Multi-temporal Pacific madrone leaf blight assessment with unoccupied aircraft systems

Authors

  • Matthew I. Barker
  • Jonathan D. Burnett
  • Tanya Haddad
  • William Hirsch
  • Dae Kun Kang
  • Kale’a Pawlak-Kjolhaug
  • Michael G. Wing

DOI:

https://doi.org/10.15287/afr.2023.2700

Keywords:

Pacifica madrone, unoccupied aircraft systems,

Abstract

: Pacific madrone leaf blight (PMLB) is a contributing agent to the declineof Pacific madrone (Arbutus menziesii) trees. Multiple fungal pathogens causePMLB, resulting in leaf spotting that can eventually kill leaves, increasing stress inindividuals, and leaving them more susceptible to deadly cankers. Spores transmit viaair and water droplets, particularly during wet Spring months. Unoccupied aircraftsystems (UAS) technologies are in their relative infancy, but UAS are becomingmore affordable and accessible. UAS promise increased efficiency in forest healthmonitoring applications, providing a safer aerial data collection method at arelatively-low cost when compared to occupied aircraft. In this study, we developand present a UAS methodology to detect PMLB with a multispectral sensor. Thismethodology combines orthomosaic products derived from high-resolution (~4 cm)multirotor platform UAS multispectral imagery with machine learning and groundassessment of PMLB to classify visual presence of blight at the individual treelevel during multiple site revisits. The resulting model detected PMLB infectionstatus of 29 field surveyed madrone trees with a kappa coefficient of , a balancedaccuracy of 0.85, and a true positive rate of 0.92. The method presented here can bereadily scaled to efficiently cover a much larger extent with a beyond-line-of-sitecapable UAS and minimal field sampling. The increased efficiency of this approachmay be critical to characterizing PMLB in the near future as it is anticipatedthat PMLB prevalence will continue to increase as a result of climate change.

References

Agisoft. 2019. Agisoft Metashape. Available from https://www.agisoft.com/.

Bagheri, N. 2020. Application of aerial remote sensing technology for detection of fire blight infected pear trees. Computers and electronics in agriculture 168: 105147. doi:10.1016/j.compag.2019.105147.

Barnes, E., Clarke, T.R., Richards, S.E., Colaizzi, P., Haberland, J., Kostrzewski, M., Waller, P., Choi, C., Riley, E., and Thompson, T.L. 2000. Coincident detection of crop water stress, nitrogen status, and canopy density using ground based multispectral data.

Baston, D. 2021. exactextractr: Fast Extraction from Raster Datasets using Polygons.

Bennett, M. and Shaw, D.C. 2008. Diseases and insect pests of Pacific madrone. [Corvallis, Or.] : Oregon State University, Extension Service.

Breiman, L. 2001. Random Forests. Machine Learning 45(1): 5-32. doi:10.1023/A:1010933404324.

Brodersen, K.H., Ong, C.S., Stephan, K.E., and Buhmann, J.M. The Balanced Accuracy and Its Posterior Distribution. In 2010 20th International Conference on Pattern Recognition. 23-26 Aug. 2010 2010. pp. 3121-3124.

Calderón, R., Navas-Cortés, J.A., Lucena, C., and Zarco-Tejada, P.J. 2013. High-resolution airborne hyperspectral and thermal imagery for early detection of Verticillium wilt of olive using fluorescence, temperature and narrow-band spectral indices. Remote sensing of environment 139: 231-245. doi:10.1016/j.rse.2013.07.031.

Cao, Q., Miao, Y., Wang, H., Huang, S., Cheng, S., Khosla, R., and Jiang, R. 2013. Non-destructive estimation of rice plant nitrogen status with Crop Circle multispectral active canopy sensor. Field Crops Research 154: 133-144. doi:https://doi.org/10.1016/j.fcr.2013.08.005.

Chen, J.M. 1996. Evaluation of Vegetation Indices and a Modified Simple Ratio for Boreal Applications. Canadian Journal of Remote Sensing 22(3): 229-242. doi:10.1080/07038992.1996.10855178.

Cohen, J. 1960. A Coefficient of Agreement for Nominal Scales. Educational and psychological measurement 20(1): 37-46. doi:10.1177/001316446002000104.

DeWald, L.E., Elliott, M., Sniezko, R.A., and Chastagner, G.A. Geographic and local variation in Pacific madrone (Arbutus menziesii) leaf blight. In Poster session presented at the 6th International Workshop on the Genetics of Tree-Parasite Interactions: Tree Resistance to Insects and Diseases: Putting Promise into Practice. Mt. Sterling, OH 2018.

Di Nisio, A., Adamo, F., Acciani, G., and Attivissimo, F. 2020. Fast Detection of Olive Trees Affected by Xylella Fastidiosa from UAVs Using Multispectral Imaging. Sensors (Basel, Switzerland) 20(17): 4915. doi:10.3390/s20174915.

DJI. 2019. Matrice 200 Series - DJI. Available from https://www.dji.com/matrice-200-series.

DJI. 2020. DJI Pilot - DJI Download Center - DJI. Available from https://www.dji.com/downloads/djiapp/dji-pilot.

Elliott, M. Diseases of Pacific Madrone. In The Decline of Pacific Madrone (Arbutus menziesii Pursh): Current Theory and Research Directions. Seattle, Washington 1999. Edited by A.B. Adams. pp. 48-60.

Elliott, M., Edmonds, R., and Mayer, S. 2002. Role of fungal diseases in decline of Pacific madrone. Northwest Science 76: 293-303.

Elliott, M., Chastagner, G.A., Dermott, G., Kanaskie, A., Sniezko, R.A., and Hamlin, J. Range-wide genetic variability in Pacific madrone (Arbutus menziesii): examining disease resistance, growth, and survival in a common garden study. In Sniezko, Richard A.; Yanchuk, Alvin D.; Kliejunas, John T.; Palmieri, Katharine M.; Alexander, Janice M.; Frankel, Susan J., tech. coords. Proceedings of the fourth international workshop on the genetics of host-parasite interactions in forestry: Disease and insect resistance in forest trees. Gen. Tech. Rep. PSW-GTR-240. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture 2012. pp. 295 - 300.

Esri. 2021. ArcGIS Pro. Esri Inc., Redlands, CA.

Friedman, J.H. 2001. Greedy function approximation: A gradient boosting machine. Annals of Statistics 29: 1189-1232.

Garza, B.N., Ancona, V., Enciso, J., Perotto-Baldivieso, H.L., Kunta, M., and Simpson, C. 2020. Quantifying Citrus Tree Health Using True Color UAV Images. Remote sensing (Basel, Switzerland) 12(1): 170. doi:10.3390/rs12010170.

Geurts, P., Ernst, D., and Wehenkel, L. 2006. Extremely randomized trees. Machine learning 63(1): 3-42. doi:10.1007/s10994-006-6226-1.

Gitelson, A.A., Kaufman, Y.J., and Merzlyak, M.N. 1996. Use of a green channel in remote sensing of global vegetation from EOS-MODIS. Remote sensing of environment 58(3): 289-298. doi:10.1016/s0034-4257(96)00072-7.

Gitelson, A.A., Viña, A., Ciganda, V., Rundquist, D.C., and Arkebauer, T.J. 2005. Remote estimation of canopy chlorophyll content in crops. Geophysical Research Letters 32(8): L08403-n/a. doi:10.1029/2005GL022688.

Greenwell, B.M. 2017. pdp: An R Package for Constructing Partial Dependence Plots. The R Journal 9(1): 421-436. Available from https://journal.r-project.org/archive/2017/RJ-2017-016/index.html [accessed.

Group, P.C. 2022. Available from https://prism.oregonstate.edu [accessed 6 Nov 2022].

Guimarães, N., Pádua, L., Marques, P., Silva, N., Peres, E., and Sousa, J.J. 2020. Forestry Remote Sensing from Unmanned Aerial Vehicles: A Review Focusing on the Data, Processing and Potentialities. Remote sensing (Basel, Switzerland) 12(6): 1046. doi:10.3390/rs12061046.

Hijmans, R.J. 2021. raster: Geographic Data Analysis and Modeling.

Hostens, D.S., Dogwiler, T., Hess, J.W., Pavlowsky, R.T., Bendix, J., and Martin, D.T. 2022. Assessing the Role of sUASSmall unoccupied aerial systems (sUAS) Mission DesignMission designs in the Accuracy of Digital Surface Models Derived from Structure-from-Motion PhotogrammetryPhotogrammetry. In sUAS Applications in Geography. Edited by K. Konsoer, M. Leitner, and Q. Lewis. Springer International Publishing, Cham. pp. 123-156.

Hunt, E.R., Daughtry, C.S.T., Eitel, J.U.H., and Long, D.S. 2011. Remote Sensing Leaf Chlorophyll Content Using a Visible Band Index. Agronomy journal 103(4): 1090-1099. doi:10.2134/agronj2010.0395.

Hunt, E.R., Doraiswamy, P.C., McMurtrey, J.E., Daughtry, C.S.T., Perry, E.M., and Akhmedov, B. 2013. A visible band index for remote sensing leaf chlorophyll content at the canopy scale. ITC journal 21: 103-112. doi:10.1016/j.jag.2012.07.020.

Kalensky, Z. and Wilson, D.A. Spectral Signatures of Forest Trees. In Third Canadian Symposium on Remote Sensing. 1975. pp. 155 -171.

Kuhn, M. 2019. caret: Classification and Regression Training.

Landis, J.R. and Koch, G.G. 1977. The Measurement of Observer Agreement for Categorical Data. Biometrics 33(1): 159-174. doi:10.2307/2529310.

Lillesand, T.M., Kiefer, R.W., and Chipman, J.W. 2015. Remote sensing and image interpretation. Seventh edition. ed. Hoboken, N.J. : John Wiley & Sons, Inc., Hoboken, N.J.

Lucas, J.A. and Dickinson, C.H. 1998. Plant pathology and plant pathogens. 3rd ed. ed. Malden, Mass. : Blackwell Science, Malden, Mass.

Maloney, P.E., Lynch, S.C., Kane, S.F., and Rizzo, D.M. 2004. Disease progression of Phytophthora ramorum and Botryosphaeria dothidea on Pacific madrone. Plant disease 88(8): 852-857. doi:10.1094/PDIS.2004.88.8.852.

Marin, D.B., de Carvalho Alves, M., Pozza, E.A., Belan, L.L., and de Oliveira Freitas, M.L. 2018. Multispectral radiometric monitoring of bacterial blight of coffee. Precision agriculture 20(5): 959-982. doi:10.1007/s11119-018-09623-9.

Marques, P., Pádua, L., Adão, T., Hruška, J., Peres, E., Sousa, A., and Sousa, J.J. 2019. UAV-Based Automatic Detection and Monitoring of Chestnut Trees. Remote Sensing 11(7): 855. Available from https://www.mdpi.com/2072-4292/11/7/855 [accessed.

Micasense. 2019, July 25. MicaSense Altum processing workflow (including Reflectance Calibration) in Agisoft Metashape Professional 1.5. Available from https://agisoft.freshdesk.com/support/solutions/articles/31000148381-micasense-altum-processing-workflow-including-reflectance-calibration-in-agisoft-metashape-professi.

Micasense. 2020. Altum - Micasense. Available from https://micasense.com/altum/.

Nesbit, P.R. and Hugenholtz, C.H. 2019. Enhancing UAV–SfM 3D Model Accuracy in High-Relief Landscapes by Incorporating Oblique Images. Remote Sensing 11(3): 239. Available from https://www.mdpi.com/2072-4292/11/3/239 [accessed.

Oerke, E.C., Gerhards, R., Menz, G., and Sikora, R.A. 2010. Precision crop protection - the challenge and use of heterogeneity. Springer, Dordrecht ;.

R Core Team. 2021. R: A Language and Environment for Statistical Computing. Vienna, Austria.

Reeves, S.L. 2007. Arbutus menziesii. Available from https://www.fs.fed.us/database/feis/plants/tree/arbmen/all.html [accessed January 11 2022].

Rouse, J.W., Jr., Haas, R.H., Schell, J.A., and Deering, D.W. 1974. Monitoring Vegetation Systems in the Great Plains with Erts. p. 309.

Sampson, A.W. and Jesperson, B., S. 1963. California range brushlands and browse plants. Berkeley : Division of Agricultural Sciences, University of California, Berkeley. pp. 127.

Sandino, J., Pegg, G., Gonzalez, F., and Smith, G. 2018. Aerial Mapping of Forests Affected by Pathogens Using UAVs, Hyperspectral Sensors, and Artificial Intelligence. Sensors 18(4). doi:10.3390/s18040944.

Sikdar, P., Mazzola, M., and Xiao, C.L. 2019. Genetic and Pathogenic Characterization of Phacidiopycnis washingtonensis from Apple and Pacific Madrone from the Western United States. Phytopathology 109(3): 469-479. doi:10.1094/PHYTO-10-17-0358-R.

Strobl, C., Boulesteix, A.-L., Zeileis, A., and Hothorn, T. 2007. Bias in random forest variable importance measures: illustrations, sources and a solution. BMC bioinformatics 8(1): 25-25. doi:10.1186/1471-2105-8-25.

Strzepek, K., Yohe, G., Neumann, J., and Boehlert, B. 2010. Characterizing changes in drought risk for the United States from climate change. Environmental research letters 5(4): 044012. doi:10.1088/1748-9326/5/4/044012.

Ting, K.M. 2017. Confusion Matrix. In Encyclopedia of Machine Learning and Data Mining. Edited by C. Sammut and G.I. Webb. Springer US, Boston, MA. pp. 260-260.

Tucker, C.J. 1979. Red and photographic infrared linear combinations for monitoring vegetation. Remote sensing of environment 8(2): 127-150. doi:10.1016/0034-4257(79)90013-0.

USDA. 2006. Pacific madrone - Plant Guide. The PLANTS Database (http://plants.usda.gov). National Plant Data Team, Greensboro, NC 27401-4901 USA.

Wing, M.G. 2019. Unmanned aircraft systems for remote sensing of vegetation vigor. JOJ Hortic Arboric 2(4).

Wing, M.G., Burnett, J., Sessions, J., Brungardt, J., Cordell, V., Dobler, D., and Wilson, D. 2013. Eyes in the Sky: Remote Sensing Technology Development Using Small Unmanned Aircraft Systems. Journal of forestry 111(5): 341-347. doi:10.5849/jof.12-117.

Wingtra. 2022. WingtraOne GEN II Technical Specifications. Available from https://wingtra.com/mapping-drone-wingtraone/technical-specifications/ [accessed 7 Nov 2022].

Wright, M.N. and Ziegler, A. 2017. ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R. Journal of Statistical Software 77(1): 1-17. doi:10.18637/jss.v077.i01.

Zarco-Tejada, P.J., González-Dugo, V., and Berni, J.A.J. 2012. Fluorescence, temperature and narrow-band indices acquired from a UAV platform for water stress detection using a micro-hyperspectral imager and a thermal camera. Remote sensing of environment 117: 322-337. doi:10.1016/j.rse.2011.10.007.

Zhang, G.-Y., Zhang, C.-X., and Zhang, J.-S. 2010. Out-of-Bag Estimation of the Optimal Hyperparameter in SubBag Ensemble Method. Communications in statistics. Simulation and computation 39(10): 1877-1892. doi:10.1080/03610918.2010.521277.

Downloads

Published

2023-07-31

Issue

Section

Research article