Peer Review History
| Original SubmissionOctober 5, 2022 |
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PONE-D-22-27354Back to life: Techniques for developing high-quality 3D reconstructions of plants and animals from digitized specimensPLOS ONE Dear Dr. Clark, 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. You will see some comments the reviewers left, specially the first reviewer. I kindly ask you please to consider her observations and recommendations to improve the manuscript before publication. The comments of the first reviewer are attached in a .pdf file to this email. Please submit your revised manuscript by Jan 05 2023 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:
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, Judith Pardo-Pérez, Ph.D 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 2. 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. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript report a protocol which is of utility to the research community and adds value to the published literature? Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the protocol been described in sufficient detail? To answer this question, please click the link to protocols.io in the Materials and Methods section of the manuscript (if a link has been provided) or consult the step-by-step protocol in the Supporting Information files. The step-by-step protocol should contain sufficient detail for another researcher to be able to reproduce all experiments and analyses. Reviewer #1: Yes Reviewer #2: Yes ********** 3. Does the protocol describe a validated method? The manuscript must demonstrate that the protocol achieves its intended purpose: either by containing appropriate validation data, or referencing at least one original research article in which the protocol was used to generate data. Reviewer #1: Yes Reviewer #2: Yes ********** 4. If the manuscript contains new data, have the authors made this data 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 article 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 highlight any specific errors that need correcting in the box below. 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: The manuscript "Back to life: Techniques for developing high-quality 3D reconstructions of plants and animals from digitized specimens" shows the work that E.G. Clark and colleagues have carried out to develop helpful protocols to create more realistic and useful 3D models to work with, specially when they present numerous artifacts. I highly appreciate the written protocols and examples, as they are easy to follow and comprehensible. However, I have several concerns: - I feel the authors should acknowledge more the previous works on 3D modelling, retrodeformation and retopology, specially when presenting each technique, as there are already published protocols on them. Together with this, I would suggest to highlight the differences of the presented workflows and techniques with the previous ones. "Why should we follow your workflows? Why are they different to the already published? Are they easier/more straightforward to follow? Why should I use Maya instead of Blender, which is open source?". These are only suggestions that could be addressed within the discussion. - I see an important issue on the "subjectivity" of the final models, as there is a lot of user interference within the workflows. The user's expertise on these software willl greatly impact the final output, and sometimes the process implies an extreme modification of the original mesh (e.g. the Petriellaea case study). Some kind of sensitivity analysis should be suggested, which can help to evaluate the reliability of the techniques, but also the user interference. - A section on "how and when to use these outputs" would be useful, as my feelings are that they couldn't be of utility when highly accurate models are needed (e.g. some FEA, geometric morphometrics, comparison works,...). Again, this is also related with the "subjectivity artifact" indicated above. - This is more a personal thought/suggestion: not all people have access to a commercial software, so I would suggest also including a workflow on an open-source program (like Blender, which has similar features as Maya). I understand the timeliness of the manuscript, but for future works this could be a nice idea to implement. I also have annotated a few more comments on the pdf. I would like to congratulate the authors for such an interesting work, I really enjoyed working on the case studies and learnt new features. Verónica Díez Díaz Reviewer #2: General comments The manuscript by Clark et al., provides an incredibly useful overview and step-by-step guide for overcoming many common problems experienced when working with 3D data. It was very well written and bound to be a highly useful and well received paper by the community. As someone who works with 3D data from both fossil and extant specimens I thought the paper was fantastic and I look forward to recommending this to my lab as a useful reference. I also think the quality of the tutorials in supplementary information were brilliant – and definitely of a standard that could be used for teaching. I have no major concerns with the manuscript and thank the authors for producing such a high quality and valuable resource. I have a couple of recommendations which are centred around ways to help signpost the key information in the paper for a reader who may use this as a quick reference guide rather than as a paper to be read from start to finish. 1. I think you could make a summary workflow figure that captures the key parts of the paper and signposts the reader to different parts of the text. E.g. If you want to remove external debris from a specimen go to this section in text and this section in supplementary. 2. I think the common problems you list in methods “Removing external debris” etc could also be listed in a highlights box so someone glancing at the paper can spot the issue they are looking for. 3. I think it might be worth emphasising the step-by-step guide in supplementary slightly more in the main text. People often overlook supplementary info especially if someone just jumped to a case study that looked particularly useful for them. 4. I think you could possibly add some annotations or colour to the figures Then two more general points to consider. I don’t think the MS necessarily needs these but could be something to consider: 1. You could mention that these techniques could also be particularly valuable for 3D reconstructions made from serial preparations that are inherently more blocky and prone to artefacts than CT data. E.g. serial sectioning, grinding or peeling. 2. Especially in the palaeo field it is very common to want to 3D print fossils. I know you mention 3D printing in the text but it could possibly be highlighted slightly more. ********** 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: Yes: Verónica Díez Díaz 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.] 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.
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| Revision 1 |
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Back to life: Techniques for developing high-quality 3D reconstructions of plants and animals from digitized specimens PONE-D-22-27354R1 Dear Dr. Clark, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. 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 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, Judith Pardo-Pérez, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Does the manuscript report a protocol which is of utility to the research community and adds value to the published literature? Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the protocol been described in sufficient detail? To answer this question, please click the link to protocols.io in the Materials and Methods section of the manuscript (if a link has been provided) or consult the step-by-step protocol in the Supporting Information files. The step-by-step protocol should contain sufficient detail for another researcher to be able to reproduce all experiments and analyses. Reviewer #1: Yes Reviewer #2: Yes ********** 3. Does the protocol describe a validated method? The manuscript must demonstrate that the protocol achieves its intended purpose: either by containing appropriate validation data, or referencing at least one original research article in which the protocol was used to generate data. Reviewer #1: Yes Reviewer #2: Yes ********** 4. If the manuscript contains new data, have the authors made this data 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 article 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 highlight any specific errors that need correcting in the box below. 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: I would like to congratulate the authors for the revision and how they have dealt with the reviewers' comments, as the work has improved considerably. Especially the inclusion of figure 5 seems to me a very smart idea, which explains in a very visual and intuitive way all the protocols and how to proceed. For my part I can add nothing more, only that the authors include the reviewers in the acknowledgements in the final version of the manuscript. I hope to see this work published soon. Verónica Díez Díaz Reviewer #2: I have no further comments. I thank the authors for taking on board my early suggestions. I think the additional changes they have made have strengthened the manuscript. ********** 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: Yes: Verónica Díez Díaz Reviewer #2: No ********** |
| Formally Accepted |
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PONE-D-22-27354R1 Back to life: Techniques for developing high-quality 3D reconstructions of plants and animals from digitized specimens Dear Dr. Clark: I'm 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 let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Judith Pardo-Pérez Academic Editor PLOS ONE |
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