crop performance were highly dependent on environmental conditions, especially rainfall. High-performing genotypes had intermediate growth and phenology, with spineless genotypes performing similarly to spiked genotypes. Phenology parameters were significantly correlated to height, with significantly weak interaction with yield traits. The genotypes produced total oil content values ranging from 20.6–41.07%, oleic acid values ranging 7.57–74.5%, and linoleic acid values ranging from 17.0–83.1%. Multispectral data were used to model crop height, NDVI and EVI changes, and crop yield. NDVI data identified the start of flowering and dissected genotypes according to flowering class, growth pattern, and yield estimation. Overall, UAV-multispectral derived data are applicable to phenotyping key agronomical traits in large collections suitable for safflower breeding programs.
    Keywords Carthamus tinctorius ; agriculture ; grain yield ; linoleic acid ; lipid content ; oils ; oilseed crops ; oleic acid ; phenology ; phenotype ; rain ; unmanned aerial vehicles ; vegetation
    Language English
    Dates of publication 2023-0304
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2651678-0
    ISSN 2077-0472
    ISSN 2077-0472
    DOI 10.3390/agriculture13030620
    Database NAL-Catalogue (AGRICOLA)

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  10. Book ; Online: A review of laser scanning for geological and geotechnical applications in underground mining

    Singh, Sarvesh Kumar / Banerjee, Bikram Pratap / Raval, Simit

    2022  

    Abstract: Laser scanning can provide timely assessments of mine sites despite adverse challenges in the operational environment. Although there are several published articles on laser scanning, there is a need to review them in the context of underground mining ... ...

    Abstract Laser scanning can provide timely assessments of mine sites despite adverse challenges in the operational environment. Although there are several published articles on laser scanning, there is a need to review them in the context of underground mining applications. To this end, a holistic review of laser scanning is presented including progress in 3D scanning systems, data capture/processing techniques and primary applications in underground mines. Laser scanning technology has advanced significantly in terms of mobility and mapping, but there are constraints in coherent and consistent data collection at certain mines due to feature deficiency, dynamics, and environmental influences such as dust and water. Studies suggest that laser scanning has matured over the years for change detection, clearance measurements and structure mapping applications. However, there is scope for improvements in lithology identification, surface parameter measurements, logistic tracking and autonomous navigation. Laser scanning has the potential to provide real-time solutions but the lack of infrastructure in underground mines for data transfer, geodetic networking and processing capacity remain limiting factors. Nevertheless, laser scanners are becoming an integral part of mine automation thanks to their affordability, accuracy and mobility, which should support their widespread usage in years to come.
    Keywords Computer Science - Computer Vision and Pattern Recognition
    Subject code 669
    Publishing date 2022-11-20
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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