Академический Документы
Профессиональный Документы
Культура Документы
Abstract
Background: Unmanned aerial vehicles (UAVs) equipped with lightweight sensors are making a significant impact
in field-based crop phenotyping. UAV platforms have been successfully deployed to acquire phenotypic data in a pre-
cise and efficient manner that would otherwise be time-consuming and costly to acquire when undertaken through
manual assessment. One example is the estimation of plant density (or counts) in field experiments. Challenges posed
to digital plant counting models are heterogenous germination and mixed growth stages that are present in field
experiments with diverse genotypes. Here we describe, using safflower as an example, a method based on template
matching for seedling count estimation at early mixed growth stages using UAV imagery.
Results: An object-based image analysis algorithm based on template matching was developed for safflower seed-
ling detection at early mixed growth stages in field experiments conducted in 2017 and 2018. Seedling detection
was successful when tested using a grouped template type with 10 subgroups representing safflower at 2–4 leaves
growth stage in 100 selected plots from the 2017 field experiment. The algorithm was validated for 300 plots each
from the 2017 and 2018 field experiments, where estimated seedling counts correlated closely with manual counting;
R2 = 0.87, MAE = 8.18, RSME = 9.38 for 2017 field experiment and R2 = 0.86, MAE = 9.16, RSME = 10.51 for 2018.
Conclusion: A method for safflower seedling count at early mixed growth stages using UAV imagery was developed
and validated. The model performed well across heterogenous growth stages and has the potential to be used for
plant density estimation across various crop species.
Keywords: Object-based image analysis, Plant phenotyping, Safflower, Seedling count, Unmanned aerial vehicle
© The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License
(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium,
provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license,
and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/
publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Koh et al. Plant Methods (2019) 15:64 Page 2 of 9
Image pre‑processing and orthomosaic The grouped template for safflower seedling was then
White balance correction for acquired images was per- applied to this safflower image layer and matches with
formed in Adobe Lightroom CC and the images were a correlation coefficient of > 0.36 were classified as saf-
geo-tagged using the 3DR Solo flight log in the free- flower seedling. The remaining matches were excluded
ware, GeoSetter version 3.4. Images were then imported as background i.e. soil, weeds or non-safflower plants.
into Pix4D Mapper version 4.2 to generate orthomosaic Further fine-tuning of the template matching accu-
image, with the coordinates of the GCPs used for geo- racy was achieved by optimising the template matching
rectification. Orthomosaic RGB images generated for the stringency/threshold. Finally, safflower seedlings were
safflower experiments had a ground sampling distance exported as a point shapefile. Primary outputs from the
(GSD) of approximately 0.19 cm/pixel. OBIA algorithm are shown in Fig. 3.
Fig. 2 Flowchart of the OBIA algorithm for safflower plant classification and seedling detection. The OBIA algorithm consists of two main parts:
safflower plant classification and seedling template matching. The final product is a point shapefile corresponding to safflower seedlings which is
imported into the ArcGIS Pro software
for safflower seedlings. Results indicated that appreci- (R = 0.584), 10 (R = 0.628) and 15 (R = 0.631) subgroups.
able gains in template quality were observed when tran- The grouped template with 10 subgroups was selected for
sitioning from single to grouped template types with 5 further optimisation as improvement in template quality
Koh et al. Plant Methods (2019) 15:64 Page 5 of 9
Fig. 3 Graphical overview of the image analysis pipeline for safflower seedling count estimation. Examples of the primary outputs in the pipeline
are presented at the plot level. Classified safflower plants (indicated in teal) are subjected to a grouped seedling template matching and detected
seedlings (indicated in red) are exported as a point shapefile into ArcGIS Pro software for plot-level summary (plots outlined in blue) of seedling
counts
was negligible (< 0.05%) with 15 subgroups which entails 0.6; threshold of 1.0 being a perfect match) on perfor-
a higher computational cost and longer processing time mance was tested. Safflower seedling count estimated
in template matching. with a template matching threshold of 0.5 had the
The performance of the template matching algo- best accuracy (R2 = 0.8668, MAE = 6.94, RSME = 9.23)
rithm was evaluated initially on 100 plots from the compared to a threshold of 0.4 (R2 = 0.8441,
2017 field experiment (Fig. 4). The effect of three tem- MAE = 11.44, RSME = 14.11) or a threshold of 0.6
plate matching stringencies (thresholds = 0.4, 0.5 and (R2 = 0.8149, MAE = 21.88, RSME = 24.06) (Fig. 4).
Koh et al. Plant Methods (2019) 15:64 Page 6 of 9
Fig. 4 Performance of plant count estimation under different template matching stringencies. Template matching thresholds of 0.4, 0.5 and 0.6
were evaluated on 100 plots from the 2017 field experiment. Estimated (digital) plant counts were compared to manual plant count
Fig. 5 Performance of plant count estimation for field experiments. Plant count was estimated (digital) for 300 plots each for 2017 and 2018
experiments and compared to those obtained by manual counting. Red line indicates the 1:1 line
visual verification of outputs. Perhaps the most attrac- a significant impact on the performance of the seed-
tive feature of the OBIA algorithm is its potential to be ling count models [8, 17]. In comparison, results in
deployed onto crops with heterogenous germination and this study indicate that the OBIA algorithm was able to
contrasting growth stages, something often seen in field detect safflower seedlings at various growth stages from
experiments with diverse genotypes or different treat- 2 to 4 leaves, largely due to the grouped template (10
ments such as varying watering or nutrient regimes. In subgroups) approach which accounts for different seed-
both wheat and rapeseed studies, the growth stage had ling growth types. Combined with the strategy of using
Koh et al. Plant Methods (2019) 15:64 Page 8 of 9
Fig. 6 Safflower seedling detection over areas with high plant overlap. Magnified views (× 1.5) of an area with safflower seedling clusters before
(a) and after (b) safflower seedling detection. Hits following template matching are indicated by red diamonds (13 plants). In contrast, manual
counting based on image is 17 plants
classified image layers containing only safflower plant determine the performance of seedling count estima-
objects as input for template matching, seedling count tion under high plant densities, particularly for differ-
estimation correlated closely with manual counts for ent safflower cultivation practises or when adopting this
both 2017 (R2 = 0.8786) and 2018 (R2 = 0.8615) experi- method for other densely sown crop species. For crops
ments. These results are comparable to the performance with small seedling and high overlaps, assuming a fairly
of seedling count models published for other crop species uniform germination and growth stage, machine learn-
[7, 8, 14–17]. ing approaches using spectral, texture and morphological
A common challenge in seedling count models is the features may be better suited for seedling count estima-
separation of plant from background, especially when tion [7, 8, 17]. However, even for seedling count models
green weeds are present. Methods employing classifica- based on machine learning approaches, complex situa-
tion based on colour [18] and shape [19] were success- tions arising from high plant overlaps remain a challenge
ful in weed identification and separation from plants. [17]. Nevertheless, the OBIA algorithm developed for
The ability to generate an image layer consisting purely safflower seedling count estimation will facilitate high-
of safflower plant objects was crucial to the success of the throughput and reliable data collection for field experi-
OBIA algorithm in this study. Although weeds were well- ments using UAV-acquired RGB imagery. Furthermore,
controlled in our field experiments, the first part of the this method could find wider application in other crop
OBIA algorithm (plant classification) can be extended to species, particularly dicot plants with seedlings similar
incorporate a myriad of segmentation and classification to safflower. This will result in significant time and cost
algorithms to achieve satisfactory plant separation from savings for large-scale agronomic and breeding field
the background in the event of a weed infestation using experiments with diverse genotypes or treatments where
spectral and spatial information, for example combining seedling count is a required phenotypic observation.
data from multiple sensors such as RGB, multispectral
and LiDAR. Conclusions
Although germination rates varied significantly A method for safflower seedling count estimation at early
between safflower genotypes and across experiments, the stages based on UAV-acquired RGB imagery was devel-
OBIA algorithm performed well across a wide range of oped and validated in this study. The method employs
seedling densities. Results from our study indicate that an OBIA algorithm based on template matching for saf-
the performance of seedling count estimation reduces flower seedling detection. Results indicate that the OBIA
slightly over areas with high plant overlaps, such as in algorithm performed well even when seedlings with con-
tight clusters. As such, further studies are required to trasting growth stages were present and has the potential
Koh et al. Plant Methods (2019) 15:64 Page 9 of 9
to be adopted for use in other crop species. This method 5. Madec S, Baret F, de Solan B, Thomas S, Dutartre D, Jezequel S, Hem-
merlé M, Colombeau G, Comar A. High-throughput phenotyping of
will facilitate high-throughput data collection for field plant height: comparing unmanned aerial vehicles and ground LiDAR
experiments using UAV platforms. estimates. Front Plant Sci. 2017;8:2002.
6. Watanabe K, Guo W, Arai K, Takanashi H, Kajiya-Kanegae H, Kobayashi M,
Acknowledgements Yano K, Tokunaga T, Fujiwara T, Tsutsumi N, et al. High-throughput pheno-
We thank Jignesh Vakani and Dennis Ward for technical support in conduct- typing of sorghum plant height using an unmanned aerial vehicle and its
ing field experiments and Emily Thoday-Kennedy for critical reading of the application to genomic prediction modeling. Front Plant Sci. 2017;8:421.
manuscript. 7. Jin X, Liu S, Baret F, Hemerlé M, Comar A. Estimates of plant density of
wheat crops at emergence from very low altitude UAV imagery. Remote
Authors’ contributions Sens Environ. 2017;198:105–14.
JCOK—designed the method and analysed the data; MH, SK, HD, JCOK— 8. Zhao B, Zhang J, Yang C, Zhou G, Ding Y, Shi Y, Zhang D, Xie J, Liao Q.
conceived and designed the experiments; SK—managed the field experi- Rapeseed seedling stand counting and seeding performance evaluation
ments; JCOK, SK, HD, MH—wrote and edited the paper. All authors read and at two early growth stages based on unmanned aerial vehicle imagery.
approved the final manuscript. Front Plant Sci. 2018;9:1362.
9. Food and agriculture data, FAOSTAT. Food and Agriculture Organisation
Funding of the United Nations. 2016. http://www.fao.org/faostat/en/#data/QC.
This study is funded by the Australian Federal, Cooperative Research Centre Accessed 13 Dec 2018.
Project CRC-P54024. 10. Wood CC, Okada S, Taylor MC, Menon A, Matthew A, Cullerne D, Stephen
SJ, Allen RS, Zhou XR, et al. Seed-specific RNAi in safflower generates a
Availability of data and materials superhigh oleic oil with extended oxidative stability. Plant Biotechnol J.
All data generated or analysed during this study are included in this published 2018;16(10):1788–96.
article. 11. SHO safflower case study. In: biobased oils. Commonwealth Scientific and
Industrial Research Organisation. 2018. https://www.csiro.au/en/Resea
Ethics approval and consent to participate rch/AF/Areas/Plant-Science/Bio-based-oils/SHO-safflower. Accessed 13
Not applicable. Dec 2018.
12. Collis B. Hopes for new industry from safflower ‘reinvention’. In: Ground-
Consent for publication Cover. Grains Research and Development Corporation. 2018. https://
Not applicable. grdc.com.au/resources-and-publications/groundcover/groundcover-133-
march-april-2018/hopes-for-new-industry-from-safflower-reinvention.
Competing interests Accessed 13 Dec 2018.
The authors declare that they have no competing interests. 13. Safflower northern region. In: GrowNotes. Grains Research and Develop-
ment Corporation. 2017. https://grdc.com.au/resources-and-publicatio
Author details ns/grownotes/crop-agronomy/safflowergrownotesnorth. Accessed 13
1
Agriculture Victoria, Grains Innovation Park, 110 Natimuk Rd, Horsham, VIC Dec 2018.
3400, Australia. 2 Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring 14. Gnädinger F, Schmidhalter U. Digital counts of maize plants by
Road, Bundoora, VIC 3083, Australia. 3 School of Applied Systems Biology, La unmanned aerial vehicles (UAVs). Remote Sens. 2017;9(6):544.
Trobe University, Bundoora, VIC 3086, Australia. 15. Chen R, Chu T, Landivar JA, Yang C, Maeda MM. Monitoring cotton (Gos-
sypium hirsutum L.) germination using ultrahigh-resolution UAS images.
Received: 9 April 2019 Accepted: 13 June 2019 Precis Agric. 2018;19(1):161–77.
16. Sankaran S, Quirós JJ, Knowles NR, Knowles LO. High-resolution aerial
imaging based estimation of crop emergence in potatoes. Am J Potato
Res. 2017;94(6):658–63.
17. Liu S, Baret F, Andrieu B, Burger P, Hemmerlé M. Estimation of wheat plant
References density at early stages using high resolution imagery. Front Plant Sci.
1. Yang G, Liu J, Zhao C, Li Z, Huang Y, Yu H, Xu B, Yang X, Zhu D, Zhang X, 2017;8:739.
et al. Unmanned aerial vehicle remote sensing for field-based crop phe- 18. Gée C, Bossu J, Jones G, Truchetet F. Crop/weed discrimination in per-
notyping: current status and perspectives. Front Plant Sci. 2017;8:1111. spective agronomic images. Comput Electron Agric. 2008;60(1):49–59.
2. Zhang C, Kovacs JM. The application of small unmanned aerial systems 19. Swain KC, Nørremark M, Jørgensen RN, Midtiby HS, Green O. Weed iden-
for precision agriculture: a review. Precis Agric. 2012;13(6):693–712. tification using an automated active shape matching (AASM) technique.
3. Holman F, Riche A, Michalski A, Castle M, Wooster M, Hawkesford M. Biosyst Eng. 2011;110(4):450–7.
High throughput field phenotyping of wheat plant height and growth
rate in field plot trials using UAV based remote sensing. Remote Sens.
2016;8(12):1031. Publisher’s Note
4. Ludovisi R, Tauro F, Salvati R, Khoury S, Mugnozza Scarascia G, Harfouche Springer Nature remains neutral with regard to jurisdictional claims in pub-
A. UAV-based thermal imaging for high-throughput field phenotyping of lished maps and institutional affiliations.
black poplar response to drought. Front Plant Sci. 2017;8:1681.