-->PONE-D-25-48731-->-->Compression benchmarking of holotomography data using OME-Zarr format-->-->PLOS ONE

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This work was supported by National Research Foundation of Korea grant funded by the Korea government (MSIT) (RS-2024-00442348, 2022M3H4A1A02074314), Institute of Information & communications Technology Planning & Evaluation (IITP; 2021-0-00272) grant funded by the Korea government, Korea Institute for Advancement of Technology (KIAT) through the International Cooperative R&D program (P0028463), and the Korean Fund for Regenerative Medicine (KFRM) grant funded by the Korea government (the Ministry of Science and ICT and the Ministry of Health & Welfare) (21A0101L1-12).

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This work was supported by National Research Foundation of Korea grant funded by the Korea government (MSIT) (RS-2024-00442348, 2022M3H4A1A02074314), Institute of Information & communications Technology Planning & Evaluation (IITP; 2021-0-00272) grant funded by the Korea government, Korea Institute for Advancement of Technology (KIAT) through the International Cooperative R&D program (P0028463), and the Korean Fund for Regenerative Medicine (KFRM) grant funded by the Korea government (the Ministry of Science and ICT and the Ministry of Health & Welfare) (21A0101L1-12).

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Additional Editor Comments:

I suggest following the reviewer comments.

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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

Reviewer #3: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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

Reviewer #3: 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

Reviewer #3: 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 paper presents a sound and thorough analysis of compression algorithms applied to HT data. The manuscript is well-structured, clearly written, and easy to follow. The experimental evaluation is solid and well designed, covering both compression and decompression performance effectively.

However, the statement that the sampling strategy “preserves data diversity representative of real-world scenarios” would benefit from additional support or justification — for instance, through a quantitative assessment of data diversity or a more detailed explanation of how representativeness was ensured during sampling.

Additionally, it could be helpful to visually highlight the best-performing algorithm(s) in the figures, which would make the comparison clearer and improve the overall readability of the experimental results.

Reviewer #2: The manuscript titled “Compression benchmarking of holotomography data using OME-Zarr format” presents a benchmarking of data compression strategies for holotomography data stored in the OME-Zarr format, using six representative datasets from five biological samples, where 4 kinds of utilization of preprocessing filters and 13 compression algorithms across multiple compression levels are tested. The work is systematic and comprehensive, and it is worth of publishing after some essential improvements and revisions. Here are the comments:

# Major

1. It is not clear what are the key insights. It would be better to clarify them at the beginning of the manuscript. It is also recommended to state how this benchmark is used to guide and improve the workflow process or corresponding compression methods, to enhance the impact of the manuscript.

2. The manuscript reads like all tests were performed on one workstation, instead of a real distributed system. It is unclear whether the test results can be reliably applied in the real-world scenario; clarifying possible limitations may help.

3. Why some datasets were collected by a customized system while others are not. It is recommended to clarify the reason.

4. It would be better to select a specific application to verify whether the benchmark can assist in promoting the workflow.

5. It is highly recommended to provide reasons on why combinations like “Pcodec (M)” and “blosc-zstd (M)” can reach the highest performance in the proposed metric.

# Minor

1. It would be better to introduce some basic concepts, such as compression ratio and the relationship between the ratio and speed performance.

2. It is recommended to state the quantitative values to describe the “Level” in Table 2.

3. It is recommended to avoid such a big blank on Page 10.

4. It would be better to mention some quantitative disadvantages of TIFF and HDF5 compared with Zarr.

Reviewer #3: The manuscript “Compression benchmarking of holotomography data using OME-Zarr format” focuses on the interesting topic of efficient data compression for very large 3D imaging database, namely Holotomography (HT).

The proposed investigation considers the OME-Zarr format, discussing how the HT data can be managed within this this compressed data storage format. As for any compression strategy, unlike preliminary preprocessing steps, the data encoding strategy is the core to achieve advanced data management in terms of compression ratio, compression and decompression bandwidth, quality of the recovered data (i.e. decoded data).

The authors provide a comprehensive analysis by including several datasets acquired in different HT systems and a systematic analysis of the widely used compression algorithms available within the OME-Zarr format.

My general opinion is that the manuscript is well-written and suitable for the publication in PLOS ONE after addressing the following major concerns

1) The authors discussed on the use of OME-Zarr format for HT data compression but without considering other potential alternative. Please provide details and discussion about other solutions even including the expected differences with respect the OME-Zarr format coding in terms of the overall efficiency.

2) Since HT devices considered in this study are commercialized by part of some authors (if I understood correctly), what is the compression data pipeline used in the past for HT data management? Please add these information underlining the advantages using the current OME-Zarr format.

3) The study reports on some performance metric including compression ratio, compression bandwidth and decompression bandwidth. Moreover the authors propose a new throughput-based evaluation metric for generalizing the quantification of the performance of a compression strategy in realistic scenarios. Although this analysis is very interesting, I believe there is a lack of a more direct metric to quantify the information loss caused by data compression. Basically, for a general reader, It would be really useful to "see" some HT images going through the preprocessing/compression/decompression stages. Basically, I suggest to include a figure reporting an uncompressed HT image (as it is obtained from the imaging system) and the same after using the decompression from the OME-Zarr format. Possibly, some similarity metrics between these images (e.g. SSIM, MSE) could help to understand the information loss of the data depending of the selected compression strategy.

4) Even if the authors claim that “Although prior studies have reported compression benchmarks in other imaging contexts [29-31], a comprehensive evaluation tailored to HT imaging has not been performed”, some studies are reported for some 3D imaging modalities also including HT. Please see and comment about the following papers

• B. Subramanian et al., “On a hybrid lossless compression technique for three-dimensional medical images,” J Appl Clin Med Phys 2021;22(8):191–203.

• O.H. Nagoor et al., “Sampling strategies for learning-based 3D medical image compression,” Machine Learning with Applications 8 (2022) 100273.

• H.M. Luu et al., “Efficiently compressing 3D medical images for teleinterventions via CNNs and anisotropic diffusion,” Med Phys 2021 Jun;48(6):2877-2890.

• P. Memmolo et al., “Loss Minimized Data Reduction in Single-Cell Tomographic Phase Microscopy Using 3D Zernike Descriptors,” Intell. Comput. 2023;2:Article 0010.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Compression benchmarking of holotomography data using OME-Zarr format

PONE-D-25-48731R1

Dear Dr. Lee,

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

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Additional Editor Comments (optional):

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: All comments have been addressed

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: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

Reviewer #2: Yes

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

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

Reviewer #1: Yes

Reviewer #2: 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: (No Response)

Reviewer #2: We appreciate the authors' efforts in addressing all the comments and improving the manuscript, which is now more systematic and informative and ready to be accepted.

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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: No

Reviewer #2: No

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