PONE-D-24-42271Discussion on pore characteristics of shale based on NMR and SEM fractal dimension

-- taking the Upper Paleozoic shale in Ordos Basin as an examplePLOS ONE

Dear Dr. zhao,

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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Fateh Bouchaala

Academic Editor

PLOS ONE

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Additional Editor Comments:

The authors should highlight the main contribution of this work to the topic of fractals or/and to the investigation of the Upper Paleozoic Shanxi Formation of the Ordos Basin. Furthermore, introduction should be re-written and English editing is needed.

Best regards

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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: No

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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: No

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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: In this paper, authors proposed to examine the pore structure and fractal characteristics of shale in the Upper Paleozoic Shanxi Formation of the Ordos Basin. The study analyses the relationship between the NMR fractal dimension and factors such as mineral composition, geochemical parameters, and physical properties, utilizing SEM imaging and artificial intelligence techniques.

The writing quality of the paper is of a moderate level, so I recommend authors to improve the general quality of the writing based on the comments hereafter especially for the introduction which is quite weak.

Technically, results in this study are interesting but I do not see novelty in the paper, and I urge authors to emphasize the novelty in the approach as I could not see it clearly. Moreover, I have several questions and suggestions to improve the paper content and quality as at this stage. They can be found in the attached file.

Reviewer #2: The manuscript does not fully adhere to the required format. For example, it uses "0. Introduction," "1. ~," and "2. ~" instead of following standard headings. Also, the line spacing on pages 12 and 15 is inconsistent, likely due to the use of MathType for in-line equations. Consider replacing these with Microsoft Word’s built-in equation editor (“Insert > Equation > Insert New Equation”). Additionally, a PDF format of the manuscript should be submitted to ensure the format remains stable during submission.

In Chapter 1, it would be beneficial to include a well location map, regional map, or geological map to illustrate the geological setting as Figure 1. I also recommend adding photos of the experimental equipment as Figures 2a, 2b, 2c, and so forth.

In Chapter 2.2, the first sentence repeats “Nuclear magnetic resonance.” Please revise to avoid redundancy.

In Figure 2(c) and (d), the blue circle you mention is missing. Please correct the figure or the associated text.

In Equation 1, you introduce , but do not define the role of . Please clarify this in the text.

Figure 4 contains four plots with arrows and descriptions that overlap with the plots. To improve readability, place the legend separately on either the right or left side of the figure.

In general, many sentences in the manuscript are overly long and complex, likely due to an attempt to condense information. For example, on the bottom of page 18: “Organic matter pores are rare in shale; only 2 samples in argon ion-polished samples have organic matter pores and a small number of pores are developed. Organic matter pores account for a small proportion of organic matter and usually cannot be connected. Organic matter pores contribute minimally to movable fluid pores and irreducible fluid pores, so the relationship between organic carbon content and NMR fractal dimension is weak.” Please revise to keep sentences shorter and clearer throughout the manuscript.

Finally, in Figure 7b, you note a negative correlation between movable fluid pores and total porosity. However, the y-axis range (2.970–2.995) is inconsistent with the previous range (2.978–2.990). Please present Figure 7b with a y-axis range of 2.978–2.990, along with the correlation coefficient value.

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Reviewer #1: Yes:  Mohamed Soufiane Jouini

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-24-42271 review.pdf

PONE-D-24-42271R1NMR and SEM fractal dimensions explore shale pore structure

—— taking the Upper Paleozoic shale in Ordos Basin as an examplePLOS ONE

Dear Dr. zhao,

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 Feb 12 2025 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:

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• 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Fateh Bouchaala

Academic Editor

PLOS ONE

Additional Editor Comments:

Comments and questions from one of the reviewers were not addressed. Please address them to improve the manuscript and make it publishable.

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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 #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 #1: Partly

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: No

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: No

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: In this paper, authors proposed to examine the pore structure and fractal characteristics of shale in the Upper Paleozoic Shanxi Formation of the Ordos Basin. The study analyses the relationship between the NMR fractal dimension and factors such as mineral composition, geochemical parameters, and physical properties, utilizing SEM imaging and artificial intelligence techniques.

Several of my comments stated in my first revision were ignored and left without response. Authors should either implement suggested improvements or reply why they refuse to implement them. They cannot ignore reviewers comments it is not acceptable. Also, the writing quality of the paper still need significant improvement.

Introduction:

The introduction is too short and does not highlight enough the work done in fractals to characterize rock properties. It need a significant re-writing.

• Authors did not highlighted the novelty in the approach as I requested in my first revision.

• 1 introduction -> Introduction

• shale reservoir -> Shale reservoir

• “At present, the fractal dimension is mainly obtained by SEM image analysis”

This statement is not true and should be corrected indeed several research studies used FIB-SEM, 3D X-Ray Micro-Computed. Please see the list of papers that you should refer to in your paper.

- Sulieman H, Jouini MS, Alsuwaidi M, Al-Shalabi EW, Al Jallad OA (2024) Multiscale investigation of pore structure heterogeneity in carbonate rocks using digital imaging and SCAL measurements: A case study from Upper Jurassic limestones, Abu Dhabi, UAE. PLoS ONE 19(2): e0295192. https://doi.org/10.1371/journal.pone.0295192

- Jouini, M.S., Alabere, A.O., Alsuwaidi, M. et al. Experimental and digital investigations of heterogeneity in lower cretaceous carbonate reservoir using fractal and multifractal concepts, (2023). Scientific Reports 13, 20306 https://doi.org/10.1038/s41598-023-47681-w

• Section 4.2: “The picture optimized by ImageJ Weka Segmentation artificial intelligence is then analyzed by Image J software: set the picture to 8-bit, carry on binary processing, close the edge of the line in the picture, close the pore, fill the hole, and apply the software analysis function to get the parameters such as pore area, perimeter, area porosity and so on[20]” Authors stated that they open the Weka Segmentation artificial intelligence tool and use it to improve the image segmentation results. However they did not specify which AI method was used what is its sensitivity advantages and limitations. Authors need to state this as it is a crucial step of the method proposed.

• Section 4.3 Traditionally, the usual formula used for Dathe's formula is based on box-counting technique to compute the fractal dimension Df:

� N(ϵ) is the number of boxes of side length ϵ that are needed to cover the structure and ϵ represents the box size.

� The equation provided in (1) is not common so please provide references at least to know who proposed it and in which context it was used.

• Several authors tried to investigate possible relationship between experimental fractal dimension (here NMR) and image fractal dimension (here SEM). Since you have all the results could you provide any comments regarding this?

Reviewer #2: The advantage of FIB-SEM experiments lies in their capability for microfabrication of materials.

SEM experiments are primarily used for observing surface morphology and compositional analysis

of materials but do not possess microfabrication capabilities. This study mainly focuses on observing

the pore structure characteristics of rock samples, thus SEM experimental analysis was adopted.

Provided a brief introduction to the method of smart pore recognition using ImageJ Weka

Segmentation and described its advantages.

Revised the sentences that needed modification as suggested by the reviewer. We are very grateful

for the valuable comments provided by the reviewer.

Made comprehensive revisions to the abstract of the paper.

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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.

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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: Yes:  Mohamed Soufiane Jouini

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-24-42271_R1 review.pdf

PONE-D-24-42271R2NMR and SEM fractal dimensions explore shale pore structure—— taking the Upper Paleozoic shale in Ordos Basin as an examplePLOS ONE

Dear Dr. Zhao,

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 Apr 19 2025 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:

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• 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Fateh Bouchaala

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear authors,

Many relevant comments from one of the reviewers were not addressed. I invite the authors to fully address these comments before submitting the next revision.

Regards

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[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.

PONE-D-24-42271R3NMR and SEM fractal dimensions explore shale pore structure—— taking the Upper Paleozoic shale in Ordos Basin as an examplePLOS ONE

Dear Dr. zhao,

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 May 19 2025 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols .

We look forward to receiving your revised manuscript.

Kind regards,

Fateh Bouchaala

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

I urge the authors to carefully review the reviewers' comments, which have not been addressed since first revised version. The reviewers' comments are reasonable and can be adequately addressed.

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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)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

**********

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

Reviewer #1: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Introduction:

- Authors stated: “Currently, there are three main methods to obtain the fractal

dimension of shale pores: SEM image analysis [14-15], nitrogen adsorption model [16] and mercury porosimetry [17].”

This statement is not true and should be corrected indeed several research studies used digital images such as thin section, FIB-SEM, 3D X-Ray Micro-Computed in addition to other experimental laboratory measurements such as NMR.

Please see the list of papers that you should refer to in your paper.

- D. Abdassah, P. Permadi, R. Sumantri. Saturation exponents derived from fractal modeling of thin sections Presented at the SPE Asia Pacific Oil and Gas Conference Held in Adelaide, Australia (1996)

- Z. Zhang, A. Weller Fractal dimension of pore-space geometry of an Eocene sandstone formation Geophysics, 79 (6) (2014), pp. 377-387

- - Sulieman H, Jouini MS, Alsuwaidi M, Al-Shalabi EW, Al Jallad OA (2024) Multiscale investigation of pore structure heterogeneity in carbonate rocks using digital imaging and SCAL measurements: A case study from Upper Jurassic limestones, Abu Dhabi, UAE. PLoS ONE 19(2): e0295192. https://doi.org/10.1371/journal.pone.0295192

- Jouini, M.S., Alabere, A.O., Alsuwaidi, M. et al. Experimental and digital investigations of heterogeneity in lower cretaceous carbonate reservoir using fractal and multifractal concepts, (2023). Scientific Reports 13, 20306 https://doi.org/10.1038/s41598-023-47681-w

Section 4.1:

Authors stated the following:” The images optimized and identified by the ImageJ Weka Segmentation intelligent recognition module are then analyzed for pore structure: set the picture to 8-bit, carry on binary processing”.

I understand that authors used software to process the segmentation and geometric characterization of pores. However, using the software should be detailed in terms of the methodology used. In my previous revision I requested to authors to explain which segmentation method is sued to “carry on binary processing”. The authors did not address this request.

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Reviewer #1: Yes:  Mohamed Soufiane Jouini

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NMR and SEM fractal dimensions explore shale pore structure

—— taking the Upper Paleozoic shale in Ordos Basin as an example

PONE-D-24-42271R4

Dear Dr. Keying,

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PLOS ONE

Additional Editor Comments (optional):

The authors improved the manuscript after multiple revisions, by addressing authors suggestions.

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