This document provides a detailed research proposal for a PhD project on using wavelet analysis to improve the accuracy of chlorophyll quantification in oil palm leaves through hyperspectral remote sensing. It includes background information on the significance of chlorophyll concentrations, an overview of the proposed methodology using wavelet transforms on reflectance spectra, research questions, and a Gantt chart outlining key milestones and a 126-week timeline. The goal is to develop a technique to generate accurate predictions of chlorophyll concentration and nitrogen content despite variations in other factors that influence leaf reflectance.
NIR in Leaf Chlorophyll Concentration EstimationIRJET Journal
This document discusses using field imaging spectroscopy and random forests to estimate leaf chlorophyll concentration in soybeans. A field imaging spectrometer system was used to collect hyperspectral reflectance data from soybean leaves. The PROSPECT radiative transfer model was used to relate the spectral data to chlorophyll content. Random forests were then used to develop a model for estimating chlorophyll content based on the spectral data. The model was able to accurately retrieve chlorophyll content from validation spectral data, demonstrating the potential of this approach for remote monitoring of crop health conditions. Future work involves applying this method from field to satellite data to allow monitoring soybean health over large areas.
JBEI Research Highlights - August 2017 Irina Silva
This document summarizes a new software tool called Rhorix that interfaces quantum chemical topology (QCT) calculations with the 3D graphics program Blender. Rhorix allows chemists to visually represent molecular structures and atoms-in-molecules using electron density from QCT calculations. This mapping provides a parameter-free means of understanding chemical phenomena based directly on quantum mechanical principles. The software will help chemists and artists visually represent chemical phenomena relevant to bioenergy through modern 3D drawing tools.
A seminar report on the chemical frontiers of living matter seminar series - ...Glen Carter
This seminar report highlights a select few presentations of cutting-edge research being done in various labs across the Paris Science et Lettre (PSL) network.
This book review summarizes a book titled "Applied Psychometry" by Narender Kumar Chadha. The book covers the fundamentals of psychometry, which is the science of measuring latent variables through paper-pencil tests and questionnaires. It discusses topics like test construction, item analysis, reliability and validity testing, ethical issues in psychological testing, and factor analysis. The book is intended to be a resource for researchers and students working in clinical, psychological and survey research where quantitative measurement of latent variables is required. Overall, the book provides a comprehensive overview of designing and validating psychometric instruments.
This research paper evaluates two methods, machine learning algorithms and radiative transfer model inversion, for estimating chlorophyll content in tea leaves with different shading treatments using hyperspectral reflectance measurements. Regression models based on machine learning, specifically kernel-based extreme learning machine, achieved the highest performance with a root mean square error of 3.04 mg/cm2 for predicting chlorophyll content in an independent test set. The PROSPECT-D radiative transfer model inversion also showed potential for quantifying chlorophyll content but requires some improvements. A total of 96 published vegetation indices were also evaluated as inputs to the machine learning models. The study aims to develop an accurate non-destructive method for estimating chlorophyll content in tea leaves grown
The document discusses three fluorescence microscopy techniques: FRET, FRAP, and TIRF microscopy. It explains the principles, instrumentation, sample preparation, applications, and future aspects of each technique. FRET involves energy transfer between fluorophores and is used to study molecular interactions and structure. FRAP examines fluorophore diffusion by photobleaching a region and monitoring recovery. It provides information about molecular mobility. TIRF microscopy uses evanescent waves to selectively excite fluorophores very near a surface and is applied to studies of cellular processes at membranes. All three techniques provide insights into biological phenomena at the molecular level.
Multi-molecular views of a stellar nurserySérgio Sacani
New detectors for radio telescopes can map emissions from many different molecules simultaneously across interstellar clouds. One such pioneering study has probed a wide area of a star-forming cloud in the Orion constellation
NIR in Leaf Chlorophyll Concentration EstimationIRJET Journal
This document discusses using field imaging spectroscopy and random forests to estimate leaf chlorophyll concentration in soybeans. A field imaging spectrometer system was used to collect hyperspectral reflectance data from soybean leaves. The PROSPECT radiative transfer model was used to relate the spectral data to chlorophyll content. Random forests were then used to develop a model for estimating chlorophyll content based on the spectral data. The model was able to accurately retrieve chlorophyll content from validation spectral data, demonstrating the potential of this approach for remote monitoring of crop health conditions. Future work involves applying this method from field to satellite data to allow monitoring soybean health over large areas.
JBEI Research Highlights - August 2017 Irina Silva
This document summarizes a new software tool called Rhorix that interfaces quantum chemical topology (QCT) calculations with the 3D graphics program Blender. Rhorix allows chemists to visually represent molecular structures and atoms-in-molecules using electron density from QCT calculations. This mapping provides a parameter-free means of understanding chemical phenomena based directly on quantum mechanical principles. The software will help chemists and artists visually represent chemical phenomena relevant to bioenergy through modern 3D drawing tools.
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This seminar report highlights a select few presentations of cutting-edge research being done in various labs across the Paris Science et Lettre (PSL) network.
This book review summarizes a book titled "Applied Psychometry" by Narender Kumar Chadha. The book covers the fundamentals of psychometry, which is the science of measuring latent variables through paper-pencil tests and questionnaires. It discusses topics like test construction, item analysis, reliability and validity testing, ethical issues in psychological testing, and factor analysis. The book is intended to be a resource for researchers and students working in clinical, psychological and survey research where quantitative measurement of latent variables is required. Overall, the book provides a comprehensive overview of designing and validating psychometric instruments.
This research paper evaluates two methods, machine learning algorithms and radiative transfer model inversion, for estimating chlorophyll content in tea leaves with different shading treatments using hyperspectral reflectance measurements. Regression models based on machine learning, specifically kernel-based extreme learning machine, achieved the highest performance with a root mean square error of 3.04 mg/cm2 for predicting chlorophyll content in an independent test set. The PROSPECT-D radiative transfer model inversion also showed potential for quantifying chlorophyll content but requires some improvements. A total of 96 published vegetation indices were also evaluated as inputs to the machine learning models. The study aims to develop an accurate non-destructive method for estimating chlorophyll content in tea leaves grown
The document discusses three fluorescence microscopy techniques: FRET, FRAP, and TIRF microscopy. It explains the principles, instrumentation, sample preparation, applications, and future aspects of each technique. FRET involves energy transfer between fluorophores and is used to study molecular interactions and structure. FRAP examines fluorophore diffusion by photobleaching a region and monitoring recovery. It provides information about molecular mobility. TIRF microscopy uses evanescent waves to selectively excite fluorophores very near a surface and is applied to studies of cellular processes at membranes. All three techniques provide insights into biological phenomena at the molecular level.
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This document discusses using imaging spectroscopy to estimate chlorophyll content in soybean leaves. It begins with an introduction to near infrared spectroscopy and its history. It then describes how a field imaging spectroscopy system was used to collect spectral data from soybean leaves. Random forests regression and the PROSPECT radiative transfer model were used to establish a model for estimating chlorophyll concentration from the spectral data. The model was able to accurately estimate chlorophyll content in soybean leaves and has potential applications for precision agriculture management and monitoring crop health at larger scales using remote sensing.
This document summarizes the development of a nanobiosensor to detect the herbicide diclofop. The nanobiosensor is based on atomic force microscopy (AFM) and uses the acetyl-CoA carboxylase (ACCase) enzyme, which is inhibited by diclofop, as the recognition element. Computational methods including molecular docking and molecular dynamics simulations were used to model the interactions between diclofop and ACCase and optimize the sensor design. Experimentally, ACCase was attached to AFM probes and force-distance curves were collected to measure the adhesion forces between the sensor and diclofop, demonstrating selective detection of diclofop over other herbicides. This
2017 - Environmental Ordination of Filamentous Bacteria in Activated SludgeWALEBUBLÉ
Reference:
Zornoza, A., Serrano, S. and Alonso, J.L. (2017) Environmental Ordination of Filamentous Bacteria in Activated Sludge. In: Abstracts of the 7th congress of European microbiologists FEMS 2017, Valencia, Spain, 9-13 July 2017.
Clinical Applications of Proton MR Spectroscopy.pdfSilvana Ciardullo
1) Proton MR spectroscopy provides greater tissue characterization than MR imaging alone by detecting metabolic abnormalities. It can be performed on most clinical 1.5T MR units in 10-15 minutes without significant additional scan time.
2) The technique detects metabolite concentrations based on peak intensities and locations on generated spectra graphs. The most commonly detected brain metabolites are NAA, creatine, choline, and lactate. Abnormal concentrations of these metabolites can indicate various neurological conditions.
3) Proton MR spectroscopy is useful for evaluating tumors, infections, demyelinating diseases, and other neurological disorders by detecting deviations from normal metabolite levels and ratios that provide physiological information about tissue status.
The influences of rooting media and hormone applications on rooting percentag...inventionjournals
ABSTRACT : Schefflera arboricola is used as an indoor plant in many places across the world besides the area it covers naturally. Therefore, it is produced intensely. However, it is usually produced through body cutting, which damages rootstock and allows obtaining only few cuttings from a plant. This study makes an attempt to determine the influences of rooting media and hormone applications on rooting percentage and some root morphological characters in cuttings taken from Schefflera arboricola in small amounts without damaging rootstock to the contrary of common practice. In this study, cuttings were treated with 1000 ppm, 3000 ppm, and 5000 ppm doses of IAA, IBA, NAA, and GA3 hormones, and rooting trials were carried out in sand, pearlite, and peat media. The research results show that the employed methods are significantly influential on rooting percentage and root morphological characters, and rooting percentage can be increased up to 75%.
Use of fluorescence lifetime technology to provide efficient protection from ...Dmitry Gakamsky
This article describes novel data analysis of fluorescence lifetime-based protein kinase assays to identify and correct for compound interference in several practical cases. This ability, together with inherent advantages of fluorescence lifetime technology (FLT) as a homogeneous, antibody-free format indepen- dent of sample concentration, volume, excitation intensity, and geometry, makes fluorescence lifetime a practical alternative to the established ‘‘gold standards’’ of radiometric and mobility shift (Caliper) assays. The analysis is based on a photochemical model that sets constraints on the values of fluorescence lifetimes in the time responses of the assay. The addition of an exponential component with free floating lifetime to the constrained model, in which the lifetimes are constants predetermined from control mea- surements and the preexponential coefficients are ‘‘floating’’ parameters, allows the relative concentra- tion of phosphorylated and nonphosphorylated substrates to be calculated even in the presence of compound fluorescence. The method is exemplified using both simulated data and experimental results measured from mixtures of dye-labeled phosphorylated and nonphosphorylated kinase substrates. A change of the fluorescence lifetime is achieved by the phosphorylated substrate-specific interaction with a bifunctional ligand, where one binding site interacts with the phosphate group and the other interacts with the dye.
Rick Stevens: Prospects for a Systematic Exploration of Earths Microbial Dive...GigaScience, BGI Hong Kong
Rick Stevens presented information about the Earth Microbiome Project (EMP), which aims to systematically characterize microbial life on Earth through a combination of extremely deep metagenomic sequencing and large-scale horizontal surveys. The EMP will establish common standards and coordinate independent projects proposed by the research community to advance large-scale microbial ecology research. It will generate over 1 petabase of sequencing data from around 1 million samples to map microbial habitats and discover new microbial diversity, genomes, and proteins.
1) The document discusses using NMR spectroscopy to analyze the metabolic profiles of clam mantle tissue and cultured lung epithelial cells. Spectra of extracts from different regions of clam mantle and control vs. cigarette smoke-exposed cells were obtained.
2) Glyceraldehyde and glucose levels were able to be quantified and showed differences between tissue and cell types. Glyceraldehyde levels suggested cigarette smoke exposure induced distress in lung cells.
3) Further identification of metabolites was needed using additional database comparisons to fully characterize the metabolic profiles obtained via NMR spectroscopy. Improvements were also needed in cell and tissue collection methods to better preserve metabolite levels.
Fluorescence recovery after photo bleachinganasshokor
FRAP (Fluorescence Recovery After Photobleaching) is a technique used to study the dynamics of molecules in living cells. It involves photobleaching a fluorescent marker in a region of the cell using a focused laser beam. The diffusion and movement of non-bleached fluorescent molecules into the bleached area is then monitored over time, allowing calculation of diffusion coefficients. Considerations in FRAP analysis include the degree of bleaching, bleach/recovery times, beam radius, and photobleaching artifacts. FRAP has various applications such as determining connectivity between cellular compartments using FLIP (Fluorescence Loss In Photobleaching) and quantifying transport between compartments.
Core-cladding mode resonances of long period fiber grating in concentration s...IOSR Journals
Long period fiber grating (LPFG) is photoinduced fiber device that facilitates the coupling of core
mode to different cladding modes resulting into series of transmission dips in the transmission spectrum. Here
we present LPFG chemical sensor to determine the concentration of Manganese in water at ppm level. We
fabricated LPFG of period 600μm in single mode communication fiber using 12W carbon dioxide laser
applying point by point method. The fabricated LPFG is directly used as chemical sensor since cladding modes
coupled to core mode directly come in contact with surrounding chemicals. Concentration of manganese in our
collected sample is found to be 0.0329ppm. The result is verified with sophisticated Atomic Absorption
Spectrometer (AAS).
This document presents a proposed "systemic strategy" to more efficiently identify functional marker candidates for abiotic stress tolerance in plants. The strategy aims to strengthen interdisciplinary efforts between plant breeding, plant nutrition, and molecular biology. It involves using ecophysiological modeling and genetic analyses to identify robust physiological parameters for important agronomic traits. Target tissues and cells critical for those parameters would then be studied at the molecular level to characterize stress-induced reprogramming. Both "top-down" whole plant approaches and "bottom-up" molecular approaches would be combined to benefit functional marker-assisted breeding for quantitative traits like stress tolerance. Research on the role of root hairs in phosphate efficiency is highlighted as one area that has made progress in this
This document summarizes research using a radio frequency sensor to detect and distinguish particle concentration. The RF sensor uses changes in dielectric permittivity to detect particles without labelling. Test results showed the sensor could detect 4 μm polystyrene particles at different concentrations and frequencies, and distinguish between 1% and 10% concentrations. Future work will further test the sensor's ability to detect different particles and concentrations at more frequencies to support its use in applications like medicine, biology and environmental monitoring.
A Mobile NMR Lab For Leaf Phenotyping In The FieldSherri Cost
The document describes a study that developed a mobile NMR lab to assess the physiological status of oilseed rape leaves grown in field conditions. A portable NMR spectrometer was placed in a van and used to measure the transverse relaxation times of leaf discs cut from plants in the field. The relaxation times detected structural changes during leaf senescence. Measurements on field-grown leaves were compared to those from controlled conditions to identify the effects of environmental variability on leaf tissues. The results demonstrated NMR can provide indicators of leaf development stage even for plants experiencing heterogeneous field conditions. This is an important step towards selecting genotypes tolerant to water and nutrient stress using non-destructive phenotyping methods.
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The document describes using thin layer chromatography and column chromatography to separate mixtures of compounds. Specifically, it discusses using column chromatography to separate a mixture of nonpolar fluorine and polar fluorenone based on their differing properties. Thin layer chromatography was then used to analyze the separation by calculating Rf values and determining if any compounds had not been fully separated based on their migration distances.
Patterson et al. used a new microscopy technique called liquid-cell transmission electron microscopy (LCTEM) to observe the crystallization of metal-organic frameworks (MOFs) in real time. This provided insights into the growth mechanisms. They observed that MOFs like ZIF-8 grow through the transport and attachment of metal ions and ligands to particle edges, not by particle coalescence. This two-step process of transport followed by edge attachment limits the growth rate. LCTEM is able to directly observe growth at the nanoscale and will provide insights to better control MOF synthesis.
The effectiveness of methods and algorithms for detecting and isolating facto...IJECEIAES
This article discusses a large number of textural features and integral transformations for the analysis of texture-type images. It also discusses the description and analysis of the features of applying existing methods for segmenting texture areas in images and determining the advantages and disadvantages of these methods and the problems that arise in the segmentation of texture areas in images. The purpose of the ongoing research is to use methods and determine the effectiveness of methods for the analysis of aerospace images, which are a combination of textural regions of natural origin and artificial objects. Currently, the automation of the processing of aerospace information, in particular images of the earth’s surface, remains an urgent task. The main goal is to develop models and methods for more efficient use of information technologies for the analysis of multispectral texture-type images in the developed algorithms. The article proposes a comprehensive approach to these issues, that is, the consideration of a large number of textural features by integral transformation to eventually create algorithms and programs applicable to solving a wide class of problems in agriculture.
Near infrared reflectance spectroscopy (NIRS) is a technique that can be used to analyze the chemical composition of feed and fishmeal by measuring the absorption of near infrared light. NIRS allows for rapid, non-destructive testing of samples to determine levels of components like protein, moisture, fat, and ash. The document discusses the principles behind NIRS, calibration procedures, applications in analyzing fishmeal and other feeds, and the advantages and limitations of using NIRS for feed analysis.
What Should I Write My College Essay About 15Amy Cernava
The document provides steps for requesting writing assistance from HelpWriting.net:
1. Create an account with a password and email.
2. Complete a 10-minute order form providing instructions, sources, deadline, and attaching a sample for style imitation.
3. Review bids from writers and choose one based on qualifications, history, and feedback, then pay a deposit to start.
4. Review the paper and authorize full payment if pleased, or request revisions using the free revision policy.
5. Confidently choose HelpWriting.net knowing needs will be fully met through original, high-quality content or a full refund.
A New Breakdown Of. Online assignment writing service.Amy Cernava
The document provides a 5-step process for requesting writing help from HelpWriting.net:
1. Create an account and provide contact information.
2. Complete a 10-minute order form with instructions, sources, deadline, and sample work.
3. Review bids from writers and choose one based on qualifications.
4. Review the completed paper and authorize payment if satisfied.
5. Request revisions to ensure satisfaction and receive a refund for plagiarized work.
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This document discusses using imaging spectroscopy to estimate chlorophyll content in soybean leaves. It begins with an introduction to near infrared spectroscopy and its history. It then describes how a field imaging spectroscopy system was used to collect spectral data from soybean leaves. Random forests regression and the PROSPECT radiative transfer model were used to establish a model for estimating chlorophyll concentration from the spectral data. The model was able to accurately estimate chlorophyll content in soybean leaves and has potential applications for precision agriculture management and monitoring crop health at larger scales using remote sensing.
This document summarizes the development of a nanobiosensor to detect the herbicide diclofop. The nanobiosensor is based on atomic force microscopy (AFM) and uses the acetyl-CoA carboxylase (ACCase) enzyme, which is inhibited by diclofop, as the recognition element. Computational methods including molecular docking and molecular dynamics simulations were used to model the interactions between diclofop and ACCase and optimize the sensor design. Experimentally, ACCase was attached to AFM probes and force-distance curves were collected to measure the adhesion forces between the sensor and diclofop, demonstrating selective detection of diclofop over other herbicides. This
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Zornoza, A., Serrano, S. and Alonso, J.L. (2017) Environmental Ordination of Filamentous Bacteria in Activated Sludge. In: Abstracts of the 7th congress of European microbiologists FEMS 2017, Valencia, Spain, 9-13 July 2017.
Clinical Applications of Proton MR Spectroscopy.pdfSilvana Ciardullo
1) Proton MR spectroscopy provides greater tissue characterization than MR imaging alone by detecting metabolic abnormalities. It can be performed on most clinical 1.5T MR units in 10-15 minutes without significant additional scan time.
2) The technique detects metabolite concentrations based on peak intensities and locations on generated spectra graphs. The most commonly detected brain metabolites are NAA, creatine, choline, and lactate. Abnormal concentrations of these metabolites can indicate various neurological conditions.
3) Proton MR spectroscopy is useful for evaluating tumors, infections, demyelinating diseases, and other neurological disorders by detecting deviations from normal metabolite levels and ratios that provide physiological information about tissue status.
The influences of rooting media and hormone applications on rooting percentag...inventionjournals
ABSTRACT : Schefflera arboricola is used as an indoor plant in many places across the world besides the area it covers naturally. Therefore, it is produced intensely. However, it is usually produced through body cutting, which damages rootstock and allows obtaining only few cuttings from a plant. This study makes an attempt to determine the influences of rooting media and hormone applications on rooting percentage and some root morphological characters in cuttings taken from Schefflera arboricola in small amounts without damaging rootstock to the contrary of common practice. In this study, cuttings were treated with 1000 ppm, 3000 ppm, and 5000 ppm doses of IAA, IBA, NAA, and GA3 hormones, and rooting trials were carried out in sand, pearlite, and peat media. The research results show that the employed methods are significantly influential on rooting percentage and root morphological characters, and rooting percentage can be increased up to 75%.
Use of fluorescence lifetime technology to provide efficient protection from ...Dmitry Gakamsky
This article describes novel data analysis of fluorescence lifetime-based protein kinase assays to identify and correct for compound interference in several practical cases. This ability, together with inherent advantages of fluorescence lifetime technology (FLT) as a homogeneous, antibody-free format indepen- dent of sample concentration, volume, excitation intensity, and geometry, makes fluorescence lifetime a practical alternative to the established ‘‘gold standards’’ of radiometric and mobility shift (Caliper) assays. The analysis is based on a photochemical model that sets constraints on the values of fluorescence lifetimes in the time responses of the assay. The addition of an exponential component with free floating lifetime to the constrained model, in which the lifetimes are constants predetermined from control mea- surements and the preexponential coefficients are ‘‘floating’’ parameters, allows the relative concentra- tion of phosphorylated and nonphosphorylated substrates to be calculated even in the presence of compound fluorescence. The method is exemplified using both simulated data and experimental results measured from mixtures of dye-labeled phosphorylated and nonphosphorylated kinase substrates. A change of the fluorescence lifetime is achieved by the phosphorylated substrate-specific interaction with a bifunctional ligand, where one binding site interacts with the phosphate group and the other interacts with the dye.
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Rick Stevens presented information about the Earth Microbiome Project (EMP), which aims to systematically characterize microbial life on Earth through a combination of extremely deep metagenomic sequencing and large-scale horizontal surveys. The EMP will establish common standards and coordinate independent projects proposed by the research community to advance large-scale microbial ecology research. It will generate over 1 petabase of sequencing data from around 1 million samples to map microbial habitats and discover new microbial diversity, genomes, and proteins.
1) The document discusses using NMR spectroscopy to analyze the metabolic profiles of clam mantle tissue and cultured lung epithelial cells. Spectra of extracts from different regions of clam mantle and control vs. cigarette smoke-exposed cells were obtained.
2) Glyceraldehyde and glucose levels were able to be quantified and showed differences between tissue and cell types. Glyceraldehyde levels suggested cigarette smoke exposure induced distress in lung cells.
3) Further identification of metabolites was needed using additional database comparisons to fully characterize the metabolic profiles obtained via NMR spectroscopy. Improvements were also needed in cell and tissue collection methods to better preserve metabolite levels.
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FRAP (Fluorescence Recovery After Photobleaching) is a technique used to study the dynamics of molecules in living cells. It involves photobleaching a fluorescent marker in a region of the cell using a focused laser beam. The diffusion and movement of non-bleached fluorescent molecules into the bleached area is then monitored over time, allowing calculation of diffusion coefficients. Considerations in FRAP analysis include the degree of bleaching, bleach/recovery times, beam radius, and photobleaching artifacts. FRAP has various applications such as determining connectivity between cellular compartments using FLIP (Fluorescence Loss In Photobleaching) and quantifying transport between compartments.
Core-cladding mode resonances of long period fiber grating in concentration s...IOSR Journals
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mode to different cladding modes resulting into series of transmission dips in the transmission spectrum. Here
we present LPFG chemical sensor to determine the concentration of Manganese in water at ppm level. We
fabricated LPFG of period 600μm in single mode communication fiber using 12W carbon dioxide laser
applying point by point method. The fabricated LPFG is directly used as chemical sensor since cladding modes
coupled to core mode directly come in contact with surrounding chemicals. Concentration of manganese in our
collected sample is found to be 0.0329ppm. The result is verified with sophisticated Atomic Absorption
Spectrometer (AAS).
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The document provides steps for requesting writing assistance from HelpWriting.net:
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3. Review bids from writers and choose one based on qualifications, history, and feedback, then pay a deposit to start.
4. Review the paper and authorize full payment if pleased, or request revisions using the free revision policy.
5. Confidently choose HelpWriting.net knowing needs will be fully met through original, high-quality content or a full refund.
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The document provides a 5-step process for requesting writing help from HelpWriting.net:
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2. Complete a 10-minute order form with instructions, sources, deadline, and sample work.
3. Review bids from writers and choose one based on qualifications.
4. Review the completed paper and authorize payment if satisfied.
5. Request revisions to ensure satisfaction and receive a refund for plagiarized work.
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1. 1
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
A practical guide for academic proposal writing
Dr. Redmond Shamshiri
University of Florida
ramin.sh@ufl.edu
http://plaza.ufl.edu/ramin.sh/
September, 2011
2. 2
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
EXAMPLE #1:
Providing supervisory committee members with one paragraph
research description, and Gant chart
Title of Research:
Retrieval of chlorophyll concentration from oil palm leaf reflectance spectra
using wavelet analysis
Program: Ph.D, M.Sc, etc.., Electrical Engineering, etc..etc..
Semester Intake: Feb. 2011
Expected date of Graduation: Feb.2014
Name of Supervisor: Prof. Dr. First Name, Last Name
Summary of Research:
The dynamics of foliar chlorophyll concentrations have
considerable significance for plant–environment interactions, ecosystem
functioning and crop growth. Hyperspectral remote sensing has a valuable
role in the monitoring of such dynamics. This study focuses upon improving
the accuracy of chlorophyll quantification by applying wavelet analysis to
reflectance spectra of oil palm leaves. Leaf-scale radiative transfer models
will be used to generate very large spectral data sets with which to develop
and rigorously test refinements to the approach and compare it with
existing spectral indices. The results are expected to demonstrate that by
decomposing leaf spectra, the resultant wavelet coefficients can be used to
generate accurate predictions of chlorophyll concentration, despite wide
variations in the range of other biochemical and biophysical factors that
influence leaf reflectance. Wavelet analysis would also outperform
predictive models based on untransformed spectra and a range of spectral
indices. This project will discusses the possibilities for further refining the
wavelet approach and for extending the technique to the sensing of a
variety of vegetation properties at a range of spatial scales.
3. 3
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
EXAMPLE #2:
Providing supervisory committee members with a complete research
proposal
Project title:
Retrieval of chlorophyll concentration from oil palm leaf reflectance
spectra using wavelet analysis
Project objectives:
This study focuses upon improving the accuracy of chlorophyll
quantification by applying wavelet analysis to reflectance spectra of oil
palm leaves. This project will also discuss the possibilities for further
refining the wavelet approach and for extending the technique to the
sensing of a variety of vegetation properties at a range of spatial scales. An
application of this research would be on variable rate application, where an
image processing method to assess oil palm leaf chlorophyll level is
required. Specific objectives are as follow:
o To address the chlorophyll spectral band accurately in the oil palm leaf
reflectance spectra
o To identify appropriate wavelet functions for this task
o To determine the optimum wavelet coefficients (at particular scales
and positions) that provide the greatest sensitivity to chlorophyll
o To investigate whether reflectance spectra or first or seconds
derivatives reflectance spectra provide the most effective inputs for
wavelet analysis
o To determine whether discrete or continuous wavelet transformations
result in more accurate chlorophyll estimates
o To develop a low cost yet more accurate real time sensor for
determination of nitrogen content in oil palm leaves to be replaced
with the high cost conventional methods.
The results are expected to demonstrate that by decomposing leaf
spectra, the resultant wavelet coefficients can be used to generate accurate
predictions of chlorophyll concentration, despite wide variations in the
range of other biochemical and biophysical factors that influence leaf
reflectance. Wavelet analysis would also outperform predictive models
based on untransformed spectra and a range of spectral indices. The
ultimate goal of this research is to further the development of this
technology through the use of a newer mathematical technique. The
wavelet transformation has been developed to convert signals and images
into frequency and spatial or time based domains (Marchant, 2003). This
technique has never been used to detect the nitrogen content of oil palm
leaves, but its properties make it a useful tool in analysis of images and
signals with transient information. Wavelet transform has a unique
property in that it can detect spatial features in a signal as well as the
frequency information that the Fourier transform can detect.
Research backgrounds
The dynamics of foliar chlorophyll concentrations have
considerable significance for plant–environment interactions, ecosystem
functioning and crop growth. Hyperspectral remote sensing has a valuable
role in the monitoring of such dynamics. The chlorophylls are essential
4. 4
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
pigments in the process of photosynthesis; therefore, it has been argued
that they are the most important organic molecules on Earth (Davies,
2004). Changes in the total concentration of foliar chlorophyll and the
relative proportions of chlorophyll a and chlorophyll b are brought about
by a variety of physiological stresses, leaf development and senescence.
Such pigment variations relate directly to the rate of primary production.
Furthermore, the chlorophylls contain a large proportion of total leaf
nitrogen therefore measurements of chlorophyll concentration can provide
an accurate indirect assessment of plant nutrient status (Moran et al.,
2000). Hence, information concerning the spatial and temporal dynamics of
leaf chlorophyll is of considerable value from a scientific viewpoint,
particularly in investigations of plant–environment interactions, and from
an applied perspective in agriculture, forestry and environmental
management. Wavelets are functions that decompose a complex signal into
component sub-signals. When applied to reflectance spectra, a model can
be established between wavelet coefficients that are assigned to the
component sub-signals and the concentrations of chemical constituents. In
the context of the remote sensing of foliar chlorophyll, wavelet analysis has
the potential to capture much more of the information contained with
reflectance spectra than previous analytical approaches which have tended
to focus on using a small number of optimal wavebands while discarding
the majority of the spectrum.
There are many commercial chlorophyll meters available which basically
measure the greenness of the plant. However chlorophyll meters are
subject to variability resulting from changes in light intensity from shade,
cloud cover, and sun intensity. Due to these concerns Kruse et al., (2004)
cautioned while the chlorophyll content can be related to the nitrogen
status in the plant, you should be careful basing fertility programs on these
readings. There are two potential problems associated with using plant
color to determine its nitrogen needs. First, if a nitrogen deficiency is
apparent, then it may be too late to apply fertilizer and expect a positive
plant response resulting in increased yield. The other major problem is that
different plants exhibit different colors in response to similar nutrient
deficiencies, i.e. there is a lack of nutrient deficiency-specific color. For
example, maize leaves become yellow-green in color if either nitrogen or
moisture deficiencies exist. This makes it difficult to distinguish the
particular deficiency for a plant based solely on color. Also, standards for
multiple plants may be required as the same nutrient deficiencies manifest
in varying colors.
Hypothesis
The hypothesis of this research is that the wavelet transform can
improve the detection of the spatial features in multi-spectral images for
determining the nitrogen content of oil palm. This research will study this
hypothesis through the use of the Matlab (Mathwork Inc) Wavelet CIR
images Toolbox. Color infrared images of oil palm leaves will be segmented
and then transformed into one-dimensional signals. These signals then will
undergo a wavelet transform to bring out specific features known to
nitrogen deficient of oil palm leaves. The final results are expected to show
a correlation factor between the transformed data and SPAD-502Plus
Chlorophyll Meter (Konica Minolta Inc) data taken of the plants as a
baseline for nitrogen stress level.
5. 5
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
Research questions
The first question to be addressed in this research is that which
family of wavelet is most appropriate for detection of nitrogen in oil palm
leaves spectra? It may be possible to select a priori the optimum family or
specific wavelet for a particular task, on the basis of mathematical criteria
or by using other factors such as the correspondence between the shape of
the wavelet and the shape of the absorption feature of interest. However,
Cocchi et al. (2003) have demonstrated the difficulty in developing an a
priori rule for identifying the most appropriate wavelet. Therefore, in the
present study, to assess the sensitivity of the analysis to the selection of the
wavelet used for decomposition, all seven compactly supported wavelet
families available within MATLAB will be tested. Hence, 53 individual
wavelet functions to be used are: the Haar wavelet, Daubechies wavelets
(shortened to db subsequently with orders ranging from to db to
db ; Symlets sym to sym8 ; Coiflets coif ' to coif ; Biorthogonal
wavelets bior . to bior .8 ; Reverse biorthogonal wavelets rbio . to
rbio .8 ; and the Discrete Meyer pseudo-wavelet dmey which
approximates the Meyer wavelet and allows discrete wavelet analysis.
Therefore, for each of the input reflectance and derivative spectra, a set of
continuous transformations and a set of discontinuous transformations will
be performed using each wavelet function in turn.
Literature review
There has been extensive research done on the multi-spectral
analysis of images. Multi-spectral images contain a number (two or more)
of monochrome images (Gonzalez and Woods, 2002). Each monochrome
image contains the amount of light reflected off the objects in the picture
for a particular spectral band. A variety of techniques on multi-spectral
images have been used for a multitude of purposes.
Several studies using hyperspectral data of vegetation have already
demonstrated the benefits of wavelet analysis for spectral smoothing and
noise removal (Bruce & Li, 2001; Schmidt & Skidmore, 2004), vegetation
classification (Henry et al., 2004; Hsu & Tseng, 2000; Huang et al., 2001;
Koger et al., 2003), discriminating nitrogen treatments (Reum & Zhang,
2005) and quantifying forest leaf area index (Pu & Gong, 2004). Indeed,
recent work by the authors has demonstrated the potential of wavelet
analysis for retrieving foliar nitrogen content (Ferwerda & Jones, 2006)
and photosynthetic pigment concentrations (Blackburn, 2007) from leaf
and canopy reflectance spectra but further research is needed to develop
the approach.
Kleynen et al. (2005) and Kim et al. (2002) used multi-spectral imaging to
inspect apples and it has been used to predict maturity in un-ripened
tomatoes (Hahn, 2002). It was also used in the inspection of poultry
carcasses (Lawrence et al., 2001; Park and Chen, 2001; Park et al., 1998)
and to detect the chlorophyll content of potatoes (Borhan et al., 2004).
Multi-spectral analysis has also been used in row crops for nitrogen
detection in corn (Kim and Reid, 2002; Noh et al., 2005), nitrogen detection
in rice (Huang et al., 2003), weed detection in cotton fields (Alchanatis et
al., 2005), and leaf surface wetness detection in corn (Ramalingam et al.,
2003).
6. 6
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
Research Methodology
The methodology of this research is to relate the reflectance of the
oil palm leaves to the amount of nitrogen in the plant. The SPAD-502Plus
measures the absorbances of the leaf in the red and near-infrared regions.
Using these two absorbances, the meter calculates a numerical SPAD value
which is proportional to the amount of chlorophyll present in the lead. The
chlorophyll present in the plant leaves is closely related to the nutritional
condition of the plant. The chlorophyll content will increase in proportion
to the amount of nitrogen present in the leaf. For a particular plant species,
a higher SPAD value indicates a healthier plant.
This wavelet analysis first removes unnecessary information from the
image and then converts the image into a one-dimensional (1-D) signal
representing the reflectance of the oil palm leaves. The obtained data is
further processed using wavelet transform to find specific features that
correspond to oil palm leaf chlorophyll stress. To implement wavelet
analysis, the 1-D signal will be deconstructed into some packets of narrows
frequency bands to find the lowest level approximations at different levels.
The maximum wavelet coefficients will be identified for interested signal
bands and then compared to SPAD meter readings which are used as the
ground-truth oil palm nitrogen level. Analysis results will indicate that
which wavelet packet at which level of deconstruction would have the
highest linear regression coefficient for oil palm nitrogen levels.
Milestones
Task Planned date Actual
date
Progress
Report
1. Discussion with supervisory committee April.01.2012
2. Proposal writing March.20.2012
3. Preliminary studies and literature
review
July.01.2012
4. Studying and purchasing Materials &
instrumentations
Sep.01.2012
5. Data collection Nov.01.2012
6. Laboratory analysis of data Jan.01.2013
7. Wavelet analysis of data April.01.2012
8. Calibration and validations June.01.2013
9. Writing the result and reports Sep.01.2013
10. Thesis submission and defense Feb.01.2014
Project activities,
There are two categories of activities associated with this project, the
research activity which leads to a Ph.D, and the transfer of the research
results to customers/beneficiaries
7. 7
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
Research activity Gant chart
Duration: 126 weeks, approximately 32 months (Normal time)
In this project, there are 10 tasks, labeled A through J. Each task has three
time estimates: the optimistic time estimate (O), the most likely or normal
time estimate (M), and the pessimistic time estimate (P). The expected time
(TE) is computed using the formula (O + 4M + P) ÷ 6.
Activity Predecessor
Time estimates (Weeks)
Expected time
(Weeks)
Opt. (O)
Normal
(M)
Pess. (P)
A. Discussion with supervisory
committee
— 1 2 3
2
B. Proposal writing — 2 4 6 4
C. Preliminary studies and
literature review
A 4 8 12
8
D. Studying and purchasing
Materials & instrumentations
A 8 24 32
22.6
E. Data collection D 12 16 24 16.6
F. Laboratory analysis of data E 12 16 24 16.6
G. Wavelet analysis of data B,C 12 16 24 16.6
H. Calibration and validations F,G 8 12 16 12
I. Writing the result and reports H 12 16 20 16
J. Thesis submission and
defense
I 8 12 16
12
Total 79 126 177 126.6667
8. 8
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
Optimistic time: The activity time if everything progresses in an ideal
manner
Most probably time: The most likely activity time under normal conditions
Pessimistic time: The activity time if we encounter significant breakdowns
and/or delays
Arcs indicate project activities
Nodes correspond to the beginning and ending activities
Event: The completion of all the activities that lead into a node is referred
to as an event
Path: A path is a sequence of connected activities that leads from the
starting node to the completion node.
ES: Earliest start time for a particular activity
EF: Earliest finish time for a particular activity
T: Expected activity time for the activity
EF= ES+T
Latest finish time:
The latest finish time for an activity entering a particular node is equal to
the smallest of the latest start times for all activities leaving the node
Activity Earliest
Start (ES)
Earliest
Finish (EF)
Latest
Start (LS)
Latest Finish
(LF)
Slack
(LS-ES)
Critical
Path?
A 0 2 0 2 0 YES
B 0 4 38 42 38
C 2 10 34 42 32
D 2 26 2 26 0 YES
E 26 42 26 42 0 YES
F 42 58 42 58 0 YES
G 10 26 42 58 32
H 58 70 58 70 0 YES
I 70 86 70 86 0 YES
J 86 98 86 98 0 YES
The critical path is ADEFHIJ.
1. What is the total time to complete the project?
The project can be completed in 98 weeks if the individual activities are
completed on schedule.
2. What are the scheduled start and finish dates for each specific
activity?
The detailed activity schedule that shows the earliest start, latest start,
earliest finish and latest finish times for each activity
3. Which activities are critical and must be completed exactly as
scheduled in order to keep the project on schedule?
The seven activities, A, D, E, F, H, I, J as the critical activities for the project
4. How long can non critical activities be delayed before they cause
a delay in total project?
The slack time available for all activities as shown in table
9. 9
Dr. Redmond Shamshiri Practical tutorial to proposal writing Sep.2011
Transfer of the research results to customers activities:
This set of activity includes:
Activit
y
Description Predecessors
A R&D product design -
B Plan market research -
C Routing (manufacturing engineering) A
D Build prototype model A
E Prepare marketing brochure A
F Cost estimates industrial
(engineering)
C
G Preliminary product testing D
H Market survey B, E
I Pricing and forecast report H
J Final report F,G,I