26-02-2013

Hyperspectral Remote Sensing Applications for Vegetation
(with special emphasis on Agriculture)

Shibendu S. Ray
Mahalanobis National Crop Forecast Centre, DAC, New Delhi – 110 012 Space Applications Centre, ISRO, Ahmedabad – 380 015 Email: shibendu.ncfc@nic.in
DST Sponsored Training Programme “Hyperspectral Remote Sensing for Agriculture”, February 1827, 2013, IARI, New Delhi

Introduction

• •

Hyperspectral remote sensing deals with large number of narrow spectral bands over a contiguous spectral range Because of its ability to detect narrow absorption features hyperspectral data are related to specific vegetation physico-chemical characteristics, ocean biological constituents, soil physical and chemical properties, mineral composition and snow characteristics Because of presence of large number of bands, hyperspectral data needs different analysis approach

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50 0.1 0 425 Soil Water 925 1425 1925 (As per IRS Bands) 0.40 Crops Habitation Plantation Soil Water Reflectance 0.00 425 725 1025 1325 1625 1925 2225 Modipuram (U.10 0.20 0.26-02-2013 Why Hyperspectral? Absorption Spectra of Plant Pigments Chlorophyll Carotene Why Hyperspectral? Hyperion Data for Different Landcovers 0. P.) Wavelength(nm) ~10 nm bandwidth 0.30 0.5 0.2 0.4 Crops Habitation Plantation 0.3 2 .

30 m Swath 7. 3nm (350-1000nm) 10 nm (100-2500 nm) (Airborne Hyperspectral Imager) AHYSI Spatial Resolution : 3.5 km 350-1075 (2500) nm range Resol.6 m Swath 129.4 m Swath : ~1. 17m Swath 14 km Multi-angular (5 angles) Causes of leaf spectral characteristics (from Jensen.6 km Spectral Range: 456-889 nm Number of Bands: 143 Band Width: 3.3-4.5 km HySi/IMS-1 64 bands 400-950 nm range Spectral separation 8 nm Spatial Resol.473 km Spatial Resolution: 4. 10/11 nm Spatial Resol.26-02-2013 Data Sources Hyperion Field Spectroradiometer 224 bands 400-2500 nm range Spectral Resol. 2000) 3 .2 nm AIMS Average Altitude: 6.5 m Spectral Range : 420-950 nm Number of Bands: 512 Spectral sampling interval: 1.1 nm CHRIS/PROBAVarious data set: Land set has 18 bands 438-1035 nm range 6-10 nm bandwidth Spatial Resol. 505.

2nd overtone / C-H stretch / C-O stretch C-O stretch / C-N stretch 2240 C-H stretch 2300 N-H stretch / C-H stretch / C-H bend. 2nd overtone / N-H bend / N-H stretch 2130 N-H stretch 2180 N-H bend.600 0. 2nd overtone / C-H deformation.400 0. 1989. O-H deformation Chemicals Chlorophyll a Chlorophyll b Chlorophyll b Chlorophyll a Protein Protein Protein. 2nd overtone 2350 CH2 bend. Nitrogen Water. Nitrogen (Adapted from Curran. Protein. Starch. Nitrogen. 3rd overtone N-H stretch N-H stretch. Protein.700 0. 1999) Canopy Spectral Profile Spectral Profile of Vraious Kharif Season Crops Paddy Sorghum 0. Nitrogen 1980 N-H asymmetry 2060 N-H bend. 1st overtone O-H stretch.200 0. Nitrogen Cellulose. Protein. Nitrogen Protein Protein.100 0. Nitrogen Lignin.000 300 Cowpea Dhaincha Sugarcane Cotton Pigeon pea Groundnut Soybean Sesamum 600 900 1200 1500 1800 2100 2400 Sunflower Castor Reflectance Wavelength (nm) 4 .300 0.500 Maize Finger millet Cluster bean Lady finger Green gram Horse gram 0. Lignin. Lucas & Curran.26-02-2013 Absorption features in vegetation reflectance spectra Wavelength [nm] 430 460 640 660 910 1020 1510 1690 1940 Cause of absorption Electron transition Electron transition Electron transition Electron transition C-H stretch. Starch. 1st overtone C-H stretch. 2nd overtone Protein Protein. Cellulose Protein Protein.

26-02-2013 Vegetation Indices Vegetation Indices 5 .

3 Spectral curve before and after continuum removal 6 . also known as the red edge inflection point (REIP).26-02-2013 Red Edge • The red edge position (REP). is defined as the wavelength around 720 nm at which the first derivative of the spectral reflectance curve reaches its maximum value. • show the spectral curves before and after this analysis is done using the software. the red edge position shifts towards longer wavelengths (red shifts) while the shift is towards shorter wavelengths (blue shift) when the plant suffers from disease or chlorosis and hence low LAI. Continuum Removal Figure 8. When a plant is healthy with high chlorophyll content and high leaf area index (LAI).

800.800.9 450. Mahrouni taluk.000 188.490.800.800.1 750.750.800. UP (IFGRI) Spectral profiles of Rabi crops .Lalitpur.960 0.2 Lentil 0.1 0.7 450.0 325 375 425 475 525 575 625 675 725 775 825 875 925 975 1025 1075 Wavelength (nm) Discriminant Analysis Step 1 2 3 4 5 6 7 Wavelength Wilk’s  F-Value 800 0.000 187.6 750.5 Reflectance (%) 0. Lalitpur-Jhansi.4 0.940.26-02-2013 Hyperspectral Study of Pulse Crop Objective: discrimination of pulse crop using hyperspectral data Area: Patha village.750.000 162.3 Pea Flowering Pea Pod Formation Crop Stage Discrimination FCC Classified Simulated LISS IV • • • Data: Airborne HySI Crop: Sorghum 3 Stages Location: Visalpur Village near Ahmedabad 7 .800 0.6 750.960 0.750.940.305 45.014 144.3 0.940.490.960 0.001 149.670.960 0.002 149. UP Chickpea Branching LENTIL 0.960 0.940.1 450.7 PEA-FLOWERING PEA-FLOW/POD CHICKPEA-POD CHICKPEA-BRANCHING 0.6 Chickpea Pod 0.

4 0. Principal Component Analysis and Band-Band Correlation (560.3 0.2 0.5 N0 N50 N100 N150 N200 N250 N300 Red edge 740/720 1.6 0.85 0.8 0.75 SIPI 0. 730 and 760nm) Many Narrowband indices evaluated for discrimination Red edge ratio and SIPI((R800 .1 1 0.7 0.2 1.R445)/(R800 + R680)) best for discrimination Similar analysis for disease detection and water stress discrimination 8 .65 0.8 0.3 1.1 0 300 N0 N50 N100 N150 N200 N250 N300 Reflectance 400 500 600 700 Wavelength (nm) 800 900 1000 1100 • • 7 levels of nitrogen applied to potato crop Lower level of nitrogen had low NIR reflectance and high red reflectance Crop Stress Detection (Nitrogen) 1.26-02-2013 Crop Stress Detection (Nitrogen) 0.4 1.9 • • • • Best Bands were selected using Stepwise Discriminant Analysis.5 0. 650.6 1.7 0.

2 -0.55** 500 700 900 1100 Wavelength (nm) • • • Correlation curves generated for potato leaf chlorophyll with reflectance & derivatives Bands selected for ratio.53** 0.373+2.75 400 600 400 500 600 700 800 900 1000 • • • Correlation map of ratio based (all possible band combinations) indices with leaf nutrients Selection of ratios with high correlation Stepwise regression for best fit model (-0.3 -0.53** Dd720/Dd750 -0.33 0.42* 0.63** 0. F=31.6 700 0 -0.63** 0.47* -0.634 r750/710.45* 0.33 Ratio based indices 0. R2 = 0.25 Correlation coefficient 0 -0.4 -0.75 0.66** -0.50* 0.69** 0.41* 0.65 0.5 -0.551.26-02-2013 Crop Parameter Estimation (Development of Indices: Chlorophyll) 0.1 Chl a Chl b Total Chlorophyll Indices Chl a Chl b Total Chl 0.2 0.7 900 800 0.59** Second derivative based ratios Dd720/Dd680 0.65 500 -0.7 -0.6 -0.45* 0.51** 0.9**) 9 .6 300 R750/R700 R750/R610 R750/R420 First derivative based ratios D740/D690 0.1 -0. using peaks and troughs of correlation curves Red-edge importance was shown in derivative based indices Crop Parameter Estimation (Development of Indices) 1000 Leaf Nitrogen 0.

PROSPECT (leaf optical properties model) requires the leaf structure parameter N. and dry matter content (g/cm2) to simulate leaf reflectance and transmittance spectra in the optical domain. the equivalent water thickness Cw (g/cm2). PROSAIL Model Calibration & LAI Estimation 10 . Cw PROSPECT Canopy Structure LAI. SAIL (Scattering by Arbitrary Inclined Leaves) is the canopy reflectance model. the chlorophyll a. Cab. 2.b content Cab (g/cm2).26-02-2013 Canopy Reflectance Model PROSPECT+SAIL LEAF CHARACTERISTICS N. soil background reflectance. which computes canopy reflectance coupled with PROSPECT and using leaf area index (LAI) and leaf angle distribution (LAD). LAD Leaf Reflectance Transmittance Soil Reflectance SAIL CANOPY REFLECTANCE Measurement Characteristics (View & Sun Angle) 1.

234 5.801 RPD 10.833 0. 505.830 0.26-02-2013 PROSAIL Inversion Software (PRIS) Hierarchical Calibration Inversion using GA Neural Network Training Inversion using NN HySi/IMS-1 Specifications 64 bands.862 0.252 9.062 6.838 0.848 0.049 0.877 5.6 m.509 6. Spectral separation 8 nm.058 2.101 6.809 4.403 3.5 km Crop Classification using HySI Data Soil Parameter Estimation using HySI Data. Swath 129. Spatial Resol.532 11 .282 R2 0. PLSR Model and Ground Observation Soil Parameter N P K SOC Sand Silt Clay RMSE 11.963 0.872 7.730 6. 400-950 nm range.

Different Classifiers 12 .3)] LCA: Lignin Cellulose Absorption Index CAI: Cellulose Absorption Index Forest Species Classification Study Area: Shoolpaneswar Forest Data Used: Hyperion Data of October Approach: Band Selection using PLSR technique.1 + R2.2 − (R2.26-02-2013 Remote Sensing of Crop Residue Soil Straw Matured Wheat Residue LCA 7 6 5 4 3 2 1 0 RESIDUE STRAW MATURED SOIL CAI 5 4 3 2 1 0 -1 -2 RESIDUE STRAW MATURED SOIL LCA =100[2*R2.

045 0.030.2 0.26-02-2013 Discrimination of Different Forest Classes Forest Research Institute (FRI) Isodata: 6 classes FRI map SAM: 6 classes Mangrove Study Avicennia alba Avicennia alba 1 0.5 0.05 Aa random leaves 0.025 0.2 0.04 0.001 L = 0.4 0.015 0.05 0.02 0.03 p-value p-value Reflectance 0.045 0.035 0.005 0 0 400 400 0 0 0 0 0 2200 400 400 600 8001000 1000 1200 1400 1600 1800 2000 1200 1400 1600 1800 2000 2200 1000 1200 1400 1600 1800 2000 2200 400600 800 600800 800 1000 1200 1400 1600 1800 200 Wavelength (nm) Wavelength (nm) 13 . 1630.005 600 600 800 800 1000 1000 1200 1200 1400 1400 1600 1600 1800 1800 2000 2000 2070 2320 0.035 Leaf reflectance spectra Random leaves 95% confidence level 0. 1750 nm 1620 1640 L = 0.3 0.044 420 0.03 0.050.025 0.6 0.03 0.8 0.1 440 0 400 1440 470 600 800 2050 0 400 600 800 1000 1200 1400 1600 1800 2000 2200 1000 1200 1400 1600 1800 2000 2200 Wavelength (nm) 0.005 0.005 0.2 Adaxial surface Abaxial surface L = 0.05 0.000 0.5 0.9 0.7 0.6 0.5 0.1 0.035 920 Reflectance 0.2 0.6 0.7 0.040.8 Reflectance 0.9 0.7 Sonneratia caseolaris Sonneratia caseolaris 1 0.02 0.035 0.3 0.4 0.025 p-value p-value 0.04 0.04 0.015 0.4 0.05 Wanelength (nm) Rhizophora mucronata Rhizophora mucronata 1 0.6 0.045 Rm random leaves Sc random leaves0.035 0.010.02 0.01 0. 720.1 400 0 400 600 800 1000 1200 1400 1600 1800 2000 2200 Adaxial surface Abaxial surface 550.015 0.01 L = 0.3 0.8 0.020.025 0.1 1130 1150 Adaxial surface Abaxial surface Reflectance 0.5 0.3 0.045 0.015 0.04 0.045 0.003 99% confidence level 0.03 0.4 0.7 0.9 0.8 0.01 0.

1 690 0 400 600 800 1000 1200 1400 1600 1800 2000 2200 600 800 1000 1200 1400 1600 1800 2000 2200 Wavelength (nm) Wavelength (nm) Mangrove Classification: Bhitarkanika Overall accuracy (%) Decrease in accuracy (%) 100 90 80 70 60 50 40 30 20 10 0 196 148 98 96 88 79 63 56 39 23 8 30 Class 1 Decrease in accuracy (%) Overall accuracy (%) 25 20 15 10 5 0 Pure/ dominant communities of Heritiera fomes Mixed communities of H.39% Kappa Coefficient (К) = 0. S.28% К = 0.3 0.3 0.019 1000 0.5 0. etc.6 Sonneratia apetala vs. fomes (with Cynometra ramiflora.1 0 400 0. caseolaris Canopies of Sonneratia apetal vs Sonneratia caseolaris 0.2 A.2 970 N. mekongensis X.7 0. Aegiceras corniculatum.5 0. A. fruticans P.97% К = 0.1 400 0 400 2080 2150 600 800 1000 1200 1400 1600 1800 2000 2200 Wavelength (nm) Wavelength (nm) Xylocarpus mekingensis vs.6 L = 0. officinalis A.69 97.97 Class 5 Others b c 14 .03 L = 0. caseolaris 400 0. granatum Canopies of Xylocarpus mekongensis vs Xylocarpus granatum 0.2 X.4 0.5 Reflectance Reflectance 0.5 Reflectance Reflectance 0. paludosa 720 430 0.7 0.7 0.6 Nypa fruticans vs.6 0.1 0 400 2310 1540 580 550 600 800 1000 1200 1400 1600 1800 2000 2200 0. apetala S. alba 0.3 0.59 75.) Mixed communities Excoecaria agallocha Avicennia sp. Rhizophora mucronata.8 0.011 1000 960 L = 0.) of (with Class 2 Class 3 Class 4 Number of bands Fringing stands of mixed Sonneratia apetala (with other landward species) Mixed communities of mangrove associates & salt tolerant grasses Class 5 FCC Minimum Distance Spectral Angle Mapper Support Vector Machine a Class 1 Class 2 Class 3 Class 4 Overall Accuracy = 65.4 0. Phoenix paludosa Canopies of Nypa fruticans and Phoenix paludosa 0.7 L = 0. granatum 0.4 0. alba Canopies of Avicennia officinalis vs Avicennia alba 0.3 0.004 0.26-02-2013 Mangrove Study Avicennia officinalis vs.2 S. X.4 0.

ARVI.10 300 Site-1 Site-8 400 500 600 700 800 900 1000 1100 WAVELENGTH (nm) Site-10 Site-6 Best Reflectance Ratio for Chlorophyll Estimation R713/R680 Correlation coefficient for Chlorophyll-a (0. MCARI etc  Other indices showing less anisotropy.80 0.50 0.50 0.80 0.30 0.60 A E Reflectance 0.ZTM. B F C G D AVERAGE SPECTRA OF WATER.20 0.70 0.40 0.  Maximum anisotropy for Red Edge.677) Analysis of CHRIS/PROBA Data Angular effects on Vegetation Indices CVof Indices CV Indices NDVI SR NDVI705 mSR705 mNDVI705 SAVI MSAVI2 OSAVI MCARI TCARI NPCI MCARI2 RdEdg ZTM PRI SIPI ARVI EVI RGRI 3 40 35 30 Percentage 25 20 15 10 5 0 1 2 Stages Of Wheat  Least anisotropy.20 0. MSAVI.10 0.00 -0.10 0.26-02-2013 Wetland Vegetation Discrimination & Water Quality In situ spectra of various wetland plant species 0.659) and Chlorophyll-a+ Pheophytine (0.SIPI and RGRI – CV <5%. CHILIKA LAGOON 0.60 Site-2 Site-3 Site-4 Site-5 Site-6 Site-7 Site-8 Site-9 Site-10 Site-11 REFLECTANCE 0.70 Site-1 0.30 0. They are ratios of bands with similar angular effects and hence tend to cancel out the common effects.NPCI and mSR705 15 .00 325 375 425 475 525 575 625 675 725 775 825 875 925 975 1025 1075 Wavelength (nm) Phragmites Ipomoea Typha Cheda Nelumbo Nympheae Chara A: Phragmites karka B: Typha angustata C: Cheda (local name) D: Ipomoea aquatica E: Nelumbo nucifera F: Nympheae stellata G: Chara sp.40 0.

4 551 705.9 894.2 mNDVI705 NDVI705 MSAVI2 OSAV I MCARI2 MCARI NDVI TCARI mSR705 RdEdg -36.4 490 674.2 529.8 696.nadir view angles Spectral Analysis Software An In-house developed software to analyze spectral profiles derived from spectroradiometer Spectral Analysis View Chart Derivative Spectra Data Smoothing Continuum Removal Red Edge Analysis Averaging Vegetation Indices Chart Chart Chart Simple Averaging Broadband Conversion Predefined Indices Index Calculator Chart Chart Chart RGR I NPCI ARVI SAVI 0 SIPI ZTM PRI EVI SR -55 -36 0 55 R 2 16 .8 0.1 1018 Vegetation Indices % Change in dnorm 40 30 20 10 0 -10 -55.37 Graph showing correlation of LAI and vegetation indices computed using CHRIS/PROBA data.6 712 909 630.2 529. -36.1 1018 % Change in dnorm 0.64 +53.6 442.6 751.26-02-2013 Analysis of CHRIS/PROBA Data (a ) 180 160 140 120 100 80 60 40 20 0 -20 -55.9 894.6 712 909 630.2 529.9 871.31 -0.8 696.6 569.6 712 909 630.2 660.9 741.9 871.2 -0.31 View angle (°) The Percent change in normalized distance from nadir between the reflectance of wheat crop in different stages.77 View angle (°) +32.31 442.6 751.4 (c ) 60 50 Grain Formation~ Milking Stage -0.3 Earhead~Milking Stage 0.6 569.9 871.6 751.3 490 674.64 View angle (°) +53.1 780.37 442.1 780.2 660. for non.6 569.1 1018 Earhead~Grain Formation % Change in dnorm LAI Vs VI 0.77 +32.2 660.9 741.9 894.9 741.1 780.64 +53.6 (b ) 40 35 30 25 20 15 10 5 0 -5 -55.4 551 705.8 696.4 551 705.3 490 674.77 +32.37 -36.

600.065 0.000 85.001 0. 850 nm WILKS’ F VALUE LAMBDA 0. 680 nm Treatments (5) Potato: Irrigation 540. 500. 760.mdb 6 Send Request Vegetation Plantation Ornamental Plants Vegetation Spectral Library GUI 2 Send req.000 53. 670. 770. 660. 790.450. Treatments (5) 800. 550. 770.001 0. 940. 1030 nm Mustard Stages (2) 400.Dates of 560. 660. for Plant List of Ornamental 4 Plant List displayed 5 Spectral View General Info Vegetatio n Analysis Spectral Details Observation Details Plant photograph Select Plant name Fig. 420. 610 nm Cotton. 480.5 3.001 86. 930.6 • • Large Dataset Stepwise discriminant analysis 17 .4 8. 440.32E-05 0. 750. 570.3 6. 450. 740. 480. 610. 720. 430.9 1568. 710.5 0. 760.172 0. 740. 700. Graphic User Interface (GUI) and query modules of spectral Library Optimum Band Selection SOURCE OF WAVELENGTHS SELECTED VARIATION Rabi Season Crops 400. 630. 830. 550. (5) 610. for Plant List of Crops Send req.16 319.701 0.26-02-2013 Development of Spectral Library Plant Info displayed on GUI on the basis of User’s Request User Send Request 1 7 Send request for Plant List of Natural Veg. 770. 970 nm Rice: Phosphorus 640.1000 nm Treatments (3) Soil Types (4) 420. 4. 680 nm (4) Kharif Season Crops 400.2 22. 590. 710. for Plant List of Plantation Natural 3 SAC. 730.700 nm Sowing (2) Rice: Nitrogen 400. 940 nm Wheat Varieties (15) 370. Send req.

01 3-nm 5-nm 15nm 25nm -0. 5.26-02-2013 Selected Narrowbands Frequency of Bands 5 4 Frequency 3 2 1 0 370 400 420 430 440 450 480 500 540 550 560 570 590 600 610 630 640 660 670 680 700 710 720 730 740 750 760 770 790 800 830 850 940 970 1000 1030 Wavelelength (nm) • • • Integration of all outputs.04 0. blue (2). NIR (2) and moisture sensitive NIR (1) region.03 400 10nm 20nm 30nm 500 600 700 Wavelength (nm) 800 900 1000 • • • • Data from nitrogen treatment of rice crop Original spectral resolution 3 nm. resampled to 1 nm Comparison of reflectance and derivative Integrated to 3. red edge (2).02 -0. 20. Bands selected on the basis of frequency of occurrence 13 optimum bands in VNIR (400-1050 nm) region These included bands in violet (2).01 0 -0. Optimum Bandwidth 1st Derivative of Reflectance at Different Bandwidth with offset First Derivative Spectra 0. red (3). 15.02 0. green (1).03 First derivative (offset) 0. 10. 30 nm 18 . 25.

800-900) 19 .0 0.15 700-800 600-700 900-1000 800-900 0.04 RMSE at varying Bandwidth 0.7 2.1 0.0 -3. Bandwidth (nm) Difference from 3 nm 3 5 10 15 20 Green Reflectance 13.8 -1.2 25 11.7 2.at varying -1.4 53.0 -5.01 0 5 10 15 20 25 30 0 Bandwidth • • Optimum bandwidth required differed for different wavelength regions 700-800 nm region: ~5 nm. Methodologies have been developed for selection of optimum bands and bandwidth for vegetation studies.0 52.6 2. It was also found suitable for more accurate bio-chemical and biophysical parameter retrieval • • • • Various software and database have been developed for better interpretation of hyperspectral data.0 0.0 13.0 -6.5 Minimum Difference -0 0. 12.3 -1.2 0 NIR Reflectance 58.0 -6.06 30 11. RMSE(500-600. in collaboration with large number of organizations including IARI.02 0.1 0.5 2.5 -1 Red Reflectance 2.0 57.5 12 Maximum Difference -0 -0.0 maximum Difference RMSE -. Narrowband data have shown higher potential in assessing crop stresses.03 0.75 0.25 52. vegetation type discrimination. 600-700 & 800-900 nm: upto 15 nm.2 2. and so on. 400-500nm and 9001000nm: upto 25 Conclusion • All these studies have been carried out under ‘Hyperspectral Remote Sensing Applications’ project of Space Applications Centre.8 12.0 56.2 -0.5 2.900-1000) 400-500 500-600 0.26-02-2013 Optimum Bandwidth Reflectance difference at peaks Reflectance (%). 600-700.9 0.05 0.0 RMSE(400-500.05 0.0 Bandwidth -2.700-800.0 55.