Introducing Hann windows for reducing edge-effects in patch-based image segmentation

Nicolas Pielawski; Carolina Wählby

doi:10.1371/journal.pone.0229839

Peer Review History

Original SubmissionOctober 18, 2019
27 Nov 2019 Decision Letter - Jie Zhang, Editor PONE-D-19-29003 Introducing Hann windows for reducing edge-effects in patch-based image segmentation PLOS ONE Dear Mr. Pielawski, 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 revise the manuscript by considering the reviewers' comments. We would appreciate receiving your revised manuscript by Jan 11 2020 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. 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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? 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: Partly Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ****** 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 ****** 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 ****** 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 authors present a procedure to address edge effects in CNN image segmentation. Their experiments are documented in detail and the manuscript is in general well-written. I do however have some recommendations that the authors should consider. References: I find it hard to believe that only 11 references were relevant for this manuscript. The authors should significantly improve their literature review, in order to place their work more rigorously within existing literature. Computational complexity: Although a mention of the general complexity of their method is shown, it would be very much helpful for the reader to display the computational time for the authors technique – along with the benchmark methods. One of the objectives in the era of big data processing is to find the right balance between improvements in accuracy, and time needed to retrieve the desired outputs and as such, this type of information can be particularly useful. Validation: I understand why the authors decided to use the SSIM as validation metric. One thing, the SSIM should be presented in detail and not just put in a reference and second, wouldn’t other established accuracy metrics (such as overall accuracy, precision, recall and F1 score) be also fruitful? Reviewer #2: The paper introduced Hann windows for patch-based image segmentation. The result shows that in terms of Structural similarity index, the Hann windows slightly outperfoms baseline. The novalty of the paper is limited. Eq 6 to Eq 10 are not clear enough, especially the definition of w(i). Only SSIM is used for evaluation, it is necessary to add commonly used metrics for segmentation tasks, such as DICE. Minor: Eq 10, should be if i <= L/2 and j <= J/2. Reviewer #3: This manuscript describes the use of windowing functions on microscope image data that is to be segmented using convolutional neural network (CNN) approaches. In specific, the manuscript compares the effectiveness of several different window functions, including Hann windows. A strength of the approach described in this manuscript is that it provides an effective way to perform CNN-based segmentation on large images by subdividing them into many smaller images, while minimizing any artifacts caused by the segmentation algorithm near the edges of each subdivided image (i.e., edge artifacts). The manuscript is well thought out and well written and only very minimal comments were identified, as described below: 1. With reference to Figure 1 and the color-bar and color look-up tables used in the figure: was a different color look-up table used for the pyramidal window? It was mentioned in the manuscript that the integrated area of the pyramidal window is not 1, while the other window functions do have an integrated area of 1. Was it necessary to compensate for this different integrated area by using a different color look-up table, or alternatively, were the data normalized prior to visualizing as a 2D heatmap? 2. The description of the different approaches and different methods is a bit confusing on page 5, for the top 3 paragraphs. For example, the first paragraph refers to "The five different approaches", while the 3rd paragraph (which is the Fig. 3 caption) refers to "the adjusted SSIM for six different methods". It is a bit unclear of what an "approach" is vs. a "method" and whether there are 5 or 6 of them. In Fig. 3a, there appear to be 5 different window functions shown. For similar reasons, the 2nd paragraph on page 5 is also confusing, in the sentence that reads "Due to a low variance in the SSIM indices for each method but a high variance between methods..." It is unclear here as well what the method is that the sentence is referring to. Clearing up the language in these 3 paragraphs is needed. Finally, along similar lines, the authors might help to clarify the vertical axis of Figure 3 by explaining that this is the improvement in SSIM over baseline, or some wording similar to this. 3. On page 6, first paragraph of the Discussion section, the 2nd sentence contains the word "theory" twice, which is a bit redundant. ****** 6. 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. 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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0229839.r001
Revision 1
13 Jan 2020 Author Response We thank the reviewers for their constructive comments and have revised the manuscript to address their concerns. REVIEWER #1 > References: I find it hard to believe that only 11 references were relevant for this manuscript. The authors should significantly improve their literature review, in order to place their work more rigorously within existing literature. The issue is relatively little discussed as many researchers have access to powerful computers or can reformulate the problem to deal with smaller images. One approach consists of cropping the borders (e.g. Rudolph, Robert, et al. "Efficient identification, localization and quantification of grapevine inflorescences in unprepared field images using fully convolutional networks." arXiv preprint arXiv:1807.03770 (2018)) but can still generate artifacts. > Although a mention of the general complexity of their method is shown, it would be very much helpful for the reader to display the computational time for the authors technique – along with the benchmark methods. Time complexity is defined as <number of patches> times <time complexity of the deep learning model> and thus it will vary from model to model, computer to computer and so on. Using overlapping windows increases the number of patches by a factor of 4 and increases the complete time complexity by the same factor. > The SSIM should be presented in detail and not just put in a reference other established accuracy metrics (such as overall accuracy, precision, recall and F1 score) be also fruitful? Agreed. We added a new metric: the DICE coefficient, which corresponds to the F1 score. REVIEWER #2 > Eq 6 to Eq 10 are not clear enough, especially the definition of w(i). The text was modified to clarify and provide a better explanation of the equations. It is necessary to add commonly used metrics for segmentation tasks, such as DICE. Agreed, we added two more experiments (see fig. 3). > Eq 10, should be if i <= L/2 and j <= J/2. Corrected. REVIEWER #3 > Was a different color look-up table used for the pyramidal window? […] Was it necessary to compensate for this different integrated area by using a different color look-up table, or alternatively, were the data normalized prior to visualizing as a 2D heatmap? The same colour look-up tables were used in the article. The un-normalized windows were normalized. > The description of the different approaches and different methods is a bit confusing on page 5, for the top 3 paragraphs. For example, the first paragraph refers to "The five different approaches", while the 3rd paragraph (which is the Fig. 3 caption) refers to "the adjusted SSIM for six different methods". It is a bit unclear of what an "approach" is vs. a "method" and whether there are 5 or 6 of them. Changed all occurrences of “approach” to “method”, and 5 to 6. There are 5 methods plus 1 baseline, clarified in the revised article. > In Fig. 3a, there appear to be 5 different window functions shown. For similar reasons, the 2nd paragraph on page 5 is also confusing, in the sentence that reads "Due to a low variance in the SSIM indices for each method but a high variance between methods..." It is unclear here as well what the method is that the sentence is referring to. Clearing up the language in these 3 paragraphs is needed. The authors might help to clarify the vertical axis of Figure 3 by explaining that this is the improvement in SSIM over baseline. The three paragraphs were partially reformulated. > On page 6, first paragraph of the Discussion section, the 2nd sentence contains the word "theory" twice. Corrected. Attachments Attachment Submitted filename: rebuttal_letter.docx https://doi.org/10.1371/journal.pone.0229839.r002
27 Jan 2020 Decision Letter - Jie Zhang, Editor PONE-D-19-29003R1 Introducing Hann windows for reducing edge-effects in patch-based image segmentation PLOS ONE Dear Mr. Pielawski, 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 address the comments of reviewer 2. We would appreciate receiving your revised manuscript by Mar 12 2020 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, Jie Zhang Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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 ******** 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 ****** 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: Yes 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: Yes 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: (No Response) Reviewer #2: The author showed the experiment result of Dice in Fig 4, but didn't give the overall performance comparision in terms of Dice and the discussion is not sufficient. ****** 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. 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 [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0229839.r003
Revision 2
14 Feb 2020 Author Response We thank the reviewers for their constructive comments and have revised the manuscript to address their concerns. > The author showed the experiment result of Dice in Fig 4, but didn't give the overall performance comparison in terms of Dice We added a new figure (fig 5), containing statistical testing of the different method with respect to the baseline and triangular/cui. > The discussion is not sufficient. The discussion section was modified and some content was added. Attachments Attachment Submitted filename: rebuttal_letter_2nd.pdf https://doi.org/10.1371/journal.pone.0229839.r004
18 Feb 2020 Decision Letter - Jie Zhang, Editor Introducing Hann windows for reducing edge-effects in patch-based image segmentation PONE-D-19-29003R2 Dear Dr. Pielawski, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Jie Zhang Academic Editor PLOS ONE Additional Editor Comments (optional): The authors have adequately addressed the reviewers' comments and the revised manuscript can be accepted. Reviewers' comments: https://doi.org/10.1371/journal.pone.0229839.r005
Formally Accepted
25 Feb 2020 Acceptance Letter - Jie Zhang, Editor PONE-D-19-29003R2 Introducing Hann windows for reducing edge-effects in patch-based image segmentation Dear Dr. Pielawski: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, please inform our press team within the next 48 hours. 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Jie Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0229839.r006

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