PCOMPBIOL-D-25-01941

A framework for evaluating predicted sperm trajectories in crowded microscopy videos

PLOS Computational Biology

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Jing Chen

Academic Editor

PLOS Computational Biology

Dimitrios Vavylonis

Section Editor

PLOS Computational Biology

Additional Editor Comments:

The reviewers complimented the value and novelty of the method. However, there are mixed opinions about the clarity of the manuscript, as well as ambiguity about the validation sample size. Please address these concerns in the revision.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Dear authors,

The topic of your research is interesting and original. There are, however, some comments mainly about the organization of the manuscript. The experimental design of the study is not described in the materials and methods part, but it seems that this information is included in the results part. For instance:

- L100: Tracking Quality’s Effect on Standard Sperm Analysis Outputs

This section could be included in the introduction part or could be discussed/compared/contrast with the results in the discussion.

- Line 129: “We then provide three experiments that illustrate poor tracking assumptions and the effects on the calculated kinematic parameters.”

This sentence could be the final in the introduction. The three experiments are not described in the materials.

- The following sections: Baseline Tracker and Dataset (L132), Experiment 1: A Poorly Configured Tracker (L152), Experiment 2: Short vs. Long Timescale Trajectories (L177), Experiment 3: Bounding Boxes vs. Centroids (L204), Evaluating Sperm Detection and Tracking (L235), Unique Considerations for Evaluating Sperm Detection (L269), Unique Consideration for Evaluating Sperm Tracking (L301), Evaluation on the Dataset (L337-44)

In the above mentioned paragraphs information about the experimental design are included in.

- The sentence “We also output Earth Mover’s Distance (EMD) scores for each kinematic parameter for the suboptimal and optimal approach when compared to the ground truth (L368-69)

This approach could be included in the materials as part of the corresponding step.

Please, re-organize the results and materials and methods part.

Reviewer #2: The manuscript presents a computational framework for evaluating sperm tracking algorithms in crowded microscopic fields. The topic is relevant and the hypothesis sound strong. The manuscript is well structured and written clearly. I enjoyed reading it, up the number of videos thats being assessed. However, there are some issues needs to be clarify.

1. The dataset used for validation is too small. Even though they used several tracking system. You could give the number of spermatozoa that are being evaluated instead of number of videos. This details should be given in the abstract.

2. The proposed metrics are adapted from existing tracking systems, so their novelty must be clearly defined in the methods.

3. The biological implications of improved tracking must be discussed more cautiously, as they didnt induced capacitation nor the fertility.

Overall, the novelty of the paper sound. However, the limitations of the study must be clearly given in the abstract and the discussion. At least why authors chose 3 videos for validating the existing tracking system such as due the number of sperm trajectories, time manner etc. For instance, whether this was due to number of trajectories, frame duration, ot computational limitations. Although, analysing longer videos provides richer motion data than traditional casa systems that are typically tracks sperms for 1-2 sec). This approach must be clearly explained if the dataset contains the number of spermatozoa that are being evaluated (300 spermatozoon), instead of number of videos. Therefore, the authors may indicate the total number of trajectories analyzed and how many overlapping trajectories are detected, rather than simplifiying the number of videos. Otherwise, this dataset may create ambiguity for the readers. This might change the overall assumptions more trustworthy.

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PCOMPBIOL-D-25-01941_reviewer.pdf

Dear Dr. Hart,

We are pleased to inform you that your manuscript 'A framework for evaluating predicted sperm trajectories in crowded microscopy videos' has been provisionally accepted for publication in PLOS Computational Biology.

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology.

Best regards,

Jing Chen

Academic Editor

PLOS Computational Biology

Dimitrios Vavylonis

Section Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Dear authors,

The manuscript is clear and well documented, with all the necessary information and explanations included.

Thank you for your cooperation.

Reviewer #2: The authors have carefully addressed the comments and the revised version is suitable for publication.

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Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —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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Reviewer #1: No

Reviewer #2: No