Inversion modeling of japonica rice canopy chlorophyll content with UAV hyperspectral remote sensing

Yingli Cao; Kailun Jiang; Jingxian Wu; Fenghua Yu; Wen Du; Tongyu Xu

doi:10.1371/journal.pone.0238530

Peer Review History

Original SubmissionMarch 27, 2020
13 May 2020 Decision Letter - Wang Li, Editor PONE-D-20-07987 Inversion Modeling of Japonica Rice Canopy Chlorophyll Content with UAV Hyperspectral Remote Sensing PLOS ONE Dear Dr Xu, 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. Editor's Comment: As an international journal, PLOS ONE aims to publish studies in a broad international community which should be reflected in any part of the paper. Thus, in addition to the comments from the reviewers, I suggest the authors update their references in a more balanced review as I saw that most of the cited literatures are published by Chinese authors or Chinese journals. 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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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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: Yes ****** 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: In this work, the possible use of UAV-HSI to predict the Chlorophyll content was evaluated. However, several questions should be explained or improved, including the writing expression, they are listed below: 1. Why use the HSI combined with UVA to detect the chlorophyll content? The introduction of significance of this work should be improved, especially in Section Introduction and Section Discussion. 2. The data processing without any black-white correction is not enough rigorous. Raw data from HSI contains tremendous amount of information including samples and noises. It’s very important to eliminate the interference of the natural lighting (or weather conditions) in this work. So, in my opinion, the system with BW correction can promote the applicability of UAV-HSI. 3. From the figures 4 to 6, the spectral reflectance in the range of 400 and 450 nm was lower than 0.1, which means low SNR (Signal to noise ratio) in this wavelengths, why did the authors still use the data to do further analysis? 4. For the selection of key spectral wavelengths, normally one detect the OD values at 663 nm and 645 nm with spectrophotometer, and then calculate the values with equations to describe the contents of chlorophyll contents, and thus these two wavelengths should be selected as key wavelengths. 5. Large area of the paddy field were selected as regions of interest, why only four japonica rice plants in test plots were used for chemical experiments? 6. The sample division for calculated and predicted datasets should be explained and provided in the manuscript. 7. Method for UAV-HSI data acquisition is unclear. 8. Unit for RMSE should be provided. 9. Why PSO-ELM was employed? 10. It would be better if authors can discuss the actual values and practical challenges of the UVA-HSI in modeling of chlorophyll content prediction. Reviewer #2: The topic of this work is very interesting for the scientific community in the field of Remote Sensing. The monitoring of rice via remote sensing is of vital importance for food and environmental security in a global context, including growth status, yield predictions, area estimates, agricultural insurance and so on. The chlorophyll content is an important indicator of the growth status of rice. The inversion rice chlorophyll content has already been carried out many times using handheld spectroradiometer. However, in this work, the authors access rice canopy chlorophyll content using hyperspectral imaging sensor with UAV platform which can be more efficient and better synchronization. The goals of the paper are very clear and very interesting, and they are obtained in a better way that can be useful. The manuscript is very well written, and I think that it is worthy to be published in this journal after revised. However, there are some questions and considerations that I would like the authors explain in the manuscript. I already marked some comment in the pdf document. ****** 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-20-07987_reviewer-.pdf https://doi.org/10.1371/journal.pone.0238530.r001
Revision 1
3 Jul 2020 Author Response We would like to thank the editor and the reviewers for their careful reviews and high quality review comments, which have significantly helped us revise and improve the quality of the paper. The comments are very constructive and extremely helpful during the revision process. All of the reviewers' comments have been addressed in the revised version. A detailed point-by-point response has been included in a separate document: “Response to Reviewers”. All modifications made in the paper has been highlighted in yellow. Attachments Attachment Submitted filename: response.pdf https://doi.org/10.1371/journal.pone.0238530.r002
31 Jul 2020 Decision Letter - Wang Li, Editor PONE-D-20-07987R1 Inversion Modeling of Japonica Rice Canopy Chlorophyll Content with UAV Hyperspectral Remote Sensing PLOS ONE Dear Dr. Tongyu Xu, 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. You will see from the below comments that the reviewer 1 still have some questions for you to further improve the paper. Please submit your revised manuscript by 13th August 2020. 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. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Wang Li Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 Reviewer #2: 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 Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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: Is it a mistake saying the hyperspectral band range is 400 to 100 nm and with a 3 nm resolution? Why the number of effective bands is 253? Please have a check and make necessary changes (100-1000 nm) . Although the authors added some references (33-38), it would be better to discuss further or compare your results with the published data. Reviewer #2: (No Response) ****** 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 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.0238530.r003
Revision 2
14 Aug 2020 Author Response Response to Comments of Reviewer Thanks for your careful review and valuable comments for the improvement of this paper. The authors appreciate your detailed comments and valuable suggestions on the technical contents. Your technical concerns and suggestions are addressed as follows. 1. Is it a mistake saying the hyperspectral band range is 400 to 100 nm and with a 3 nm resolution? Why the number of effective bands is 253? Please have acheck and make necessary changes (100-1000 nm) Response: Thanks for your question. We have clarified the number of effective bands in Section II-B of the revised paper as follows: The frequency range of the data acquired by the hyperspectral imaging sensor is 400 to 1000 nm. The data is preprocessed by using spectral difference calculations with a hyperspectral resampling interval set to 2.35 nm, which results in 255 bands over the spectral range between 400 to 1000 nm. The two bands on the upper and lower boundaries of the spectrum are removed, which leads to 253 effective bands. 2. Although the authors added some references (33-38), it would be better to discuss further or compare your results with the published data Response: Thanks for your suggestion about further comparison with the published data in the literature. Following your suggestion, we compared the characteristics bands obtained in this paper and those published in the literature. The five characteristic bands extracted in this study are 410 nm, 481 nm, 533 nm, 702 nm, 798 nm. The two bands in 702 nm and 798 nm are are consistent with the 705 nm and 750 nm range used for chlorophyll content retrieval index in [33]. The characteristic bands of 410 nm, 481 nm, and 533 nm in this paper are similar to those bands used in the study of the rice jointing stage in the literature [34]. Comprehensive analysis shows that there are overlaps and differences in the spectral regions of the characteristic bands among different studies. The differences in characteristic bands are mainly caused by differences in strain varieties, growth periods, environmental conditions, and data processing methods. The above point is clarified in Section IV of the revised paper. Attachments Attachment Submitted filename: response.pdf https://doi.org/10.1371/journal.pone.0238530.r004
19 Aug 2020 Decision Letter - Wang Li, Editor Inversion Modeling of Japonica Rice Canopy Chlorophyll Content with UAV Hyperspectral Remote Sensing PONE-D-20-07987R2 Dear Dr. Xu, 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, Wang Li Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0238530.r005
Formally Accepted
24 Aug 2020 Acceptance Letter - Wang Li, Editor PONE-D-20-07987R2 Inversion Modeling of Japonica Rice Canopy Chlorophyll Content with UAV Hyperspectral Remote Sensing Dear Dr. Xu: 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. Wang Li Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0238530.r006

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