Infrared Spectroscopy
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Infrared Spectroscopy Keith D Shepherd. Optimizing Fertilizer Recommendations for Africa (OFRA) Project Inception 25-27 November 2013. Surveillance Science.

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Infrared Spectroscopy Keith D Shepherd

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Infrared spectroscopy keith d shepherd

Infrared Spectroscopy

Keith D Shepherd

Optimizing Fertilizer Recommendations for Africa (OFRA) Project Inception

25-27 November 2013


Surveillance science

Surveillance Science

UNEP. 2012. Land Health Surveillance: An Evidence-Based Approach to Land Ecosystem Management. Illustrated with a Case Study in the West Africa Sahel. United Nations Environment Programme, Nairobi.

http://www.unep.org/dewa/Portals/67/pdf/LHS_Report_lowres.pdf

  • Increase sample density in landscapes

  • Direct prediction of soil-plant responses to management

  • Measure frequency of problems and associated risk factors in populations using statistical sampling designs & standardized measurement protocols

Shepherd KD and Walsh MG (2007) Infrared spectroscopy—enabling an evidence-based diagnostic surveillance approach to agricultural and environmental management in developing countries. Journal of Near Infrared Spectroscopy 15: 1-19.


Spectral shape relates to basic soil properties

Spectral shape relates to basic soil properties

  • Mineral composition

  • Iron oxides

  • Organic matter

  • Water (hydration, hygroscopic, free)

  • Carbonates

  • Soluble salts

  • Particle size distribution

 Functional properties


Infrared spectroscopy

Infrared spectroscopy

Dispersive VNIR

FT-NIR

FT-MIR Robotic

FT-MIR Portable

Brown D, Shepherd KD, Walsh MG (2006). Global soil characterization using a VNIR diffuse reflectance library and boosted regression trees. Geoderma 132:273–290.

Shepherd KD and Walsh MG (2007) Infrared spectroscopy—enabling an evidence-based diagnostic surveillance approach to agricultural and environmental management in developing countries. Journal of Near Infrared Spectroscopy 15: 1-19.

Terhoeven-Urselmans T, Vagen T-G, Spaargaren O, Shepherd KD. 2010. Prediction of soil fertility properties from a globally distributed soil mid-infrared spectral library. Soil Sci. Soc. Am. J. 74:1792–1799

Handheld MIR ?

Mobile phone cameras ?


Calibration

Calibration

Soil organic carbon

  • Spectralpretreatments

  • Derivatives, smoothing

  • Data miningalgorithms:

  • PLS +

  • SupportVectorMachines

  • Neural networks

  • MultivariateAdaptiveRegressionSplines

  • BoostedRegressionTrees

  • RandomForests

  • BayesianAdditiveRegressionTrees

Training

Out-of-bag validation

Soil pH

R package soil.spec

Soil spectral file conversion, data exploration and regression functions


Spectral prediction performance

Spectral prediction performance


Infrared spectroscopy keith d shepherd

Spectral libraries


Infrared spectroscopy keith d shepherd

  • Submit batch of spectra online

  • Uncertainties estimated for each sample

  • Samples with large error submitted for reference analysis

  • Calibration models improve as more samples submitted

  • All subscribers benefit


Infrared spectroscopy keith d shepherd

Spectral fingerprinting

X-ray diffraction spectroscopy

Total X-ray fluorescence spectroscopy

Infrared spectroscopy


Spectral lab network

Spectral Lab Network

  • Planned

  • Eggerton University, Kenya

  • MoA, Liberia

  • IER, Arusha, Tanzania

  • FMARD, Nigeria

  • NIFOR, Nigeria

  • CNLS, Nairobi

  • BLGG, Kenya (mobile labs)

  • IAMM, Mozambique

  • AfSIS, Sotuba, Mali

  • AfSIS, Salien, Tanzania

  • AfSIS, Chitedze, Malawi

    • CNLS, Nairobi, Kenya

    • ICRAF, Nairobi, Kenya

  • CNRA, Abidjan, Cote D’Ivoire

  • KARI, Nairobi, Kenya

  • ICRAF, Yaounde, Cameroon

  • ObafemiAwolowo University, Ibadan, Nigeria

  • IAR, Zaria, Nigeria

  • ATA, Addis Ababa, Ethiopia (+ 5 on order)

  • IITA, Ibadan, Nigeria

  • IITA, Yaounde, Cameroon

  • ICRAF, Nairobi, Kenya


Plant compost fertilizer analysis

Plant, compost, fertilizer analysis

  • IR for plant N/protein, organic resource quality/decomposition

  • Handheld XRF for plant P, K, Ca, Mg, micronutrients (in progress)

  • Handheld XRF for fertilizer quality control (in progress)

Shepherd KD, Palm CA, Gachengo CN and Vanlauwe B (2003) Rapid characterization of organic resource quality for soil and livestock management in tropical agroecosystems using near infrared spectroscopy. Agronomy Journal 95:1314-1322.

Shepherd, KD, Vanlauwe B, Gachengo CN Palm CA (2005) Decomposition and mineralization of organic residues predicted using near infrared spectroscopy. Plant and Soil 277:315-333.


Calibrating plant response to ir

Calibrating plant response to IR

http://afsis-dt.ciat.cgiar.org


Mtt finland foodafrica soil micronutrients

MTT-Finland FoodAfricaSoil Micronutrients

Evidence-based micronutrient management

Healthy crops

Healthy livestock

Healthy soils

Healthy people


Land health surveillance out scaling

Land HealthSurveillance Out-scaling

Global-Continental Monitoring Systems

Vital signs

CRP pan-tropical sites

AfSIS

Regional Information Systems

National surveillance

systems

Tibetan Plateau/ Mekong

Evergreen Ag / Horn of Africa

Ethiosis

Project baselines

SLM Cameroon

Parklands Malawi

Rangelands E/W Africa

Cocoa - CDI

MICCA EAfrica


Critical success factors

Critical success factors

  • Consistent field sampling protocol

  • Soil-Plant sample labeling, drying, preparation, sub-sampling, shipping, back-up storage

  • Data management, linking

  • Judicious selection of samples for reference analysis

  • Consistency of reference analyses

  • Use MIR as a soil covariate

  • Direct calibration of MIR to plant/soil response

http://worldagroforestry.org/research/land-health/spectral-diagnostics-laboratory


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