PONE-D-23-17337Calibration of Commercial Fisheries Echo Sounders for the Estimation and Management of Fishery ResourcesPLOS ONE

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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: Partly

Reviewer #2: Yes

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

Reviewer #1: I Don't Know

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This manuscript proposes a simplified echosounder calibration method for commercial fisheries vessels to provide quantitative data for fish stock assessment. The method is based on overpass over seabed areas with known backscattering properties, in place of time-consuming calibration procedures using reference targets, commonly used in fisheries research. The manuscript reports from a large and comprehensive work with interesting and impressive results.

In my opinion, the manuscript is promising but has some important shortcomings in its present form. My recommendation is therefore that a major revision should be carried out before the manuscript may be accepted.

To Review Question 1, the manuscript seems to report from a work that is technically sound, but the manuscript itself needs revision to reach appropriate rigor in its treatment of theory (well known from literature), experiment, and conclusions.

To Review Question 2, there is little statistical analysis in the work. Some details are lacking or need clarification.

To Review Question 3, I found this somewhat difficult to answer. The data are available from the authors “upon reasonable request”, without specification of why they are not openly available online.

To Review Question 4, the manuscript is mostly intelligible and written in standard English, but it would benefit from some improvements.

The authors state that “the calibration of general echo sounders has never been carried out using the backscattering strength of the seabed” (page 6 line 85). In my opinion, the manuscript should account for, and compare with, other uses of the seabed as sonar calibration reference, such as, e.g., Eleftherakis et al., Mar. Geophys. Res. 39 (2018), Weber & Ward, J. Acoust. Soc. Am. 138 (2015), Roche et al., Mar. Geophys. Res. 39 (2018). The reviewer found the two latter references via the Master’s theses of Guimarães (2020), and Cândido (2022).

The manuscript should define the quantities used more precisely and keep clear separation between their natural and logarithmic forms. Several equations need to be corrected and/or explained more clearly in the surrounding text. Details are noted under “Detail comments” below. A thorough foundation for the equations built upon in the manuscript are given in the report series “Fisken og havet” (The Fish and the Sea), available online at Institute of Marine Research (https://www.hi.no/en/hi/nettrapporter?query=&serie=fisken-og-havet): No. 10/2013, Lunde et al., “Power budget and echo-integrator equations for fish abundance estimation”, and No. 7/2014, Lunde and Korneliussen, “A unifying theory explaining different power budget formulations used in modern scientific echosounders for fish abundance estimation”.

In my opinion, the manuscript should provide more details about how the echo sounder measurements and data processing were conducted. This would support quantitative discussion of measurement uncertainty and possible transferability to other general echo sounder models than those used in the study.

Detail comments

Page 2 line 24: Please check the sentence, “To carry out the quantification of fisheries echo sounders quantitatively …”

Page 4 line 55: The sentence should provide some foundation, e.g., a reference, for the claim that the processes used to survey fishery resources “show no improvement”.

Page 5 line 63: Please consider reformulating the sentence “As the data measured by conventional general echo sounders are not quantifiable, quantifying the data …”. As it stands it seems to imply that the authors will quantify something which is not quantifiable.

Page 7 line 96 and Page 9 line 125: In my opinion, “spherically spreading” or “spherically diverging” would be preferable to “diffuses and attenuates”.

Page 7 line 99: Please clarify the statement “Notably, in quantitative echo sounders, TVG processing can be processed automatically; this is the characteristic difference between quantitative and general echo sounders”. Does this mean, generally, that a general echo sounder does not feature TVG? What implications may this have for the measurement uncertainty, or resolution, of a general echo sounder, when the reception voltage level “digit” is given as an 8-bit integer (page 8 line 107)?

Page 8 line 118: Please clarify the formulation “returned in the source direction by a unit distance”.

Page 8 line 122: Equation (2) does not include the backscattering cross-section of the target. Please change or explain.

Page 8 line 122: Equation (2) is also dimensionally unbalanced. Inclusion of a reference distance R_0 in the spherical spreading and absorption factors would complete it, if G_R is dimensionless.

Page 8 line 123: The formulation “sound pressure of the transmitted wave” seems unclear. Does it refer to the transmitted sound pressure amplitude on the sound beam axis at a reference distance from the source, and, if so, is the target also positioned on the sound beam axis?

Page 8 line 124: Judging by Equation (2), it does not seem correct that the gain G should be in units of dB.

Page 9 line 133: The text should define all the logarithmic quantities in Equation (4), such as making clear that KTR = 10 log_10 K_TR.

Page 9 line 133: From the definition of K_TR above, Equations (4) and (8) seem to define EL as an electrical quantity rather than a sound pressure level as in the classical sonar equation EL = SL – 2TL + TS. The authors refer to Traynor and Ehrenberg, 1990, but I cannot see that they define EL as in the manuscript. The definition of EL must be clarified.

Page 9 line 142: Does Figure 2b exemplify an actual sampling volume? It seems to me that the smallest quantifiable sampling volume would span the whole two-way beam pattern of the transducer, typically illustrated as a conical shell volume corresponding to the two-way equivalent beam solid angle.

Page 10 line 146: Equation (5) does not include the volume backscattering coefficient. Please change or explain.

Page 10 line 147: Consider writing, e.g., “The backscattering volume” or “The ensonified volume of scatterers” rather than “The scattered volume”. Similar formulations are found also elsewhere in the manuscript.

Page 10 line 148: Consider clarifying that psi is the two-way equivalent beam solid angle.

Page 10 line 160: It should be made clear that SV in Equation (9) is not the logarithmic quantity from Equation (8).

Page 11 line 161 and Page 14 line 225: The target strength (TS) is conventionally defined as logarithmic and thus not used as a divisor. Dividing by a mean backscattering cross-section (sigma_bs) can be valid. The authors are encouraged to align their description with the commonly used echo integration formulations as in, e.g., References 27 and 29.

Page 11 line 168: A discussion of the differences between the four measurement frequencies, and possible significance of these differences, would be useful.

Page 11 line 177: It would be useful if Table 1 include the beam angles and two-way beam solid angles of the echo sounders.

Page 12 line 181: Please clarify the formulation “the seabed had not changed significantly”. The formulation is clearer but still somewhat unspecific in the Conclusions, Page 30 line 471.

Page 14 line 225: In my opinion, a more detailed discussion of the secondary validation comparing fish abundance estimated from SA would be useful. Factors such as school size, density, uniformity across the sound beam, edge effects, etc., and how such effects were treated, may influence the measurement results.

Page 15 line 235: Please clarify if by “acoustic index” here it is meant the same as “acoustic indicator” later in the manuscript.

Page 15 line 235: Please clarify the reasoning indicated by sentence “… the seabed has the strongest scatterer in the ocean; therefore, the maximum echo in one ping can be considered the primary reflection …”

Page 15 line 235: How was the maximum echo amplitude from the seafloor calculated? Could there be differences (integration time, sample rate, etc.) between the quantitative and general echo sounders, and between different models of general echo sounders? What importance could this have for the proposed calibration method?

Page 17 line 262: What were the measurement parameters, such as seawater salinity and temperature, transmit power / source level, acoustic beam width, and capability to manoeuvre the calibration ball, and how may they affect the measurement uncertainty and the uncertainty of the theoretical value for the TS of the calibration ball?

Page 18 line 280: It would be useful to include a discussion of what uncertainty and variability should be expected for the four anchovy target strengths, both in the present measurements and in the values from literature. For example, a listing of the 45 extracted SA values could be helpful.

Page 19 line 296: The fish abundance listed in Table 2 for the 120 kHz measurement frequency is only one-third of the results for 38 kHz and 15 kHz, which seem to show excellent agreement. It seems that Table 2 could be discussed in further depth, ideally based on a notion of what measurement uncertainties to expect in general and what is needed for the proposed method to be worthwhile.

Page 19 line 301: Is the mentioned difference of 0.3 dB the same value as used to calibrate (adjust) the values listed in Table 2 as “Cal using calibration ball”?

Page 19 line 303: This passage may be reworked if details of the measurement parameters and their importance are added, see my comment to Page 17 line 262.

Page 19 line 305: Please explain how the 0.5 dB calibration measurement uncertainty was estimated – preferably in the description of the measurements (above). It would be useful to modify the very general claim “the results of this study were very accurate” to refer more specifically to the agreement between measured and theoretical TS of the calibration ball without adjustment of the data from the general echo sounders.

Page 20 line 308: What are the beam angles for the echo sounders used in this study (ref. the comment to Table 1)?

Page 20 line 311: The sentence “Therefore, …” should be more specific in its description of why calibrated general echo sounders can be used as “quasi-quantitative” echo sounders.

Page 20 line 314: The sentence may over-state the accuracy of the general echo sounder, if based only on the calibration ball measurement. Please consider revising the statement, or revealing more details of the measurements to found the claim more firmly.

Page 21 line 322: Please clarify what is means that the “echo number” is 4608. Is it the number of echoes that were acquired and used, and is it the same between the echo sounders?

Page 21 line 322: What is meant by “extracted at one ping”? Does this refer to the statistics of single echoes as opposed to the averages within grid cells discussed later?

Page 21 line 324: Please clarify the formulation “… primary reflections saturated”. Did the seabed echoes saturate the quantitative echo sounders, explaining why these measurements are missing from Table 3? The word “thus” may be somewhat overused.

Page 21 line 328: Please specify that the values in Table 3 are given in decibels, and what reference is used for the dB value.

Page 22 line 334: The minimum SV based on the secondary reflection seem very low. The text could benefit from a discussion of factors that could cause weak secondary echoes compared to the primary echoes (in addition to the brief discussion on grain size on Pages 24-25). Is the mean value based on all the recorded values, and could there be some benefit in introducing a cut-off value or some other means to reduce the influence of weak measured echoes?

Page 22 line 345: Table 4: Same comment as for Table 3. Also, are all results in Table 4 mean values per grid cell, as opposed to single-echo statistics in Table 3?

Page 25 line 374: Please define what is meant by the echo convergence time.

Page 24 line 375: Please reconsider the statement that the acoustic impedance of sand particles is smaller than that of seawater.

Page 25 line 377: Please consider revising the statement that it is the acoustic impedance of gravel that makes the reflection more diffuse. Could it be that the echo from a gravel seabed has more of a scattering-dominated characteristic, due to roughness, rather than specular reflection from a smoother sand or sediment bottom?

Page 26 line 400: Please clarify what is meant by “saturated”.

Page 26 line 402: Please revise the statement “if the discharged sound waves are strong … the sound waves may get reflected before being attenuated”. As explained earlier in the paper, propagating sound waves are always attenuated.

Page 26 line 407: Please revise the statement “Therefore, the backscattering strength tends to be a non-linear phenomenon”. The text leading to the statement does not imply nonlinearity in the process of backscattering but may point to weaknesses in the applicability of the proposed calibration method to the echo sounders used.

Page 27 line 420: What does the achieved agreement mean for possible application of general echo sounders for quantitative survey measurements of fish abundance?

Page 29 line 442: Please clarify the sentence “The seabed data captured …”

Page 29 line 448: In my opinion, the work would benefit from a further discussion of why the adjustments in SV measured by the general echo sounders are so large while the TS of calibration balls were measured with only 0.3 dB difference from theoretical values.

Page 31 line 470: The Conclusions chapter introduces new and important items related to both possible applications, technical aspects of quantitative measurement of the secondary bottom reflection, and the frequency dependence of backscattering strength. These items should be introduced in the appropriate introduction and discussion sections earlier in the text.

Reviewer #2: Summary:

The main content of the manuscript is the development of a simple calibration method using the seabed backscattering strength. This technique offers a solid framework for calibrating echo sounders used in commercial fisheries, enhancing resource estimation and management. The authors tested their metholodogy comparing with echo sounders calibrated using a calibration ball in multiple scenarios.

Major comments:

The manuscript shows a lot of promise, but some major issues need to be addressed before it can be published from my point of view:

• I found the manuscript difficult to read at some points, specially the “Results and discussion” section. Most of the large amount of data they describe in these paragraphs may be tabulated and then only comment the relevant features in the text, thus considerably improving the readibility. Besides that, the authors abuse of the usage of the semicolon at many points, creating very long sentence which are difficult to understand easily. Finally, I command the authors to separate the discussion of Tables 3 and 4 into different paragraphs for more clarity.

• I miss more connection between the “Mechanics of general echo sounders” and the “Results and discussion” sections. The computations that yield the tables should be clearly referenced to facilitate the understanding of non-expert readers.

• All the research performed in the “Results and discussion” section should be accompained by spread measures of the data, i.e., it is not sufficient to provide mean values of the quantities, but also the standard deviations must be detailed.

• I feel that the future work can be extended in some directions. For example, echo sounder are widely used in dFAD fishing, and their calibration is crucial both for fisherman and for research due to the large amount of data they provide. Have you considered to use this new calibration system to the echo sounder equipped in dFADs?

Minor comments:

Abstract

• L22. Change semicolon by full stop.

• L24. I feel “quantification of fisheries echo sounders quantitatively” to be redundant.

• L27. “Therefore” is not necessary here.

• L28. I suggest changing “The method involves using” by “Our approach is based on the usage of”

• L31. The semicolon is not necessary: “...the seabed echoes, which were calibrated by comparing…”

Introduction

• L44. Are being depleted.

• L49. I suggest to substitute “fishes” by “biomass present”.

• L51. I suggest to substitute “quantify” by “estimate”.

• L52. “Several disadvantages”, but only one is mentioned.

• L63-65: This sentence is not clear. Please, clarify.

• L74: I suggest to substitute “Due to” by “For”.

• L76-77. I feel “In this method, we used the backscattering strength of the seabed” to be redundant looking at how the previous sentence ended.

• L80. I suggest to substitute “measure the backscattering strength of the seabed” by “the backscattering strength of the seabed can be measured”.

• L84. What is “inter-ship calibration”? It has not been defined.

Methods

• L91. Change semicolon by full stop.

• L102-103. I suggest to omit the formulas in Fig 1, as they are commented afterwards, so the footnote fully describes the image.

• L106. Change semicolon by full stop.

• L110. The equation in the text are subjected to the same puntuaction rules, so a full stop or a comma (as in this case) must be placed at the end of equation (1).

• L115. What are single echo and group echoes? Please, clarify.

• L115. I suggest to substitute “; therefore, it is” by “, so it is”.

• L121. It find referencing an equation that does not already appear in the text a bit weird. I suggest to substitute “using Eq (2) [17]” by “as” and move the reference [17] after describing the variables.

• L122. The final comma is missing.

• L123-125. I suggest to describe all the parameters involved in Eq (2) just after the equation, and then the authors may point out related observations such as “the factor of transmit and received” and the characteristic of R^{-2}.

• L128. What does “with the characteristic of exp(-2\\alpha R)2 mean?

• L130. Equation (3) is not an equation, as there is no equality. Moreover, the authors must mention in what basis are the logarithms expressed.

• L133. K_{TR} was used in L125, but KTR is used in this line.

• L138-140. P_{0} and R have already been described, and the rest of the parameters are described below. I strongly recommend the authors to better explain the images instead of defining the parameters which are detailed in the text.

• L149. Same comment as in L121.

• L150. The full stop is missing.

• L152. Change semicolon by full stop.

• L153. Again, this is not an equation. Please, describe precisely the relation between the parameters.

• L155. The full stop is missing.

• L156-159. I suggest the authors to motivate better why SA is preferred over SV.

• L158. I suggest to substitute “Notably, SA” by “This quantity is”.

• L160. The R1 and R2 are not defined.

• L161. I suggest to add “in Eq. (4)” after “TS”.

• L161. The number of target species is denoted as “n” in the following section. The authors should consider to include this notation here.

• L166. I do not support the usage of Figure 3, since it does not add any value to the manuscript.

• L167. I suggest removing “in this study” since it is unnecessary here.

• L185. Change semicolon by full stop.

• L185. Add “in this study” after “measurement lines2.

• L185. A linking word is missing before “The depth…”. “Besides that” suits well here.

• L199. There are sentences where low numbers are in letter and others that are in numbers. I suggest taking the same criterion everywhere (preferably, with letter. i.e., “ten” instead of “10”).

• L229. Change semicolon by full stop.

• L236. Change semicolon by full stop.

• L241. I suggest rephasing this sentence as “We treated the record as an error…”

• L242. I suggest rephasing this sentence as “assumed that secondary reflections of the seabed were not captured…”

• L255. The authors of the references were not named until this point (Wentworth). Please, take the same criterion everywhere.

• L256. I suggest changing “based” by “depending”.

Results and discussion

• L265. State the water temperature and salinity.

• L265. A linking word is missing before “There was…”. “Therefore” suits well here.

• L284. The authors of the references were not named until this point (Amakasu et al). Please, take the same criterion everywhere.

• L297. The authors say the differences were low, but there are a 110000 difference between 4th row and 6th row in Table 2, which I think is not negligible.

• L303-306. This four-line sentence is difficult to read. Consider rephrasing it.

• L322. What is the echo number?

• L336. Change semicolon by full stop.

• L360. Replace “10” by “ten”.

• L370. Replace “10” by “ten”.

• L374-375. I do not understand “The difference in acoustic impedance of the medium is large, the reflection is large”.

• L387. What does “acoustic impedance”?

• L403. Change semicolon by full stop.

• L406. I suggest to substitute “; however,” by “, although”.

• L411. Replace “1” by “one”.

• L416. I suggest to move the reference [52] just after “According to a previous study...”.

Conclusions

• L482. Replace “½” by “one-half”.

• L490. Change semicolon by full stop.

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Reviewer #2: No

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PONE-D-23-17337R1Calibration of Commercial Fisheries Echo Sounders for the Estimation and Management of Fishery ResourcesPLOS ONE

Dear Dr. Zhu,

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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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: (No Response)

Reviewer #3: (No Response)

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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 #1: Yes

Reviewer #3: No

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

Reviewer #1: Yes

Reviewer #3: No

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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: No

Reviewer #3: No

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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 #1: Yes

Reviewer #3: No

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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 have made considerable changes to the manuscript. The changes have been detailed in an intelligible way, but not all comments have been addressed sufficiently. The manuscript still has some shortcomings. My recommendation is that another revision is called for before the manuscript may be accepted.

To Review Question 3, I have not been able to read clearly from the submittal whether all the data will be made publicly available or not.

Major comments

Revision 1 (R1) does not seem to respond to the first two of my original three major comments. These are repeated and amended below. The page and line number references have been updated to match R1.

1. The authors state that “the calibration of general echo sounders has never been carried out using the backscattering strength of the seabed” (page 5 line 85). In my opinion, the manuscript should account for, and compare with, other uses of the seabed as sonar calibration reference, such as, e.g., Eleftherakis et al., Mar. Geophys. Res. 39 (2018), Weber & Ward, J. Acoust. Soc. Am. 138 (2015), Roche et al., Mar. Geophys. Res. 39 (2018). The reviewer found the two latter references via the Master’s theses of Guimarães (2020), and Cândido (2022).

2. The manuscript should define the quantities and equations used more precisely and in line with the well-established literature in the field. Some, but not all, details are noted under “Detail comments” below. A thorough foundation for the equations built upon in the manuscript are given in the report series “Fisken og havet” (The Fish and the Sea), available online at Institute of Marine Research (https://www.hi.no/en/hi/nettrapporter?query=&serie=fisken-og-havet): No. 10/2013, Lunde et al., “Power budget and echo-integrator equations for fish abundance estimation”, and No. 7/2014, Lunde and Korneliussen, “A unifying theory explaining different power budget formulations used in modern scientific echosounders for fish abundance estimation”. I strongly recommend to use the terms and definitions found in these references, or to refer to literature that establishes the particular terms and definitions of the manuscript.

Below I have made some detail comments to the changes made in R1.

Detail comments

Page 6 line 96: An original formulation containing “diffuses and attenuates” was replaced in R1 by “The echoes include distance attenuation, e.g., spherically diverging attenuations caused by the propagation of sound waves”. I propose to rephrase once more, to make it clear that it is not the attenuations that diverge. If the two mechanisms of attenuation considered are absorption and spherical spreading, I propose that these two are mentioned, without “e.g.”.

Page 7 line 121: A series of comments were resolved by adjusting Equation (2) and the section around it. The sentence on Line 121 now includes the terms “single echo”, “single object”, “backscattering strength”, “target strength", “reflector”, and “distribution density”. I propose to rephrase this sentence and possibly divide it into multiple sentences explaining more clearly what Equation (2) describes.

Page 8 line 126: Please clarify what “terminals” the transmission sound pressure P_0 refers to, and what is meant by “normalized to the 1 m range”. Standard wording is found in acoustics textbooks and e.g. the “Fisken og havet” reference mentioned in my second major comment.

Page 8 line 130: Please clarify the definition of “ts” as a “linear measure of” the backscattering cross-section. A standard definition is TS = 10 log_10 (sigma_bs / r_0^2). This or any alternative definition should be clearly defined in mathematical terms.

Page 8 line 133: Please reconsider the description “the sound waves absorb energy from the components of seawater”.

Page 8 line 139: The echo level is usually defined as the free-field sound pressure level due to backscattering, incident at the position of the sonar transducer. The alternative definition given here as a received voltage squared after front-end amplification warrants a further, mathematically stringent, explanation.

Page 10 line 148: Consider clarifying that psi is the two-way equivalent beam solid angle.

Page 11 line 168: A discussion of the differences between the four measurement frequencies, and possible significance of these differences, would be useful. Please clarify what is meant by that “each frequency has different frequency characteristics”, and why this is an argument for using backscattering strength to compare measurements taken at different frequencies.

Page 11 line 196: Thank you for adding beam angles to Table 1. When comparing measurements of the seafloor, are not also the two-way beam solid angles psi needed?

Page 18 line 304: Please rephrase “a 38.1 mm WC sphere gives a sound speed c of 1520.2 m/s”.

Page 29 line 465: Consider inserting “measured”, “observed”, or “apparent” in the sentence – “there was no change in the measured SV values of the seabed primary reflection”.

Page 32 line 524: What does the achieved agreement mean for the achievable measurement accuracy in terms of SV when general echo sounders are used for quantitative survey measurements of fish abundance?

Reviewer #3: From the perspective of this reviewer, while technique of using the seabed for calibration is well established, especially within the hydrographic community, the application to the use of fish finders, as far as this reviewer is aware, is the novelty of this work. However, the manuscript as currently presented does not seem to provide enough evidence to substantiate many of the claims made in the results and the discussion, and the manuscript, overall, lacks the focus that is conveyed in the abstract.

Further, from an acoustics perspective, many of the definitions and processes described in the methods and then used throughout the paper are both inconsistent internally within the manuscript and fail to follow field-specific conventions (e.g., see those presented by MacLennan et al., 2002). In addition to confusing an informed reader, this adds further skepticism to the reported results as some of the important details of the methods and analyses are either unreported or construed. There are many elements to the manuscript that in its current form read as disjointed, and additional analyses, clarity, or figures (detailed below) are needed to convey the findings the authors to conclude.

Specific comments:

Consider a title that notes the use of seabed backscatter

Line 39, specify what is meant by “them”, i.e., change to “resource”

Line 43, “scientifically” is not needed

Line 48, “short time” is unclear, consider rephrasing that they can efficiently estimate biomass over a wide area.

Line 48, Remove “In addition”, not necessary in this statement.

Line 55, 2nd and 3rd commas are not necessary

Line 58, move “to survey resources” to the end of the sentence

Line 67, remove “in the sea”

Paragraph at line 70, really needs to include a lot of references, and discuss what already is/isn’t being done with regards to seabed calibration. There is lot of work in the seafloor mapping field, plus some work with water column fisheries echosounders (See De Robertis and Hjellvic). They need to develop more on why using the seabed works, which currently has 0 references.

Line 94, What is meant by “upgrade”?

Line 92, Replace distance with range throughout this paragraph. What is the ‘essential role’? Clarify what is meant here.

Line 98, TVG does not improve the reception sensitivity, it amplifies the received signal as a function of range. Clarify.

Line 103/Figure 1, r is range. The proper term is SV¸ where the ‘V’ is subscript. See Maclennan et al., 2002 A consistent approach to definitions and symbols in fisheries

acoustics”. Fix throughout.

Line 119, The use of 20log and 40log for volume and individual scattering, respectively, needs to be clarified in the paper. Are you doing both, and if so, provide the equations.

Line 130, σbs is linear, clarify and replace ‘ts’ in equation 2 with σbs. Fix throughout.

Line 139, Again, use σbs in place of ‘ts’, as is consistent with MacLennan et al., 2002.

Line 156/Equation 4, Proper use is subscript of the V, as in sV.

Figure 2, This figure indicates the basic concepts and terminology used in fisheries acoustics and seems to be excessive to include in this manuscript. In addition, these figures already exist in common acoustic literature. This one in particular looks similar to Figure 1 and Figure 2 in Furusawa 2021. Consider removing or citing previous work instead.

Paragraph at 167 and equation 7, The area backscattering coefficient is sa and the units here are incorrect, again see MacLennan et al., 2002.

Line 169, This sentence is unclear. What does layer number have to do with sA? This statement can be removed.

Line 174, R1 and R2 represent the lower and upper ranges of the volume over which sV is being integrated. Clarify this sentence.

Line 175, ‘ts’, as a lower case form, is not a valid representation of the linear form of target strength. Target strength is a logarithmic unit, thus σbs is the linear form. The parenthetical here is incorrect.

Line 176, This is confusing, if you correctly give the units for sa (m2 m-2) then you can clarify that the resulting unit when dividing by σbs (which has units of m2) is target species per unit area.

Figure 3, What are the axes on the seabed backscattering strength maps on the right? Labels are necessary to interpret these. Label the subfigures as (a), (b), and (c) to be able to directly reference them in the text.

Line 189, The figure caption needs to include specific details defining ‘seabed backscattering strength’. Remove the term ‘acoustic indicator’ and refer specifically to SV when discussion volume backscattering strength. The seabed maps look interpolated. Are they? Specify in the caption.

Line 199, Figure 3 does not substantiate the claim that the sediment and slope had not changed significantly, and there is no indication of bathymetry. Consider adding bathymetric contours to the Sv representations in Figure 3.

Line 205, Remove ‘Besides that’

Line 212, What depth was the sphere suspended? Were multiple depths used to confirm the linearity of the response from the general echosounder?

Line 217, Replace ‘know’ with ‘measure’

Line 218, Define ‘peak’ here, which should be referring to the peak backscatter or target strength of the calibration sphere.

Line 218, Remove ‘with a wide beam’ and ‘with a narrow beam’

Line 221, What are the parameters?

Line 225, “to prevent recording the waves reflected from air bubbles”. Does this refer to preventing entrainment of bubbles underneath the transducer? Please clarify.

Line 229, Include sites in the map on figure 1.

Line 235, Did you use a single observation of the maximum TS observed or a mean of an ensemble of observations? Report the number of TS measurements used to calculate the on-axis measurement.

Line 241, Please elaborate what is meant by this sentence.

Line 243, 250, It is unclear how these different calibrations were applied in the processing. Were the echosounder observations corrected afterwards using an offset? Or were data reprocessed using a modified gain based on the observed target strength/seabed measurement? Please expand.

Line 252/Figure 4, Please include at least the depth/range axis and labels on the echograms. Identify the yellow line of the quantitative echogram in the caption. Analysis grid is not defined anywhere in the text. Further, the use of ‘analysis range’ throughout the text is unclear, given the meaning of ‘range’ for volume integration as explained in the methods. Use a different term throughout the text that indicates that this is the horizontal grid.

Line 257, The company name for Echoview is currently Echoview Software Pty Ltd.

Line 258, ‘ts’ should be σbs. This sentence is redundant with previous methods, simply state that fish abundance was calculated for fish schools based on integration of volume backscatter as previously described.

Line 261, Define reaction size and school reactions.

Line 266, ‘treated as fish schools’? Simply state were not included in the analysis.

Line 268, ‘Echoes below the seabed line’ is unclear. Are you referring to the integration volume immediately below the sounder-detected seabed? How was the seabed line detected?

Line 277-280, These two things do not seem to be related as written. Yes, the pitch/roll of the vessel has a significant impact on the observation of the seabed as a result of changes in the incident angle with the seafloor. Was range then used as an indicator of angle? I.e., were only echoes where the seafloor was a consistent range window averaged, assuming that the observations represented the same vessel position? This is highly sensitive to vessel movement and complete flat seabed structure. Were measurements of pitch and roll available to validate this?

Line 282, Clarify that this was 1-m below the detected seabed.

Line 285, This needs to be defined earlier as it has already been used multiple times throughout the text and figures.

Line 286, Earlier it is stated this was done in 50 m grid. Please clarify in either place. Also, due to the confusion between terms, is this the power average (average of the linear values, sV, then converted back into log space)?

Line 290, This information needs to be included in the caption for Figure 1, or Figure 1 should be divided into two figures which can be used in the into/methods (the transect map) and the results (the seabed maps).

Line 294, This is the first time sediments are mentioned. This needs to be described earlier in the survey methods, including how the sediments were collected, and here, additional details into the grain size methods should be included. Define the grain sizes used to distinguish the 3 classes.

Line 306, Again, include the complete unit for TS here, which is dB re 1 m2

Line 304-313 As in the methods, clarify if these are single observations of the maximum TS or an average of the highest values, and if so how many observations were included.

Line 322, use the correct notation, sA, throughout

Line 324-330, sA is not a log unit as being reported. Are these values referring to SV?

Line 332/Table 2, Here as well, these cannot be measurements of sA or any areal unit as they are being reported in decibels. Please correct or clarify.

Line 338-346, Shouldn’t these estimates be roughly the same at both frequencies for the quantitative echosounder?

This indicates that potentially an incorrect target strength values was used. Are these values from the integration using the sphere calibration or the seabed calibration?

Line 354, That is a large range with significant implications for the target strength, and it is assumed that the sound speed did not change over the course of the survey. The difference in TS can be driven by many other factors that are internal to the processing of the echosounder. Please discuss here.

Line 360-372, There is currently very little evidence for the claims described in this paragraph outside of the single aggregation of reported values in the paragraph at 339. This needs to be revised or school-by-school results for animal densities need to be included which will remove the variability of comparing different frequencies, from which statistics can be drawn which can include possible error due to both the calibration and target strength values at the differing frequencies.

Line 377, The difference between -168 and -15 dB is still a ~40% difference in backscattering strength. This is considered not significant?

Line 386/Table 3, include the number of observations in the table.

Line 392, I would argue that they did (-25 vs -16.8 is a massive difference in the secondary reflection). Clarify.

Line 399/Figure 5, It has yet to be stated what the intention behind including the data on the secondary reflections is. Why are they included, and what the meaning behind their measurements? Why are you not showing the same figure for the primary bottom, which is a significantly stronger interface and thus the one that should be used for the calibration?

Line 405/Table 4, Shouldn’t the values for the 50 m grid match shoes reported in Table 3? Why are they not? It is unclear what the difference behind the data being presented are.

Line 414, Define saturated here. If the values were saturated, how are the values being presented in the tables variable?

Line 419, What is the implication of the choice of grid size? Expand.

Line 424, In the methods, only 3 groups are mentioned. Please clarify either here or in the methods.

Line 435, The table does not do a great job demonstrating this. A figure, or including mean Sv on the ternary as a color for each site would be very useful.

Line 441, Table 5 does not substantiate this claim.

Line 448, The convergence time of the echo is not previously described or any results shown.

Line 464, Again, what does this refer to? If the values were ‘saturated’, wouldn’t that mean they would be a maximum value? Are you referring to some sort of color or integration threshold? If something is being saturated, how are you collecting measurements?

Line 475-479, This needs to be discussed much earlier in the manuscript to justify the focus of the results on the use of the secondary bottom. It should be explained both in the intro and then reiterated in the methods.

Line 484, This, like the previous statement regarding incidence, assumes a lot about the ability of the boat to remain perfectly level and the seafloor to be uniformly flat. Given that it is unlikely that both of things are perfectly true, you likely need to do more to address variability due to the pitch, roll of the vessel. Given the beam angles, minor changes (fractions of degrees) can lead to a lot of variance. There is likely also a tradeoff, as gridding over a larger area means that the likelihood that the seafloor varies is greater as well.

Line 503, So was the same data used to calculate the average as is being presented to indicate the variability in Sv? This is very confusing.

Line 509, From the abstract, I expected this to be the focus of the manuscript, however the results and discussion of this intercalibration and the integration of the anchovy schools is buried to the end of the paper. Reporting Sv across different frequencies is meaningless for a reader to interpret, and instead should focus on the estimated fish density as reported earlier. Rather than using the entire school, layers/intervals within the school can be used to increase the sample number in addition to the dual-frequency estimates of each system. Further, the sphere itself can be integrated to do a similar comparison.

Line 528, This is the first place that the objective of the manuscript is stated and references the secondary seabed. This needs to be stated earlier, and the justification for not using the primary seabed needs to be expanded.

Line 540, But the gravel areas and sandy areas show roughly the same variability reported in your results?

Line 544, This is not discussed enough earlier, see previous comments regarding roll.

Line 547, Isn’t that the purpose of this study?

Line 557, This contradicts the previous paragraph stating that specific requirements need to be met.

Line 559, What is meant by error prone? These are not the reasons these have become industry standards. The second clause of this sentence needs a reference, 15 kHz is not as common as 18 kHz.

Line 567, This is too general of a statement.

Line 568, ‘eco sounders’ should be echosounders. What is meant by ‘automatically’? Expand.

Line 567, What is a survey system? Survey of what? Be specific. Clarify or remove as this is better explained in the following sentences.

References

Dalen, J., and Lovik, A. 1981. The influence of wind‐induced bubbles on echo integration surveys. Journal of the Acoustical Society of America, 69: 1653–1659

MacLennan, D. N., Fernandes, P. G., and Dalen, J. 2002. A consistent approach to definitions and symbols in fisheries acoustics. ICES Journal of Marine Science, 59: 365-369.

Hjellvik V., De Robertis A.Vessel comparison on the seabed echo: influence of vessel attitude, 2007US Department of Commerce, NOAA Technical Memorandum NMFS-AFSC-171 pg. 34

Alex De Robertis, Vidar Hjellvik, Neal J. Williamson, Christopher D. Wilson, Silent ships do not always encounter more fish: comparison of acoustic backscatter recorded by a noise-reduced and a conventional research vessel, ICES Journal of Marine Science, Volume 65, Issue 4, May 2008, Pages 623–635, https://doi.org/10.1093/icesjms/fsn025

Furusawa, Masahiko (2021) "Volume Scattering and Echo Integration in Fisheries Acoustics Revisited," Journal of Marine Science and Technology: Vol. 29: Iss. 2, Article 1.

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Reviewer #3: No

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PONE-D-23-17337R2Calibration of Commercial Fisheries Echo Sounders Using Seabed Backscatter for the Estimation of Fishery ResourcesPLOS ONE

Dear Dr. Zhu,

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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 #1: (No Response)

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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 #1: Yes

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

Reviewer #1: I Don't Know

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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

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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 #1: Yes

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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: Page 2 (abstract), Line 23 and Page 4, Line 55: Please clarify “at a high frequency” – that the acoustic frequency is high or that data are gathered often?

Page 2 (abstract), Line 29: Please clarify “averaged over a certain range” – does this mean over a certain area?

Page 5 Line 81: Please check the sentence: Is it the measurements using a calibrated general echosounder that will be used as a standard value for the seabed in that area?

Page 5 Line 83: I advise to specify clearer what “the validation opportunity” could be, e.g., when the fishing vessel has opportunity to pass over an area where a reference value has been established.

Page 6 Line 93: Consider rephrasing the sentence for conciseness. What is it to “calculate an echo”, and what is it to “quantify the data”?

Page 6 line 96, Page 8 line 101: The term “spherical spreading” is preferable over “diffuse attenuation”.

Page 6 line 99: If the absorption law is exp(-2\\alpha R), the unit of \\alpha should be Np/m not dB/m.

Page 6 Line 99: Consider removing “Therefore, “. Alternatively, remove the whole sentence since the purpose of TVG was already stated in Line 94.

Page 6 Line 101, Page 15 Line 259, Page 24 Line 383: It is stated in the first location that some recent general fisheries echosounders include TVG. What is the difference between such TVG and what is here referred to as “automatic TVG”? Since this is emphasized as a characteristic difference between quantitative and general echosounders I advise to describe the difference in more length. On Line 259 it is stated that general echosounders do not include TVG, while a different formulation again is used on line 383. Please check agreement throughout the text. Also consider to reduce the number of times this is mentioned.

Page 7 line 122, Page 8 line 130: Please check the sentence, it seems to imply that an area is being backscattered.

Page 8 line 136: It may be useful to define two absorption coefficients, or alternatively use 10^(-\\alpha R/20) as the amplitude absorption factor throughout. The units of \\alpha in this line is dB/m, while the \\alpha in Equation (2) is in Np/m if exp means the natural exponential function.

Page 8 line 139: Please check if a “log” is missing from “KTR is 10 K_TR.”

Page 8 line 139: TS is 10 log (\\sigma_bs / r_0^2). Similarly for definitions of logarithmic quantities throughout, please check if reference quantities are missing.

Page 9 line 151: Please check the sentence. Can it be divided?

Page 10-11 table 1: It would be helpful for the reader with a brief explanation already here about of these high transmit powers were chosen. Korneliussen et al., ICES Journal of Marine Science, 65(6), 2008, contains recommendations that could be relevant for comparison.

Is the “Beam angle” in the table equal to what is referred to as the beam width in the text? (Often, the beam width is understood as two times the -3 dB beam angle.)

Page 13 line 223: It is stated that direct comparison between measured target strengths between the general and scientific echosounders is difficult because the measurement frequencies are different. A verification is therefore made by comparing the measurement results in terms of fish abundance. Is this the whole motivation for measuring on fish in the present work? The text should explain clearly how this approach overcomes the problem that the frequencies are different, and why the measurements on fish are desirable in addition to measurements on the calibration ball.

Page 14 line 246: Please review the sentence “When comparing …”, which is difficult to follow.

Page 18 line 290: Please adjust to clarify the calibration state of the echosounder for this first measurement (and for the other results reported). Was it made before any calibration attempts, with factory adjustment values, or after some other form of calibration? Was the initial KTR of the 15 kHz echosounder different from the new value reported at Line 302?

Page 21 line 346: Something seems to be missing from this sentence.

Page 22 line 349: Is this section heading meant to encompass all the text until the next numbered “Results and discussion” heading? It appears that not all of it focuses on “1 ping” measurements. For example, consider adjusting the heading text.

Page 24 line 392: Consider to revise the statement “… echo sounders were found to be larger … ”

Page 27 line 432: This section should discuss why the mean value of S_Vmean increases so strongly with the grid size.

Page 27 line 433: It would be helpful with a discussion of why the maximum values are the same for all the grid sizes.

Page 31 line 490: This still seems unclear. I have not been able to read from the text exactly what signals saturate the receiver. With “saturation of the fish backscattering strength”, is it meant that echoes from fish saturate the receiver? If so, the text would benefit from a discussion of how this leads to an overestimate of abundance.

Page 31 line 492: If the two calibration methods lead to the same abundance measurement results, were the calibration factors almost equal and this result already expected?

Page 32 line 507: Please revise to clarify what is meant by that the slope of the seabed was not smaller than one-half of the beam width. For example, is the slope the angle between the seabed plane and the horizontal? Perhaps a brief definition of slope could be included where the word is first used.

Page 33 line 515: Consider removing the word “While”.

Page 33: With regard to possible reasons for the observed variations, did you also consider the variability in the first two reflections (bottom and surface) affect the sound beam and thus e.g. the footprint (backscattering area) contributing to the second bottom reflection? How were the weather conditions, with respect to scattering at the surface? Alternatively, would it be possible to reduce the transmit power while calibrating, to be able to use the first bottom echo, combined with a study of the uncertainty resulting from changing the transmit power between high and low? This would of course increase the personnel workload somewhat.

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Reviewer #1: No

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Calibration of Commercial Fisheries Echo Sounders Using Seabed Backscatter for the Estimation of Fishery Resources

PONE-D-23-17337R3

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