PONE-D-20-08690

Forest dynamics and canopy structure from a high resolution remotely piloted aircraft imagery in the Central Amazon

PLOS ONE

Dear Dr. Araujo,

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.

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We look forward to receiving your revised manuscript.

Kind regards,

Jana Müllerová, Ph.D

Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

The paper is interesting and research well structured. Therefore only minor revision is recommended. Please make sure you address all the issues raised by the reviewers, especially to define aims and research gaps you want to address in your study, add details on data collection and processing, and formulate clear conclusions.

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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

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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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: No

Reviewer #2: No

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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

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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: The study is exploring the usage of high resolution orthomosaics from UAV to identify the crowns within an Amazon forests but also authors are combining the data with data from ground measurements started in 1996. Altogether 1244 trees from 51 subplots (20x20) are investigated. The number of trees and also the temporal ground data are great basis for all analysis. The main idea is not to assess the performance of UAV for crown delineation but to use it as one of the data sources to come with conclusions. In general, I like the whole concept of the study, where authors are taking the UAV in account and they are aware of the shortcomings of it (not seeing understory trees). The main result is that 40% of trees are canopy trees but they are accounted for 70% of aboveground carbon stocks and wood productivity.

I have comments mainly for methods. I have not found flaws or main issues in introduction, results or discussion.

TITLE

I would rather use “Unmanned aerial vehicle” or “Unmanned aircraft system”. I understand that the RPAS is a most formal term but nowadays it is not used frequently within manuscripts. But if you decided to use this formal name correct the title: Forest dynamics and canopy structure from a high resolution remotely piloted aircraft system imagery in the Central Amazon.

DATA AVAILABILITY

You have stated that your data are fully available. Could you add it also to the article? Especially the way how to access them. This will give additional value to your paper in my opinion.

Suppl. Shp: I have downloaded “Shapefile_Crowns_WGS84_UTM20S” but I it was not possible to open it. It seems empty because the extent is 0,0,0,0.

METHODS

In general, you should add more details in the part dedicated to data collection and processing. It is not clear how did you georeferenced the data from UAV but also those on the ground. Or everything was in local coordinates? If you have used to georeferenced and scale your data based on Flytrex then you should add more info about this device and the reliability of it.

Secondly, the crown fitting with ground data is not very clear.

L146: Please add information for the overlap. Whether it is related to ground or crown.

L146-147: What is the accuracy of the Flytrex core 2.0. You should add it to the article.

L182: would be good to add also the number of trees that were considered for that analysis.

Reviewer #2: The presented study compares forest inventory data with tree crowns visible in high resolution UAV imagery. This study reveals that there is no trivial connection between forest structure from the ground and from the air, and that a combination of both perspectives can provide important insights. The manuscript thereby provide interest to a wide readership. The manuscript is generally well written and the methods seem sound.

General comments:

I recommend to streamline the introduction and define a proper research gap. After reading the introduction for the fist time I had problems to get a clear picture of the overall research aim. The research questions are very well defined but came a bit as a surprise to me. I guess you should drop some details and focus on a clear red thread (too much detail may distract from the overall red thread).

The results regarding the visibility in the imagery as a function of the diameter distributions are indeed interesting! The same applies for the growth rates. The manuscript as a whole will certainly benefit from clearer guidance on these aspects in the introduction.

Regarding the DBH and canopy trees relationship: Did you compare different species or at least genera? It is very likely that the different species show a very different relationship since they are likely to have different strategies. Some species may show a conservative growth and accumulate a lot of resources (e.g. high wood density). Other species may be more competitive and grow fast in height but not in DBH (they may aim to overtop neighbors). I was missing at least a discussion on this. A separation into species or genera (at least the dominant ones) may also allow to fit better models. I guess you would also see a very strong pattern in the species distribution as a function of canopy trees since shadow-tolerant species usually feature smaller heights.

I missed a conclusion section where you distil your main findings. This would also enable to create a nice frame for the manuscript and relate to your initial research questions.

I hope this review helps to further improve the manuscript. Best regards, Teja Kattenborn

Detailed comments:

Title: I think the title does not really resemble the content of your paper. I guess it would be better to include the aspect of comparing UAV with inventory data – this is what I understood the research gap and should, hence, be reflected in the title.

l.27 Crucial for what? To me the research gap is somewhere between the lines, but ideally the research gap should be explicitly formulated. Are you primarily interested in the forest structure and dynamics or in the methodology of deriving the latter?

l.31 The term ‚canopy trees‘ sounds odd to me, since every tree contributes to the canopy. This becomes even more clear when considering that a canopy can have multiple layers. At least you should clearly define what you mean with canopy trees before using such concept.

l.46 Limitted in terms of what? And does the number of studies matter or is it rather the missing knowledge that matters?

l.51 LiDAR does penetrate up to the ground. This should be reflected here.

l.63-72 I do not really understand how this paragraphs contributes to formulating the research gap. To me this is rather off-topic or distracting, respectively.

l.97 I cannot really follow the red line of your introduction. You start with tropical forest, then with remote sensing, then you jump again to forest structures and again to remote sensing. I recommend to streamline your introduction and address one topic after another. For instance along these lines: 1) Knowledge on the forest structuere in tropical forest remains scarce. There are different models and empirical findings. Inventory data alone is unlikely to reveal the structural diversity and causal processes. Remote sensing offers insights from another perspective. Combining Inventory data and remote sensing is key to address the above mentioned research gap.

l.104 There is no reference here. I guess this one suitable: Kattenborn, T., Lopatin, J., Förster, M., Braun, A. C., & Fassnacht, F. E. (2019). UAV data as alternative to field sampling to map woody invasive species based on combined Sentinel-1 and Sentinel-2 data. Remote Sensing of Environment, https://doi.org/10.1016/j.rse.2019.03.025

l.117 This section most importantly misses a motivation on why you chose this study area.

l.151-156 This description is a bit short in my opinion. To my experience from various similar works, linking UAV and in-situ data can be very challenging. Did you use a RTK-based GNSS? Based on what criteria did you assign a species to a stem coordinate? When looking at the RGB imagery with the red polygons it seems to me that there are some uncertainties with the delineation of the tree crowns. For instance polygon #1022, #1018 and #1035 seem to cover different tree species / individuals. How can you be sure that these interpretations are plausible? Consider to elaborate on your methods and discuss potential problems.

l.163 There might be gap constellations that enable a tree to receive direct sunlight for the major part of the day although these trees might not be fully visible from the bird perspective. From a process-based perspective such trees could be considered as ‘canopy trees’. You should consider to discuss such problems, since your method may not perfectly resemble the inherent process of the system.

Table 2 Maybe it would be worth to visualize the distributions vs your observations. I guess this would greatly help the reader to get an understanding of the data structure and the distributions.

l.294 This sentence may imply that you applied an automated crown delineation. Remote Sensing itself cannot detect trees, but an algorithm or interpreter can do. Consider to revise this sentence.

l.303 Here it appears that tree growth only depends on light. One would have to know the growth rate of small trees with sufficient access to light to make such a statement – at least I would state this more carefully. Especially considering that tropical forests are often rather limited by nutrients rather than by light. It could also be that the larger root system of bigger trees is indeed being the causal factor that drives higher growth rates. I do not want to state that your statement is entirely wrong – I just recommend to be more careful.

l.339 I do not really agree here. You indeed showed that there are some statistical patterns, but you did not present causal relationships (see comments above on species, nutrients, etc…).

l.343ff This connects to the issue I addressed above – given these aspects, how can you be sure that you delineated the trees appropriately? This should be discussed in my opinion.

l.361 I totally agree – maybe this aspect could be nicely paraphrased by saying that different perspectives, i.e. the ‘ground’ and the ‘bird perspective’, are needed to fully understand the complex structure of forests. In the light of your results it may also be worth to discuss that passive optical remote sensing is certainly limited in revealing the forest structure or its biomass. In this regard I was also missing reference to other studies that used more sophisticated sensors (e.g. LiDAR) to describe forest structures.

The data is not made available yet. There is no inventory data, no orthoimagery and the supplied shapefile is empty.

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Reviewer #1: No

Reviewer #2: Yes: Teja Kattenborn

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PONE-D-20-08690R1

Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

PLOS ONE

Dear Dr. Araujo,

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.

Please submit your revised manuscript by Nov 21 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. 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,

Jana Müllerová, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

Dear authors. I am happy to see that your manuscript improved very much, now it is clear and informative. Only very few issues remain. After you addressed those, your paper will be ready for publication. Good job indeed!

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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 #2: All comments have been addressed

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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 #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

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 #2: Yes

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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 #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 #2: The revised manuscript clearly improved in clarity and reading flow. All of my previous comments were addressed and misunderstandings were clarified. The manuscript reads nicely and the results are now more elegantly highlighted in the added conclusion section.

Besides some details (see below), the only further suggestion I have relates to a comment of the previous review: I suggested to study the species as a factor of canopy proportions, DBH and growth rates. I undersand, that your data may not enable to do such analysis. Nevertheless, I would (briefly! - maybe 1-2 sentences) discuss that looking deeper into species/genus-specific relationships may shed additional light on the forest structural heterogeneity. Especially, considering that some species are by design shadow tolerant (there is no need to reach the canopy to thrive), whereas other species (competitive species) may only succeed on the long run, if the eventually reach the canopy. There may, for example, be only a few species with exceptional high canopy heights containing the majority of timber. I would consider to add such thoughts to 1) explain the scatter in your results and 2) provide an outlook for future work.

Good job!

Teja Kattenborn

Minor Details:

l.141 Remove full stop before braket.

l.149 Consider to state that you generated the products using Agisoft.

l.310 Full stop after and not before the bracket.

Fig.5 In the text, you primarily refer to DBH, whereas in the figures you use ‘Diamter’ as axis label. Consider to also use DBH in the figures. Diameter is rather unspecific (and could, for example, also refer to crown diameter).

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Reviewer #2: Yes: Teja Kattenborn

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Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

PONE-D-20-08690R2

Dear Dr. Araujo,

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.

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Kind regards,

Jana Müllerová, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Congrats to your paper, it is now ready for publication. Regards

Reviewers' comments: