Dear Dr. Coskun,

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 Jun 08 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.

• 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,

Ashad Kabir, PhD

Academic Editor

PLOS ONE

Journal Requirements:

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

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

3. Please amend your list of authors on the manuscript to ensure that each author is linked to an affiliation. Authors’ affiliations should reflect the institution where the work was done (if authors moved subsequently, you can also list the new affiliation stating “current affiliation:….” as necessary).

4. Please ensure that you refer to Figure 1 in your text as, if accepted, production will need this reference to link the reader to the figure.

5. Please remove your figures from within your manuscript file, leaving only the individual TIFF/EPS image files, uploaded separately. These will be automatically included in the reviewers’ PDF.

6. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

Additional Editor Comments :

The reviewers have raised several major concerns. Please carefully consider all comments and ensure that each one is thoroughly addressed in revision.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: No

**********

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

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: No

**********

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: No

**********

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

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: No

**********

Reviewer #1: The topic is very interesting and necessary because currently there are many software for data visualization but limited articles with comparisons on them.

The introduction is too short, the authors should provide other research articles on data visualization (although limited but there are if you google), then draw the novelty of this study.

Figures quality are low, so I cannot read some of the texts in Figure 3 and 4. Please improve the quality.

Line numbers should be added.

Reviewer #2: 1. The abstract should present to the reader in an objective way: Objective, Methodology, Findings, and the relevance of the research. I suggest that you reconstruct the abstract focussing on the points presented;

2. The introduction does not contextualise the subject, it does not present the problem, the objectives, a summary of the methodology, the main findings.

3. The article is not structured as a scientific article, but as a summarised version of a book chapter.

I suggest that the authors reorganise the article and resubmit it at a later date.

Reviewer #3: This study seeks to explore the diverse applications of biomedical visualization in various societal contexts and propose an evaluation framework for scoring visualizations using a bespoke algorithm. Furthermore, this research aims to present an example of interactive data visualizations for research-oriented datasets, achieved through both the scoring of research-based figures and the development of a fully interactive web-based visualization platform.

The motivation behind this study appears to be compelling; however, the overall structure of the paper lacks clarity, making it difficult to follow. It would be beneficial if the authors aligned the figures more closely with the corresponding text to enhance readability and coherence.

Furthermore, the structure of the paper deviates notably from conventional norms. For instance, the introduction is too brief to adequately convey the core ideas underpinning the work; no related literature is reviewed; and it is difficult to discern the principal components of the proposed strategy or the rationale behind the introduced metrics.

**********

what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step.

Dear Dr. Coskun,

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.<h3 style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 宋体; color: rgb(0, 0, 0); text-align: justify;"><samp>This paper proposes a new algorithmic framework, M.E.D.V.I.S., which quantifies the quality of biomedical images using four metrics: complexity, color usage, white space, and number of visualizations. It then compares and evaluates this framework against 26 commonly used visualization tools. The authors also developed an interactive visualization platform, SpatioView, to enhance the presentation of spatial omics data, emphasizing the importance of standardization and reproducibility in image design.</samp><o:p></o:p></h3><h3 style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 宋体; color: rgb(0, 0, 0); text-align: justify;"><samp>Minor revision suggestions:</samp><o:p></o:p></h3><h3 style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 宋体; color: rgb(0, 0, 0); text-align: justify;"><samp>1. Further quantify the rationality of scoring weights.Although four scoring metrics have been proposed, the weights of each metric for the final “good/bad” classification are not yet clear. It is recommended to add weight sensitivity analysis or expert scoring comparisons to enhance the persuasiveness of the evaluation system.</samp><o:p></o:p></h3><h3 style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 宋体; color: rgb(0, 0, 0); text-align: justify;"><samp>2. The article provides a detailed introduction to SpatioView, but the demonstration examples are too brief. It is recommended to supplement with screenshots of higher-resolution or typical data to enhance its visual appeal and persuasiveness.</samp><o:p></o:p></h3><h3 style="margin-right: 0cm; margin-left: 0cm; font-size: 12pt; font-family: 宋体; color: rgb(0, 0, 0); text-align: justify;"><samp>3. It is recommended to include feedback from trials of M.E.D.V.I.S. or SpatioView in actual research or teaching settings to strengthen the argument for its practicality.</samp><o:p></o:p><samp> </samp></h3>

Please submit your revised manuscript by Sep 25 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.

• 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 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,

Wenhao Ouyang

Academic Editor

PLOS ONE

Journal Requirements:

If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 

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:

This paper proposes a new algorithmic framework, M.E.D.V.I.S., which quantifies the quality of biomedical images using four metrics: complexity, color usage, white space, and number of visualizations. It then compares and evaluates this framework against 26 commonly used visualization tools. The authors also developed an interactive visualization platform, SpatioView, to enhance the presentation of spatial omics data, emphasizing the importance of standardization and reproducibility in image design.

Minor revision suggestions:

1. Further quantify the rationality of scoring weights: Although four scoring metrics have been proposed, the weights of each metric for the final “good/bad” classification are not yet clear. It is recommended to add weight sensitivity analysis or expert scoring comparisons to enhance the persuasiveness of the evaluation system.

2. SpatioView visualization display effects are weak: The article provides a detailed introduction to SpatioView, but the demonstration examples are too brief. It is recommended to supplement with screenshots of higher-resolution or typical data to enhance its visual appeal and persuasiveness.

3. Lack of user feedback or validation in real-world application scenarios: It is recommended to include feedback from trials of M.E.D.V.I.S. or SpatioView in actual research or teaching settings to strengthen the argument for its practicality.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: N/A

**********

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

Reviewer #1: The authors have significantly improved the manuscript, so I have no further questions regarding it.

Cheers,

Reviewer #2: Dear Authors

The research article “What is a ‘Good’ Figure: Scoring of Biomedical Data Visualization” presents a comprehensive approach to evaluating the quality of biomedical figures using computational and design-oriented metrics. The need for such a framework arises from the widespread variability and subjectivity in figure design across biomedical research publications and tools.

To address this, the authors developed M.E.D.V.I.S. (Metrics for Evaluation and Discretization of Biomedical Visuals using an Iterative Scoring Algorithm), an algorithm that analyzes figures based on four core features: visual complexity, color usage, whitespace ratio, and number of distinct visualization elements. By combining unsupervised machine learning techniques—PCA, t-SNE, UMAP for dimensionality reduction—and clustering via K-means, figures are categorized into performance groups. Each image receives a scoring dashboard with actionable feedback, aiding researchers in improving figure clarity.

The team also conducted a comparative benchmark of 26 visualization tools ranging from coding-based platforms (Python/Plotly, MATLAB) to GUI-based systems (Tableau, Excel, FusionCharts). Tools were ranked by usability (time to render a simple figure), customization potential, financial cost, and required technical knowledge. Tableau and IBM Watson were identified as strong multi-purpose tools, while coding environments offered unmatched flexibility but steeper learning curves.

To showcase practical implementation, the authors ran three case studies:

- Figure Scoring Analysis: Applying M.E.D.V.I.S. to real-world figures, revealing disparities in perceived and algorithmic figure quality and highlighting issues like redundancy, caption formatting inconsistencies, and design imbalances.

- Visualization Style Comparison: Testing different software on the same spatial genomic dataset, showing how aesthetics and interpretability shift across platforms and chart types.

- SpatioView Platform Development: Introducing an interactive, browser-based tool for visualizing high-dimensional spatial multi-omics data. Built using PyScript and HTML, it allows dynamic user exploration without coding, though challenges remain with runtime performance and library limitations (e.g., support for UMAP/Diffmap).

In the discussion section, the article outlines persistent challenges in biomedical visualization:

- The subjectivity of design choices, which can introduce bias.

- The lack of reproducibility across platforms, especially non-coded environments.

- The steep learning curve and educational gaps in training biomedical researchers on visualization principles.

The conclusion reinforces the value of standardization. M.E.D.V.I.S. and SpatioView together represent important steps toward automated evaluation, accessibility, and interactive exploration of complex biomedical data. These tools lay the groundwork for reproducible, interpretable, and inclusive figure design across academia and industry.

Improvement Opportunities:

- Broader Testing: Apply M.E.D.V.I.S. to a larger, more diverse figure corpus to validate performance across domains (e.g. histopathology, neuroimaging).

- Accessibility Features: Integrate checks for visual accessibility (e.g. color contrast ratios, font sizes, alternative text) to ensure inclusiveness.

- Scoring Weight Optimization: Use expert feedback to refine the influence of each criterion—some may disproportionately impact clarity (e.g. whitespace vs. color).

- Cross-platform Reproducibility: Emphasize methods for preserving figure integrity across GUI and script-based tools, perhaps via exportable templates.

- User Experience Evaluation: Conduct usability studies for SpatioView with biomedical audiences to iteratively improve its design and performance.

English Language Evaluation:

The manuscript employs formal and technically sound academic English. It demonstrates strong domain-specific vocabulary and structured scientific writing. Highlights include:

- Effective use of passive voice and transitional phrases typical of peer-reviewed journals

- Clear section headers and organized content progression

- Minor redundancies and occasional verbose constructions could benefit from tightening

- Some syntax inconsistencies (e.g., mixed use of British and American spelling in citations)

- Terminology refinement would help avoid confusion (e.g., "visual count" vs. "number of visualizations")

Overall, the language is appropriate for scientific publication but could benefit from professional copyediting for conciseness and consistency.

The current version is much better than the first one, but there are still points for improvement, which I've listed above.

I wish you a good review.

**********

what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy

Reviewer #1: No

Reviewer #2: Yes:  Dr. Marcio Basilio

**********

[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

What is a “Good” Figure: Scoring of Biomedical Data Visualization

PONE-D-25-05417R2

Dear Dr. Coskun,

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

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

An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager®  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support .

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Wenhao Ouyang

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

This manuscript has been revised based on the comments from the peer review process and has reached the level suitable for publication.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #2: All comments have been addressed

Reviewer #4: All comments have been addressed

**********

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

Reviewer #2: (No Response)

Reviewer #4: Yes

**********

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

Reviewer #2: N/A

Reviewer #4: Yes

**********

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

The PLOS Data policy

Reviewer #2: Yes

Reviewer #4: Yes

**********

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

Reviewer #2: Yes

Reviewer #4: Yes

**********

Reviewer #2: Technical Report to the Authors

Manuscript: What is a “Good” Figure: Scoring of Biomedical Data Visualization

Manuscript Number: PONE-D-25-05417R2

1. Context

This technical report refers to the second revised version (R2) of the manuscript submitted to PLOS ONE, titled “What is a ‘Good’ Figure: Scoring of Biomedical Data Visualization.”

A comparative analysis between this version and the previous one (R1) shows that the authors have diligently and consistently implemented the recommendations provided by the editorial board and peer reviewers. The modifications introduced strengthen the methodological soundness, improve the clarity of the argumentation, and significantly enhance the visual and structural quality of the paper, thereby fully meeting the journal’s standards for originality, rigor, and editorial compliance.

2. Summary of improvements implemented

2.1. Methodological reinforcement

The authors incorporated significant advances that consolidate the validity and reliability of the proposed model:

Inclusion of the Weight Sensitivity Analysis Framework, demonstrating the robustness of the M.E.D.V.I.S. algorithm to variations in the weighting of evaluation criteria (complexity, color usage, whitespace, and number of visualizations).

Addition of a usability test with human evaluators, comparing automated classifications and human judgments, with 85% agreement and accuracy close to 90%.

Expansion of the results and case study sections, notably through the enhancement of SpatioView, now presented with high-resolution images and a detailed description of its interactive functions.

These additions directly address the reviewers’ requests for empirical validation and justification of the weighting logic used in the algorithm.

2.2. Structure and scientific clarity

The text has been fully reorganized according to the IMRaD structure (Introduction, Methods, Results, and Discussion), ensuring better flow and section delimitation.

The Introduction now provides a more comprehensive contextualization, with updated references and a clear statement of the research gap, problem definition, and contribution.

The Discussion has been substantially expanded to include limitations, implications, and future research perspectives, in alignment with best scientific reporting practices.

2.3. Visual quality and editorial compliance

All figures were reprocessed at 600 DPI, improving contrast, readability, and caption clarity.

New supplementary figures (Supplementary Figures S2 and S8) were included to reinforce analytical transparency.

The manuscript now fully complies with PLOS ONE editorial standards, including metadata structure, author affiliations, ethics statements, data availability, and conflict of interest declarations.

3. General assessment

The current revision presents a substantially strengthened manuscript, transforming an initial conceptual proposal into a complete and verifiable empirical study.

The improved clarity, coherence between objectives, methods, and results, and the achieved level of empirical evidence justify publication in its current form.

The paper provides a relevant contribution to the biomedical visualization field by proposing and validating a standardized, replicable method for assessing the quality of scientific figures, with direct applications in research, education, and scientific communication.

4. Final recommendation

Considering:

the full incorporation of reviewer recommendations;

the substantial improvement in methodological and editorial quality;

and the internal consistency of the findings presented;

I recommend the acceptance of the manuscript in its current form, with no further revisions required.

Signature:

Reviewer – PLOS ONE

Reviewer #4: I have carefully evaluated the revised version of the manuscript. The authors have satisfactorily addressed all previous concerns and substantially improved the overall quality of the paper. The methodology, data presentation, and discussion are now clear and coherent.

The manuscript meets the journal’s standards for scientific rigor and clarity. I recommend acceptance of this paper in its current form.

**********

what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy

Reviewer #2: Yes:  Prof. Dr. Marcio Pereira Basilio

Reviewer #4: No

**********