PONE-D-21-35862AI-DRIVEN QUANTIFICATION OF GROUND GLASS OPACITIES IN LUNGS OF COVID-19 PATIENTS USING 3D COMPUTED TOMOGRAPHY IMAGINGPLOS ONE

Dear Dr. Saha,

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. Your manuscript has been evaluated by two experts in the field and their comments are attached here below for you reference. You will see that, in particular, the reviewers requested additional details about the methods and datasets used in this study.

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We look forward to receiving your revised manuscript.

Kind regards,

Francesco Bianconi, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

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2. Thank you for stating the following in the Acknowledgments Section of your manuscript:

“Ashish Sharma would like to acknowledge support from the National Cancer Institute U24CA215109. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. T. K. Satish Kumar and Rajiv K. Kalia (RKK) would like to acknowledge the support of Zumberge Research and Innovation Fund at the University of Southern California. RKK would like to thank Sarah Kalia for helpful discussions.”

Please note that funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“Ashish Sharma would like to acknowledge support from the National Cancer Institute U24CA215109. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. T. K. Satish Kumar and Rajiv K. Kalia (RKK) would like to acknowledge the support of Zumberge Research and Innovation Fund at the University of Southern California. RKK would like to thank Sarah Kalia for helpful discussion”

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

3. Thank you for stating the following financial disclosure:

“Ashish Sharma would like to acknowledge support from the National Cancer Institute U24CA215109. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. T. K. Satish Kumar and Rajiv K. Kalia (RKK) would like to acknowledge the support of Zumberge Research and Innovation Fund at the University of Southern California. RKK would like to thank Sarah Kalia for helpful discussion”

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."

If this statement is not correct you must amend it as needed.

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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: Yes

Reviewer #2: Yes

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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 proposed method is good. Manuscripts have been written with the standards of Scientific Writing Publications. Manuscript need equip with a recapitulation of test results for all tested data. References from old journal articles changed to the latest issue.

Reviewer #2: the author proposed a manuscript which has a title "AI-DRIVEN QUANTIFICATION OF GROUND GLASS OPACITIES IN LUNGS OF COVID-19 PATIENTS USING 3D COMPUTED TOMOGRAPHY IMAGING". This research come up with a hot issues nowdays. The manuscript is explained structurely.

But need some explaination for some parts as follow

1. in line 252, author mentions that the network is the same as VGG-16 but author reduce the first four convolutiion layers into two. It was done to achieve best performance. how author proof this one ?

2. author mention that, the MosMedData is used in this research. what is the image size ? because if author modified model from VGG-16 which has its on pixel size ? what kind of preprocessing was done to the dataset ?

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Reviewer #1: No

Reviewer #2: Yes: Ir. Rahmat Hidayat

[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.

AI-DRIVEN QUANTIFICATION OF GROUND GLASS OPACITIES IN LUNGS OF COVID-19 PATIENTS USING 3D COMPUTED TOMOGRAPHY IMAGING

PONE-D-21-35862R1

Dear Dr. Saha,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted once it meets all outstanding technical requirements.

Within one week, you will receive an e-mail detailing the required amendments. When these have been addressed, you will receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Francesco Bianconi, Ph.D.

Academic Editor

PLOS ONE