Plant phenomics & precision agriculture simulation of winter wheat growth by the assimilation of unmanned aerial vehicle imagery into the WOFOST model

Tianle Yang; Weijun Zhang; Tong Zhou; Wei Wu; Tao Liu; Chengming Sun

doi:10.1371/journal.pone.0246874

Peer Review History

Original SubmissionSeptember 14, 2020
13 Nov 2020 Decision Letter - Abel Chemura, Editor PONE-D-20-28606 Simulation of winter wheat growth by the assimilation of unmanned aerial vehicle imagery into the WOFOST model PLOS ONE Dear Dr. Sun, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. There is need for more information for making the WOFOST modelling more transparent to the reader by adding the used parameters and settings.In addition, the authors should describe in detail the extraction of LAI from UAV imaging and how accurate that process it. Please submit your revised manuscript by Dec 28 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. 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Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: I Don't Know ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: his paper represents a study of simulation of winter wheat growth by the assimilation of unmanned aerial vehicle imagery into the WOFOST model at the finer spatial resolution. And readers are very interested in the topic. Generally, this paper is well written, some comments can be found as followed, (1) Suggest conduct an sensitivity analysis to determine the optimized parameters, I think that specific leaf area (SLATB0, SLATB0.5, SLATB2) and maximum CO2 assimilation rate (AMAXTB1, AMAXTB1.3) is not suitable for reinitialized because CO2 assimilation rates are relative constant values for wheat. (2) I didn’t see how the retrieve the LAI from UAV imagery and evaluation of accuracy of LAI. More texts need to be added to clarify this point. (3) The uncertainty of observation and model in the assimilation method. This actually to be very important for improving the performance of DA. More texts need to be added to clarify this issue. (4) I suggest that don’t cite the Chinese papers in the manuscript, because English readers are not easy to understand the content of Chinese papers. Meanwhile added the latest DA literature to support your viewpoint. (1) Huang et al.,. Assimilation of remote sensing into crop growth models: current status and perspectives. Agricultural and Forest Meteorology. 276-277, 2019,107609. (2) Jianxi Huang et al., Evaluation of regional estimates of winter wheat yield by assimilating three remotely sensed reflectance datasets into the coupled WOFOST–PROSAIL model. European Journal of Agronomy. 2019,102, pp.1-13;(3) Jianxi Huang et al., Assimilating a synthetic Kalman filter leaf area index series into the WOFOST model to estimate regional winter wheat yield. Agricultural and Forest Meteorology. 216, 2016. pp.188-202. (4) Jianxi Huang, Hongyuan Ma, Wei Su, Xiaodong Zhang， Yanbo Huang, Jinlong Fan, Wenbin Wu. Jointly assimilating MODIS LAI and ET products into the SWAP model to estimate winter wheat yield. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing. 8(8), 2015.pp. 4060--4071. (5) Wen Zhuo et al., Assimilating Soil Moisture Retrieved from Sentinel-1 and Sentinel-2 Data into WOFOST Model to Improve Winter Wheat Yield Estimation. Remote Sens. 2019, 11(13), 1618 (5) English of this paper need to be further polished by professional editor. Reviewer #2: Review for Plos One Title : Simulation of winter wheat growth by the assimilation of unmanned aerial vehicle imagery into the WOFOST model 1. Introduction It is written in lines 48-50 that the parameter optimization method is superior in terms of assimilation results. This statement should be clearly explained and supported by a bundle of citations. To the knowledge of the Reviewer, other methods such as updating method using EnKF have quite high performance especially in the consideration of the measurement uncertainties. In addition, the operability of the proposed assimilation method should be adequately discussed? When do we acquire data to assimilate them during the growing season? The originality of this contribution relies on the fact that, although UAV is widely used in crop monitoring, most studies related to assimilation methods use high-altitude remote sensing (RS) and not UAV data. The interest of UAV-based RS should be better highlighted in terms of scales, operability, spatial and temporal resolution with respect to, for instance, satellite-based RS. In the introductive section, the proposed research work should be better detailed and supported by the state of the art in order to specify the scientific objectives with regard to the considered material and methods. For the Reviewer, the formulation of the paper objectives are too general. 2. Material and methods The material and methods section appears not complete enough to better understand the research scope and limitations of the proposed method. Why two experiments are considered in response to the research objectives? The measurement methods for LAI and crop yield are not described at all, which renders difficult the interpretation of the results. Also, please give the crop density in terms of grains per meter square. Although WOFOST is quite known in the community, the key principle of modelling, the considered assumptions and values of major parameters (line 191) should be given for the sake of completeness and research reproducibility. Also, please give the definition of R2 in Equation 1. The extraction of LAI from UAV imaging is not described. This is a critical point to explain, present and discuss in terms of methodology, operability and accuracy. What are the sensors used? What is the altitude? What is the regression? … It is not clear for the Reviewer when data assimilation is performed. Is it at each remotely sensed LAI? If so, this should be better highlighted via a Figure. Is it necessary to perform assimilation at all measurement point? Equation 4 and 5 are not mathematically valid. Please adapt them. Line 199, please correct “A comparison in made in …” Line 203, please define earlier in the paper the notion of localized model. Line 227, please give the definition of the confidence interval. Line 273, CRM is negative 3. Discussion The scale of the study should be criticized. The Authors present their model as valid at the regional scale. Is it realistic with UAV technology? ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0246874.r001
Revision 1
6 Jan 2021 Author Response Reviewer #1: his paper represents a study of simulation of winter wheat growth by the assimilation of unmanned aerial vehicle imagery into the WOFOST model at the finer spatial resolution. And readers are very interested in the topic. Generally, this paper is well written, some comments can be found as followed, (1)Suggest conduct an sensitivity analysis to determine the optimized parameters, I think that specific leaf area (SLATB0, SLATB0.5, SLATB2) and maximum CO2 assimilation rate (AMAXTB1, AMAXTB1.3) is not suitable for reinitialized because CO2 assimilation rates are relative constant values for wheat. R: The parameters for initialization adjustment in this article are all determined by the results of sensitivity analysis. Taking into account the local varieties and cultivation measures, compare the leaf area and the maximum CO2 assimilation rate (AMAXTB1, AMAXTB1.3) for reinitialization to make the results more accurate. (2) I didn’t see how the retrieve the LAI from UAV imagery and evaluation of accuracy of LAI. More texts need to be added to clarify this point. R: The extraction of LAI from UAV images and the content of LAI accuracy evaluation have been explained in detail in another article. (3) References R: Replaced Reviewer #2: Review for Plos One 1. Introduction It is written in lines 48-50 that the parameter optimization method is superior in terms of assimilation results. This statement should be clearly explained and supported by a bundle of citations. To the knowledge of the Reviewer, other methods such as updating method using EnKF have quite high performance especially in the consideration of the measurement uncertainties. In addition, the operability of the proposed assimilation method should be adequately discussed? When do we acquire data to assimilate them during the growing season? The originality of this contribution relies on the fact that, although UAV is widely used in crop monitoring, most studies related to assimilation methods use high-altitude remote sensing (RS) and not UAV data. The interest of UAV-based RS should be better highlighted in terms of scales, operability, spatial and temporal resolution with respect to, for instance, satellite-based RS. In the introductive section, the proposed research work should be better detailed and supported by the state of the art in order to specify the scientific objectives with regard to the considered material and methods. For the Reviewer, the formulation of the paper objectives is too general. R: (1) The parameter optimization method mentioned in this article is actually a general term for EnKF, SAA, and ordinary least squares. In the research, ordinary least squares were selected. (2) This study mainly carried out data acquisition in the five key stages of wheat growth: jointing stage, heading stage, flowering stage, filling stage, and mature stage. 2. Material and methods The material and methods section appears not complete enough to better understand the research scope and limitations of the proposed method. Why two experiments are considered in response to the research objectives? The measurement methods for LAI and crop yield are not described at all, which renders difficult the interpretation of the results. Also, please give the crop density in terms of grains per meter square. Although WOFOST is quite known in the community, the key principle of modelling, the considered assumptions and values of major parameters (line 191) should be given for the sake of completeness and research reproducibility. Also, please give the definition of R2 in Equation 1. The extraction of LAI from UAV imaging is not described. This is a critical point to explain, present and discuss in terms of methodology, operability and accuracy. What are the sensors used? What is the altitude? What is the regression? … It is not clear for the Reviewer when data assimilation is performed. Is it at each remotely sensed LAI? If so, this should be better highlighted via a Figure. Is it necessary to perform assimilation at all measurement point? Equation 4 and 5 are not mathematically valid. Please adapt them. Line 199, please correct “A comparison in made in …” Line 203, please define earlier in the paper the notion of localized model. Line 227, please give the definition of the confidence interval. Line 273, CRM is negative R: (1) The data of the second year is used to verify the results; (2) The leaf area index measurement method: 15 plants were sampled in the experimental plot, and the length and width coefficient method was used to determine the leaf area, and then the specific leaf weight method was used to calculate the leaf area index. Yield measurement: In the mature period of wheat, the number of ears per unit area was investigated in each plot, and 30 single ears were taken for indoor experiment to calculate the three factors of yield (number of ears, number of grains per ear, and thousand-grain weight). Take 1m2 area of wheat from each plot, thresh and test the yield. (3) In this study, the inspire 1RAW drone produced by DJI is equipped with a Zenmuse X5R aerial camera for data collection. The flying height of the drone is 9 meters. (4) What is regression (5) The localized model refers to the adjustment of related parameters so that the model can simulate the growth of wheat in the study area. (6) This study mainly carried out data acquisition and assimilation in five key stages of wheat growth: jointing stage, heading stage, flowering stage, filling stage, and mature stage. 3. Discussion The scale of the study should be criticized. The Authors present their model as valid at the regional scale. Is it realistic with UAV technology? R: The combination of UAV remote sensing and WOFOST model is applied to the simulation of crop agronomic parameters. This method is still in the exploratory stage. Cheng et al. used a combination of multispectral UAV and WOFOST model to estimate corn yield. This proves that this method is feasible. (Cheng Z, Meng J, Shang J, et al. Generating Time-Series LAI Estimates of Maize Using Combined Methods Based on Multispectral UAV Observations and WOFOST Model[J]. Sensors, 2020, 20(6006):6006.) Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0246874.r002
28 Jan 2021 Decision Letter - Abel Chemura, Editor Simulation of winter wheat growth by the assimilation of unmanned aerial vehicle imagery into the WOFOST model PONE-D-20-28606R1 Dear Dr. Sun, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Abel Chemura Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors made a good revision following reviewers's comments and the manuscript is greatly improved. The manuscript can be accepted for publication in present form. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No https://doi.org/10.1371/journal.pone.0246874.r003
Formally Accepted
30 Sep 2021 Acceptance Letter - Abel Chemura, Editor PONE-D-20-28606R1 Plant Phenomics & Precision Agriculture Simulation of winter wheat growth by the assimilation of unmanned aerial vehicle imagery into the WOFOST model Dear Dr. Sun: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Abel Chemura Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0246874.r004

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