Detection of crown rot in wheat utilising near-infrared spectroscopy: towards remote and robotic sensing

Paper


Humpal, Jacob, McCarthy, Cheryl, Percy, Cassy and Thomasson, J. Alex. 2020. "Detection of crown rot in wheat utilising near-infrared spectroscopy: towards remote and robotic sensing." Thomasson, J. Alex and Torres-Rua, Alfonso F. (ed.) Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping V (SPIE 2020). Online 27 Apr - 08 May 2020 United States. https://doi.org/10.1117/12.2557949
Paper/Presentation Title

Detection of crown rot in wheat utilising near-infrared spectroscopy: towards remote and robotic sensing

Presentation TypePaper
AuthorsHumpal, Jacob (Author), McCarthy, Cheryl (Author), Percy, Cassy (Author) and Thomasson, J. Alex (Author)
EditorsThomasson, J. Alex and Torres-Rua, Alfonso F.
Journal or Proceedings TitleProceedings of SPIE: Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping V
Journal Citation11414, pp. 1-7
Number of Pages7
Year2020
Place of PublicationUnited States
ISBN9781510636057
9781510636064
Digital Object Identifier (DOI)https://doi.org/10.1117/12.2557949
Web Address (URL) of Paperhttps://spie.org/Publications/Proceedings/Paper/10.1117/12.2557949
Conference/EventAutonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping V (SPIE 2020)
Event Details
Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping V (SPIE 2020)
Event Date
27 Apr 2020 to end of 08 May 2020
Event Location
Online
Abstract

Forty percent wheat yield reduction is reported globally due to crown rot (Fusarium pseudograminearum). An emerging approach for sensor-based disease discrimination is the use of spectral reflectance with combinations of wavebands and varying bandwidths, which has potential to reduce the impact of environmental factors on spectral sensitivity detection accuracy. Transferring such technology from a laboratory to field environment presents challenges, particularly in regard to producing adequately robust models. An experiment was conducted in which near-infrared spectral reflectance data was captured in a glasshouse environment, for cultivars of spring bread wheat with varying resistances to F. pseudograminearum. A contact sensor sensitive to nearinfrared (900–1700 nm) wavebands was used. Raw sensor data was calibrated and transformed, allowing for variable waveband size. Optimised machine learning disease identification models were compared across the nine weeks following inoculation with F. pseudograminearum. Models were compared for the ability to accurately detect crown rot across weeks. The results show crown rot detection ability with accuracies ranging from 49–74%, as well as a temporal patterning effect as the season progresses. An artificial neural network classifier (ANN) performed best with a top accuracy of 74.14%, of the six machine learning algorithms trialed. Waveform differences between plus and minus treatments indicate that the sensing approach has potential to be scaled to a camera-based system for use on remote sensing platforms. Further work is being conducted to understand the viability of such an approach, which is an important step towards both robotic and RPA-based disease discrimination.

KeywordsNIR, Spectroscopy, Crown Rot, Disease Detection
ANZSRC Field of Research 2020400909. Photonic and electro-optical devices, sensors and systems (excl. communications)
309999. Other agricultural, veterinary and food sciences not elsewhere classified
300409. Crop and pasture protection (incl. pests, diseases and weeds)
Public Notes

File reproduced in accordance with the copyright policy of the publisher/author.

Byline AffiliationsCentre for Agricultural Engineering
Centre for Crop Health
Texas A&M University, United States
Institution of OriginUniversity of Southern Queensland
Permalink -

https://research.usq.edu.au/item/q796x/detection-of-crown-rot-in-wheat-utilising-near-infrared-spectroscopy-towards-remote-and-robotic-sensing

Download files


Submitted Version
SPIE_Humpal_v2_submitted.pdf
File access level: Anyone

  • 72
    total views
  • 69
    total downloads
  • 0
    views this month
  • 2
    downloads this month

Export as

Related outputs

Non-visual common root rot disease detection using NIR spectrum and machine learning methods
Xiong, Yiyi, McCarthy, Cheryl, Humpal, Jacob and Percy, Cassandra. "Non-visual common root rot disease detection using NIR spectrum and machine learning methods." 2023 11th International Conference on Agro-Geoinformatics (Agro-Geoinformatics). Wuhan, China 25 - 28 Jul 2023 IEEE (Institute of Electrical and Electronics Engineers). https://doi.org/https://ieeexplore.ieee.org/xpl/conhome/10233256/proceeding
A review on common root rot of wheat and barley in Australia
Xiong, Yiyi, McCarthy, Cheryl, Humpal, Jacob and Percy, Cassandra. 2023. "A review on common root rot of wheat and barley in Australia." Plant Pathology. 72 (8), pp. 1347-1364. https://doi.org/10.1111/ppa.13777
Evidence for the plant recruitment of beneficial microbes to suppress soil‐borne pathogens
Liu, Hongwei, Li, Jiayu, Carvalhais, Lilia C., Percy, Cassandra D., Verma, Jay Prakash, Schenk, Peer M. and Singh, Brajesh K.. 2021. "Evidence for the plant recruitment of beneficial microbes to suppress soil‐borne pathogens." New Phytologist. 229 (5), pp. 2873-2885. https://doi.org/10.1111/nph.17057
Fusarium pseudograminearum and F. culmorum affect the root system architecture of bread wheat
Saad, Ahmed, Christopher, Jack, Martin, Anke, McDonald, Stephen and Percy, Cassandra. 2023. "Fusarium pseudograminearum and F. culmorum affect the root system architecture of bread wheat." The Crop Journal. 11 (1), pp. 316-321. https://doi.org/10.1016/j.cj.2022.08.013
Investigation of Two QTL Conferring Seedling Resistance to Fusarium Crown Rot in Barley on Reducing Grain Yield Loss under Field Environments
Zheng, Zhi, Powell, Jonathan, Gao, Shang, Percy, Cassandra, Kelly, Alison, Macdonald, Bethany, Zhou, Meixue, Davies, Philip and Liu, Chunji. 2022. "Investigation of Two QTL Conferring Seedling Resistance to Fusarium Crown Rot in Barley on Reducing Grain Yield Loss under Field Environments." Agronomy. 12 (6), pp. 1-14. https://doi.org/10.3390/agronomy12061282
Winter Cereal Reactions to Common Root Rot and Crown Rot Pathogens in the Field
Saad, Ahmed, Macdonald, Bethany, Martin, Anke, Knight, Noel L. and Percy, Cassandra. 2022. "Winter Cereal Reactions to Common Root Rot and Crown Rot Pathogens in the Field." Agronomy. 12 (10), pp. 1-18. https://doi.org/10.3390/agronomy12102571
Review of Current State of Autonomous Technology in Agriculture
Baillie, Craig and Humpal, Jacob. 2021. Review of Current State of Autonomous Technology in Agriculture. Toowoomba, Australia. University of Southern Queensland.
NIR sensing and machine learning to rapidly assess crown rot in wheat
Humpal, Jacob, McCarthy, Cheryl, Percy, Cassandra and Thomasson, J. Alex. 2020. "NIR sensing and machine learning to rapidly assess crown rot in wheat." GRDC Grains Research Update: Driving Profit Through Research. Goondiwindi, Australia 03 - 04 Mar 2020 Australia.
Detection of early infestations of Fall armyworm (FAW) in sweet corn and maize
McCarthy, Alison and Humpal, Jacob. 2021. Detection of early infestations of Fall armyworm (FAW) in sweet corn and maize. Toowoomba, Australia. University of Southern Queensland.
Review of Technologies, Regulations and Operating Standards for Field Based Autonomous Agricultural Machinery
Baillie, Craig, Torrance, Logan, Long, Derek, Brett, Peter and Humpal, Jacob. 2020. Review of Technologies, Regulations and Operating Standards for Field Based Autonomous Agricultural Machinery. Toowoomba, Australia. University of Southern Queensland.
Machine vision learning for crop disease and quality parameters
Humpal, Jacob, McCarthy, Cheryl, Thomasson, J. Alex and Percy, Cassy. 2018. "Machine vision learning for crop disease and quality parameters." 21st Precision Agriculture Symposium (2018). Adelaide, Australia Australia.
Automation: opportunities for adoption in agriculture
Humpal, Jacob and Baillie, Craig. 2022. "Automation: opportunities for adoption in agriculture." GRDC Update Papers.
Space Agriculture: Sensing Crops in Space
Humpal, Jacob, McCarthy, Cheryl, Baillie, Craig, Percy, Cassy and Brett, Peter. 2022. "Space Agriculture: Sensing Crops in Space." GRDC Update Papers.
An improved method for selection of wheat genotypes for tolerance to crown rot caused by Fusarium pseudograminearum
Kelly, Alison, Macdonald, Bethany, Percy, Cassandra and Davies, Philip. 2021. "An improved method for selection of wheat genotypes for tolerance to crown rot caused by Fusarium pseudograminearum." Journal of Phytopathology. 169 (6), pp. 339-349. https://doi.org/10.1111/jph.12970
Preliminary evaluation of real-time sensing of harvester losses by machine vision
McCarthy Chery. 2022. "Preliminary evaluation of real-time sensing of harvester losses by machine vision ." 43rd Annual Conference of the Australian Society of Sugar Cane Technologists (ASSCT 2022). Mackay, Australia 19 - 22 Apr 2022 Australia. Australian Society of Sugar Cane Technologists. pp. 108-110
Comparison of disease severity caused by four soil-borne pathogens in winter cereal seedlings
Saad, Ahmed, Macdonald, Bethany, Martin, Anke, Knight, Noel L. and Percy, Cassandra. 2021. "Comparison of disease severity caused by four soil-borne pathogens in winter cereal seedlings." Crop and Pasture Science. 72 (5), pp. 325-334. https://doi.org/10.1071/cp20245
Disease responses of hexaploid spring wheat (Triticum aestivum) culms exhibiting premature senescence (dead heads) associated with Fusarium pseudograminearum crown rot
Knight, Noel L., Macdonald, Bethany, Percy, Cassy and Sutherland, Mark W.. 2020. "Disease responses of hexaploid spring wheat (Triticum aestivum) culms exhibiting premature senescence (dead heads) associated with Fusarium pseudograminearum crown rot." European Journal of Plant Pathology. 159 (1), pp. 191-202. https://doi.org/10.1007/s10658-020-02158-8
Deep learning - method overview and review of use for fruit detection and yield estimation
Koirala, Anand, Walsh, Kerry B., Wang, Zhenglin and McCarthy, Cheryl. 2019. "Deep learning - method overview and review of use for fruit detection and yield estimation." Computers and Electronics in Agriculture. 162, pp. 219-234. https://doi.org/10.1016/j.compag.2019.04.017
Deep learning for real‑time fruit detection and orchard fruit load estimation: benchmarking of ‘MangoYOLO’
Koirala, A, Walsh, K.B, Wang, Z and McCarthy, C. 2019. "Deep learning for real‑time fruit detection and orchard fruit load estimation: benchmarking of ‘MangoYOLO’." Precision Agriculture. 20 (6), pp. 1107-1135. https://doi.org/10.1007/s11119-019-09642-0
Discrimination of wheat crown rot utilising wavelet based models in the NIR spectrum
Humpal, Jacob. 2020. Discrimination of wheat crown rot utilising wavelet based models in the NIR spectrum. PhD Thesis Doctor of Philosophy. University of Southern Queensland. https://doi.org/10.26192/gkp6-xx10
PREDICTA®B update and new tests for 2018
McKay, Alan, Simpfendorfer, Steven, Gupta, Vadakattu, Bithell, Sean, Moore, Kevin, Daniel, Richard, Percy, Cassy, White, Jo, Sparks, Adam and Hollaway, Grant. 2018. "PREDICTA®B update and new tests for 2018." GRDC Update Papers.
A review of autonomous navigation systems in agricultural environments
Shalal, N., Low, T., McCarthy, C. and Hancock, N.. 2013. "A review of autonomous navigation systems in agricultural environments." SEAg 2013: Innovative Agricultural Technologies for a Sustainable Future. Barton, Australia 22 - 25 Sep 2013
Row and water front detection from UAV thermal-infrared imagery for furrow irrigation monitoring
Long, Derek, McCarthy, Cheryl and Jensen, Troy. 2016. "Row and water front detection from UAV thermal-infrared imagery for furrow irrigation monitoring." 2016 IEEE/ASME International Conference on Advanced Intelligent Mechatronics (AIM 2016). Banff, Canada 12 - 15 Jul 2016 https://doi.org/10.1109/AIM.2016.7576783
Markers for seedling and adult plant crown rot resistance in four partially resistant bread wheat sources
Martin, A., Bovill, W. D., Percy, C. D., Herde, D., Fletcher, S., Kelly, A., Neate, S. M. and Sutherland, M. W.. 2015. "Markers for seedling and adult plant crown rot resistance in four partially resistant bread wheat sources." Theoretical and Applied Genetics: international journal of plant breeding research. 128 (3), pp. 377-385. https://doi.org/10.1007/s00122-014-2437-1
Orchard mapping and mobile robot localisation using on-board camera and laser scanner data fusion – Part B: mapping and localisation
Shalal, Nagham, Low, Tobias, McCarthy, Cheryl and Hancock, Nigel. 2015. "Orchard mapping and mobile robot localisation using on-board camera and laser scanner data fusion – Part B: mapping and localisation." Computers and Electronics in Agriculture. 119, pp. 267-278. https://doi.org/10.1016/j.compag.2015.09.026
Orchard mapping and mobile robot localisation using on-board camera and laser scanner data fusion – Part A: tree detection
Shalal, Nagham, Low, Tobias, McCarthy, Cheryl and Hancock, Nigel. 2015. "Orchard mapping and mobile robot localisation using on-board camera and laser scanner data fusion – Part A: tree detection." Computers and Electronics in Agriculture. 119, pp. 254-266. https://doi.org/10.1016/j.compag.2015.09.025
Evaluation of stereovision for extracting plant features
Mohammed Amean, Z., Low, T., McCarthy, C. and Hancock, N.. 2013. "Evaluation of stereovision for extracting plant features." SEAg 2013: Innovative Agricultural Technologies for a Sustainable Future. Barton, Australia 22 - 25 Sep 2013 Canberra, Australia.
Symptom development and pathogen spread in wheat genotypes with varying levels of crown rot resistance
Malligan, C. D., Sutherland, M. W. and Wildermuth, G. B.. 2009. "Symptom development and pathogen spread in wheat genotypes with varying levels of crown rot resistance." Guest, David (ed.) 17th Biennial Australasian Plant Pathology Society Conference (APPS 2009): Plant Health Management: An Integrated Approach. Newcastle, Australia 29 Sep - 01 Oct 2009 Toowoomba, Australia.
A preliminary evaluation of vision and laser sensing for tree trunk detection and orchard mapping
Shalal, Nagham, Low, Tobias, McCarthy, Cheryl and Hancock, Nigel. 2013. "A preliminary evaluation of vision and laser sensing for tree trunk detection and orchard mapping." Katupitiya, Jayantha, Guivant, Jose and Eaton, Ray (ed.) Australasian Conference on Robotics and Automation (ACRA 2013). Sydney, Australia 02 - 04 Dec 2013 Australia.
Automatic plant branch segmentation and classification using vesselness measure
Mohammed Amean, Z., Low, T., McCarthy, C. and Hancock, N.. 2013. "Automatic plant branch segmentation and classification using vesselness measure." Katupitiya, Jayantha, Guivant, Jose and Eaton, Ray (ed.) Australasian Conference on Robotics and Automation (ACRA 2013). Sydney, Australia 02 - 04 Dec 2013 Australia.
Commercialisation of precision agriculture technologies in the macadamia industry
Rees, Steven, Dunn, Mark, Werkman, Peter and McCarthy, Cheryl. 2009. Commercialisation of precision agriculture technologies in the macadamia industry. Toowoomba, Australia. University of Southern Queensland.
Preliminary evaluation of shape and colour image sensing for automated weed identification in sugarcane
McCarthy, Cheryl, Rees, Steven and Baillie, Craig. 2012. "Preliminary evaluation of shape and colour image sensing for automated weed identification in sugarcane." Bruce, R. C. (ed.) 34th Annual Conference of the Australian Society of Sugar Cane Technologists (ASSCT 2012). Palm Cove, Australia 01 - 04 May 2012 Australia.
Symptom development proceeds at different rates in susceptible and partially resistant cereal seedling infected with Fusarium pseudograminearum
Percy, C. D., Wildermuth, G. B. and Sutherland, M. W.. 2012. "Symptom development proceeds at different rates in susceptible and partially resistant cereal seedling infected with Fusarium pseudograminearum." Australasian Plant Pathology. 41 (6), pp. 621-631. https://doi.org/10.1007/s13313-012-0146-2
Development and evaluation of a prototype precision spot spray system using image analysis to target guinea grass in sugarcane
Rees, S. J., McCarthy, C. L., Baillie, C. P., Burgos-Artizzu, X. P. and Dunn, M. T.. 2011. "Development and evaluation of a prototype precision spot spray system using image analysis to target guinea grass in sugarcane." Australian Journal of Multi-Disciplinary Engineering. 8 (2), pp. 97-106.
Automated internode length measurement of cotton plants under field conditions
McCarthy, C. L., Hancock, N. H. and Raine, S. R.. 2009. "Automated internode length measurement of cotton plants under field conditions." Transactions of the ASABE. 52 (6), pp. 2093-2103.
On-the-go machine vision sensing of cotton plant geometric parameters: first results
McCarthy, Cheryl, Hancock, Nigel and Raine, Steven. 2008. "On-the-go machine vision sensing of cotton plant geometric parameters: first results." Billingsley, John and Bradbeer, Robin (ed.) 13th Annual Conference on Mechatronics and Machine Vision in Practice. (M2VIP 2006). Toowoomba, Australia 05 - 07 Dec 2006 Germany. pp. 305-312 https://doi.org/10.1007/978-3-540-74027-8_26
Development of molecular markers for crown rot resistance in wheat: mapping of QTLs for seedling resistance in a '2-49' x 'Janz' population
Collard, B. C. Y., Grams, R. A., Bovill, W. D., Percy, C. D., Jolley, R., Lehmensiek, A., Wildermuth, G. B. and Sutherland, M. W.. 2005. "Development of molecular markers for crown rot resistance in wheat: mapping of QTLs for seedling resistance in a '2-49' x 'Janz' population." Plant Breeding. 124 (6), pp. 532-537. https://doi.org/10.1111/j.1439-0523.2005.01163.x
Infection of wheat tissues by fusarium pseudograminearum
Knight, N. L., Percy, C., Lehmensiek, A., Herde, D. J. and Sutherland, M. W.. 2008. "Infection of wheat tissues by fusarium pseudograminearum." Appels, Rudi (ed.) 11th International Wheat Genetics Symposium 2008 (IWGS 2008). Brisbane, Australia 24 - 29 Aug 2008 Sydney, Australia.
Applied machine vision of plants: a review with implications for field deployment in automated farming operations
McCarthy, C. L., Hancock, N. H. and Raine, S. R.. 2010. "Applied machine vision of plants: a review with implications for field deployment in automated farming operations." Intelligent Service Robotics. 3 (4), pp. 209-217. https://doi.org/10.1007/s11370-010-0075-2
Machine vision-based weed spot spraying: a review and where next for sugarcane?
McCarthy, Cheryl, Rees, Steven and Baillie, Craig. 2010. "Machine vision-based weed spot spraying: a review and where next for sugarcane?" Bruce, R. C. (ed.) 32nd Annual Conference of the Australian Society of Sugar Cane Technologists (ASSCT 2010). Bundaberg, Australia 11 - 14 May 2010 Australia.
Apparatus and infield evaluations of a prototype machine vision system for cotton plant internode length measurement
McCarthy, Cheryl, Hancock, Nigel and Raine, Steven R.. 2010. "Apparatus and infield evaluations of a prototype machine vision system for cotton plant internode length measurement." Journal of Cotton Science. 14 (4), pp. 221-232.
Applied machine vision in agriculture at the NCEA
McCarthy, Cheryl and Billingsley, John. 2009. "Applied machine vision in agriculture at the NCEA." Banhazi, T. M. and Saunders, C. (ed.) SEAg 2009: Agricultural Technologies In a Changing Climate. Brisbane, Australia 13 - 16 Sep 2009 Brisbane, Australia.
Cattle liveweight estimation using machine vision assessment of objective body measurements: first results
McCarthy, C., Billingsley, J., Finch, N., Murray, P. and Gaughan, J.. 2010. "Cattle liveweight estimation using machine vision assessment of objective body measurements: first results." 28th Biennial Australian Society of Animal Production Conference. Armidale, Australia 11 - 15 Jul 2010 Brisbane, Australia.
Development of a prototype precision spot spray system using image analysis and plant identification technology
Rees, Steven, McCarthy, Cheryl, Artizzu, X. P. B., Baillie, Craig and Dunn, Mark. 2009. "Development of a prototype precision spot spray system using image analysis and plant identification technology." Banhazi, T. M. and Saunders, C. (ed.) SEAg 2009: Agricultural Technologies In a Changing Climate. Brisbane, Australia 13 - 16 Sep 2009 Brisbane, Australia.
A preliminary field evaluation of an automated vision-based plant geometry measurement system
McCarthy, Cheryl, Hancock, Nigel and Raine, Steven R.. 2007. "A preliminary field evaluation of an automated vision-based plant geometry measurement system." Prusinkiewicz, Przemyslaw, Hanan, Jim S. and Lane, Brendan (ed.) 5th International Workshop on Functional Structural Plant Models (FSPM07). Napier, New Zealand 04 - 09 Nov 2007
Automated machine vision sensing of plant structural parameters
McCarthy, C. L., Hancock, Nigel and Raine, Steven R.. 2007. "Automated machine vision sensing of plant structural parameters." Biological Sensorics 2007: Critical Technologies for Future Biosystems. Minneapolis, Australia 15 - 17 Jun 2007 St. Joseph, MI, United States.
The application of molecular markers for partial resistance against fusarium crown rot in hexaploid and tetraploid wheats
Sutherland, Mark, Bovill, W. D., Horne, M., Lehmensiek, A., Eberhard, F., Percy, C., Wildermuth, G. B., Simpfendorfer, S. and Hare, R.. 2008. "The application of molecular markers for partial resistance against fusarium crown rot in hexaploid and tetraploid wheats." 10th International Fusarium and Fusarium Genomics Workshop 2008. Sardinia, Italy 30 Aug - 02 Sep 2008 Sardinia,Italy.
On-the-go machine vision sensing of cotton plant geometric parameters: first results
McCarthy, Cheryl, Hancock, Nigel and Raine, Steven R.. 2006. "On-the-go machine vision sensing of cotton plant geometric parameters: first results." Billingsley, John (ed.) 13th Annual Conference on Mechatronics and Machine Vision in Practice. (M2VIP 2006). Toowoomba, Australia 05 - 07 Dec 2006 Berlin, Heidelberg.
A preliminary evaluation of machine vision sensing of cotton nodes for automated irrigation control
McCarthy, Cheryl, Hancock, Nigel and Raine, Steven R.. 2006. "A preliminary evaluation of machine vision sensing of cotton nodes for automated irrigation control." Irrigation Australia 2006: Irrigation Association of Australia National Conference and Exhibition. Brisbane, Australia 09 - 11 May 2006 Brisbane.
Effectiveness of partial resistance sources in hexaploid wheats against fusarium pseudograminearum isolates
Percy, C. D., Wildermuth, G. B. and Sutherland, Mark W.. 2005. "Effectiveness of partial resistance sources in hexaploid wheats against fusarium pseudograminearum isolates." Cahill, David (ed.) 15th Biennial Australasian Plant Pathology Society Conference. Geelong, Australia 26 - 29 Sep 2005 Geelong, Australia.