A comparative study on the use of microscopy in pharmacology and cell biology research

Agatha M. Reigoto; Sarah A. Andrade; Marianna C. R. R. Seixas; Manoel L. Costa; Claudia Mermelstein

doi:10.1371/journal.pone.0245795

Peer Review History

Original SubmissionAugust 24, 2020
30 Nov 2020 Decision Letter - Yuval Garini, Editor PONE-D-20-26569 How is microscopy used in pharmacology research? PLOS ONE Dear Dr. Mermelstein, 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 Jan 14 2021 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: 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Yuval Garini, 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Additional Editor Comments (if provided): The manuscript presents a study on the use of microscopy in the fields of pharmacology and cell biology as a control. Three journals are allocated and studied, two in pharmacology and one in cell biology. Different microscopy methods were analyzed: bright field, phase contrast, DIC, polarization, conventional fluorescence, confocal, TEM and SEM. The results show different volume of usage in these two fields. In addition, common words were tested in the titles and found ‘Cell’ to be dominant in both fields. The work is interesting, and the subject is important, but there are major issues that should be corrected and added before it can be published. Major comments: Except for the reviewer comments, please refer to the following comments as well. 1. Some important microscopy methods are not included in the subjects that are tested, including Super resolution microscopy that lately immerged as a very important method. 2. Although the issue of ‘in vivo’ and ‘live cell’ are mentioned in the introduction, these are important issues that should also be part of the study. Otherwise, we are left with partial knowledge, as it is not clear what the usage of the microscopy is. 3. It seems that two journals are not enough for the study of a discipline, and definitely a single journal for the control cell biology discipline (with much less articles relative to the pharma discipline number or articles). 4. For the pharmaceutical analysis, it is important to know what kind of study is described in the manuscript. One can assume that studying histological sections will necessitate microscopy, while studying drug tablets not necessarily requires microscopy. Mixing these together may bias the results and certainly the conclusions. 5. In relation to the previous comment, it seems that the value of general statement “use of microscopy in pharmaceutical” is not very high, as it depends what is the actual study. The authors should refine their analysis accordingly. 6. It is important to correlate the use of microscopy with the research theme – such as tablets – tissues – drug efficiency – biomarkers and so on. A ‘comparative analysis” (line 172) similar to that, but for subjects of matter, seemed to be very important. 7. One of the conclusions is: “we can conclude that the pharmacology research field could gain novel horizons by including 215 new microscopy techniques in their studies.” It does not seem to be a relevant conclusion, definitely not based on the study that is described. For such a statement to be true, one has to explore the type of study, the methods that are used, and compare similar studies that are done with or without microscopy. That is why point 6 is so important – The use of the technique depends on the application and the subject of study. Microscopy is definitely a great method, but its use, just like any other method, depends on the need. 8. As another comment related to points 6-7, it will be interesting to have a 'negative control' that uses a subject like biochemistry ot other, in order to teat the use of microscopy. THe point to emphasize is that the use of a method is strongly correlated with the need. [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? 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: No ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: This work studies the use of microscopy in pharmacological research. To do this, the authors propose to do a bibliometrics analysis to review scientific publications during the year 2019 on two pharmacology journals (BJP and FP) and one cell biology journal for control. The following data is recollected - Whereas microscopy techniques are used. - Which technique was used, single or combined with others. - The difference in the subject based on relative frequency of words in the title. The authors analyze the data a conclude that microscopy techniques are infra utilized in pharmacology. While I believe the topic is interesting, the analyses performed fail to support the claims make by the authors. A big rewrite must be done so the authors clarify their claims and analyses. As it is, It is not written clearly enough to be accesible and new results should be included to streghen the claims. Therefore I can not recommend it for publication. Some mayor issues: - In 211 it is stated that cell biology and pharmacology fields have completely different uses of microscopy techniques”. I do not find clear if the techniques are used for different purposed or it refers that microscopy techniques are more commonly used in cell biology. - The usage of microscopy is compared using word cloud in the titles in section 192. The use of “cell”, “protein” and “receptor” but no further analysis is given. It do not feel that it is sufficient criteria to state “that differences in microscopy usage cannot be attributed to differences in the subject of study “. Also there is diferent spellings for some words (like signaling/signalling) that can be observed in the word clouds that it is not properly explained. - No specific reasons are given for using such a small sample of journals (3), even if the number of scientific articles is big enough to guarantee that the analysis was not performed by hand. -It would be clarifying to add the results to which techniques are mostly use together and if there is any reason for these combinations. - Finally, the number of references is small and fails to introduce the previous work done in this field. The authors mention the combination of different techniques but fail to cite examples where pharmacology research has improved by the use of microscopy. For example: Usaj MM, Styles EB, Verster AJ, Friesen H, Boone C, Andrews BJ. High-Content Screening for Quantitative Cell Biology. Trends Cell Biol. 2016;26(8):598–611. Finally some typos and minor issues - The results section presents the data in an unhelpful manner. Some restructuring must be done in this section. -Line 48 How important it is to … -> How important is it to look -Line 102 Provide Wordle Software as a citation. ****** 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 [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. https://doi.org/10.1371/journal.pone.0245795.r001
Revision 1
31 Dec 2020 Author Response Dear Dr. Yuval Garini, I submitted the manuscript entitled "How is microscopy used in pharmacology research?" (PONE-D-20-26569) for publication in PLOS ONE. The reviewers of my manuscript recommended major revision. I made the modifications in the manuscript and in its figures and I included a point-by-point response to the reviewer’s comments, which were useful to improve the data presentation and interpretation. The whole manuscript text was revised and rewritten, and new figures were added. We decided to change the title of the manuscript to “A comparative study on the use of microscopy in pharmacology and cell biology research” because of the addition of new data. I thank the Referees for their careful and appropriate analysis. The detailed corrections are as follows. Editor comments: The manuscript presents a study on the use of microscopy in the fields of pharmacology and cell biology as a control. Three journals are allocated and studied, two in pharmacology and one in cell biology. Different microscopy methods were analyzed: bright field, phase contrast, DIC, polarization, conventional fluorescence, confocal, TEM and SEM. The results show different volume of usage in these two fields. In addition, common words were tested in the titles and found ‘Cell’ to be dominant in both fields. The work is interesting, and the subject is important, but there are major issues that should be corrected and added before it can be published. FEITO 1 - Some important microscopy methods are not included in the subjects that are tested, including Super resolution microscopy that lately immerged as a very important method. Although the issue of ‘in vivo’ and ‘live cell’ are mentioned in the introduction, these are important issues that should also be part of the study. Otherwise, we are left with partial knowledge, as it is not clear what the usage of the microscopy is. Author’s response – We now included in the new version of the manuscript “super resolution microscopy” and “live cell/in vivo microscopy”, along with nine other microscopy methods (bright field, phase contrast, differential interference contrast, polarization, conventional fluorescence, confocal fluorescence, transmission and scanning electron microscopy, and cryoEM). FEITO 2 - It seems that two journals are not enough for the study of a discipline, and definitely a single journal for the control cell biology discipline (with much less articles relative to the pharma discipline number or articles). Author’s response – We now included data from 8 leading scientific journal from the pharmacology, cell biology, biochemistry, and general biomedical sciences fields. The selected journals were British Journal of Pharmacology (BJP), Journal of Pharmacy and Pharmacology (JPP), Frontiers in Pharmacology (FP), Journal of Cell Biology (JCB), Journal of Cell Science (JCS), Cells (CEL), Journal of Biological Chemistry (JBC) and Proceedings of the National Academy of Sciences (PNAS). FEITO 3 - For the pharmaceutical analysis, it is important to know what kind of study is described in the manuscript. One can assume that studying histological sections will necessitate microscopy, while studying drug tablets not necessarily requires microscopy. Mixing these together may bias the results and certainly the conclusions. In relation to the previous comment, it seems that the value of general statement “use of microscopy in pharmaceutical” is not very high, as it depends what is the actual study. The authors should refine their analysis accordingly. It is important to correlate the use of microscopy with the research theme – such as tablets – tissues – drug efficiency – biomarkers and so on. A ‘comparative analysis” (line 172) similar to that, but for subjects of matter, seemed to be very important. Author’s response – We now attempted to correlate the use of microscopy with the research theme of each article. Since the themes can be diverse, we focus on analyzing the use of cell cultures, since it is reasonable to expect that microscopes are needed for the proper visualization of cells because of their dimensions. In articles that used cell cultures, we analyzed the percentage of microscopy figures in relation to the total number of figures of the articles. We thank the reviewer for this important suggestion that highly improved our manuscript. FEITO 4 - One of the conclusions is: “we can conclude that the pharmacology research field could gain novel horizons by including new microscopy techniques in their studies.” It does not seem to be a relevant conclusion, definitely not based on the study that is described. For such a statement to be true, one has to explore the type of study, the methods that are used, and compare similar studies that are done with or without microscopy. That is why point 3 is so important – The use of the technique depends on the application and the subject of study. Microscopy is definitely a great method, but its use, just like any other method, depends on the need. Author’s response – We now revised the whole manuscript, including the Conclusions, to incorporate new data on the use of cell cultures together with microscopy. In this way we tried to separate the articles in two types: research at the cellular level or at the whole animal/human level. FEITO 5 - As another comment related to points 3-4, it will be interesting to have a 'negative control' that uses a subject like biochemistry or other, in order to treat the use of microscopy. The point to emphasize is that the use of a method is strongly correlated with the need. Author’s response – As I explained above, we now included data from 8 leading scientific journal from the pharmacology, cell biology, biochemistry (as a negative control), and general biomedical sciences fields. I think that these new results have greatly improved our manuscript. Reviewer #1: FEITO 1 - This work studies the use of microscopy in pharmacological research. To do this, the authors propose to do a bibliometrics analysis to review scientific publications during the year 2019 on two pharmacology journals (BJP and FP) and one cell biology journal for control. The following data is recollected - Whereas microscopy techniques are used. - Which technique was used, single or combined with others. - The difference in the subject based on relative frequency of words in the title. The authors analyze the data a conclude that microscopy techniques are infra utilized in pharmacology. While I believe the topic is interesting, the analyses performed fail to support the claims made by the authors. A big rewrite must be done so the authors clarify their claims and analyses. As it is, it is not written clearly enough to be accessible and new results should be included to strengthen the claims. Therefore, I cannot recommend it for publication. Author’s response – We now included data from 8 leading scientific journal from the pharmacology, cell biology, biochemistry, and general biomedical sciences fields. The selected journals were British Journal of Pharmacology (BJP), Journal of Pharmacy and Pharmacology (JPP), Frontiers in Pharmacology (FP), Journal of Cell Biology (JCB), Journal of Cell Science (JCS), Cells (CEL), Journal of Biological Chemistry (JBC) and Proceedings of the National Academy of Sciences (PNAS); and data from 11 types of optical and electron microscopy techniques: bright field, phase contrast, differential interference contrast (DIC), polarization, conventional fluorescence, confocal fluorescence, super resolution, live cell imaging, transmission and scanning electron microscopy (TEM and SEM, respectively), and cryoEM. The whole manuscript text was revised and rewritten to strengthen our claims and analysis. FEITO 2 - In 211 it is stated that cell biology and pharmacology fields have completely different uses of microscopy techniques. I do not find clear if the techniques are used for different purposed or it refers that microscopy techniques are more commonly used in cell biology. Author’s response – We now changed this sentence as well as we reviewed the whole manuscript. FALTA 3 - The usage of microscopy is compared using word cloud in the titles in section 192. The use of “cell”, “protein” and “receptor” but no further analysis is given. It does not feel that it is sufficient criteria to state “that differences in microscopy usage cannot be attributed to differences in the subject of study”. Also, there is different spellings for some words (like signaling/signalling) that can be observed in the word clouds that it is not properly explained. Author’s response – We revised all the words present in the word clouds to resolve the different spellings problem (American versus English language). We also reviewed the word cloud section. FEITO 4 - No specific reasons are given for using such a small sample of journals (3), even if the number of scientific articles is big enough to guarantee that the analysis was not performed by hand. Author’s response – As I explained above, we now included data from 8 leading scientific journal from the pharmacology, cell biology, biochemistry, and general biomedical sciences fields. The selected journals were British Journal of Pharmacology (BJP), Journal of Pharmacy and Pharmacology (JPP), Frontiers in Pharmacology (FP), Journal of Cell Biology (JCB), Journal of Cell Science (JCS), Cells (CEL), Journal of Biological Chemistry (JBC) and Proceedings of the National Academy of Sciences (PNAS); and data from 11 types of optical and electron microscopy techniques: bright field, phase contrast, differential interference contrast (DIC), polarization, conventional fluorescence, confocal fluorescence, super resolution, live cell imaging, transmission and scanning electron microscopy (TEM and SEM, respectively), and cryoEM. The whole manuscript text was revised and rewritten to strengthen our claims and analyses. FALTA 5 -It would be clarifying to add the results to which techniques are mostly use together and if there is any reason for these combinations. Author’s response – We now included a new supplementary figure (Table 1) with the information related to which techniques are mostly used together and we discuss some of these combinations. FEITO 6 - Finally, the number of references is small and fails to introduce the previous work done in this field. The authors mention the combination of different techniques but fail to cite examples where pharmacology research has improved by the use of microscopy. For example: Usaj MM, Styles EB, Verster AJ, Friesen H, Boone C, Andrews BJ. High-Content Screening for Quantitative Cell Biology. Trends Cell Biol. 2016;26(8):598–611. Author’s response – We now included more references to introduce the previous work done in this field. 7 - Finally, some typos and minor issues FALTA - The results section presents the data in an unhelpful manner. Some restructuring must be done in this section. Author’s response – The Results section of the new version of the manuscript was restructured to make our results easily understandable. FEITO -Line 48 How important it is to … -> How important is it to look Author’s response – FEITO -Line 102 Provide Wordle Software as a citation. Author’s response – We now provided a citation for Wordle software. We hope that the modifications made in the new version of the manuscript have properly addressed the criticism and suggestions made by the referee, and that the improvements made in the manuscript will be sufficient for its publication in PLOS ONE. I would like to state that all listed authors qualify for authorship and agreed in the submission of the manuscript. The final version of the manuscript has been seen and approved by all coauthors. The authors declare that they have no conflict of interest. With kind regards, Claudia Mermelstein Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0245795.r002
4 Jan 2021 Decision Letter - Yuval Garini, Editor PONE-D-20-26569R1 A comparative study on the use of microscopy in pharmacology and cell biology research PLOS ONE Dear Dr. Mermelstein, Thank you for submitting your revised 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, pending minor revisions. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. All the comments of the reviewers were carefully answered as requested, but there are still minor revisions and suggestions as mentioned below. Please submit your revised manuscript by Feb 18 2021 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: 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Yuval Garini, Ph.D. Academic Editor PLOS ONE Editor Comments: The manuscript is now improved according to all the comments and requests by the reviewers. There are still few issues to be refined as listed below. 1. PNAS was one of the journals that was evaluated. Note however, that PNAS is a general journal that publish articles in many subjects that are outside the scope of cell biology, or even biology. Consider how to take this into account (i.e. when quoting in page 8 the percentage of OM, the value is lower, 32%, but I believe that if this will be normalized by the percentage of bio-related publications from all publications, the number will become more similar to that of the cell-bio journals). 2. Page 8: “Optical microscopy (OM) was much more used than electron microscopy (EM), probably because EM is more labor-intensive than OM”: There are many reasons for the broader use of optical microscopy rather than EM, except for the labor issue. It is also because it is faster, possible to label multiple probes simultaneously, works on live cells, the structure is not damaged during the preparation, it is fully quantitative, and even though the resolution is not as good, it is still good enough to provide sub-cellular information. Most likely, it is more accurate to claim that EM is used only where very high resolution is needed, and OM cannot provide that resolution. 3. Page 9: “and an image of the object of study should be almost a requirement for these studies”. It is not clear where is this fact coming from? Please check the argument, and if necessary, please provide a reference. 4. Page 10 lines 222: Cryo-EM is most likely being used for basic-science studies, which explains the low-percentage use. 5. I may have missed it, but it will be useful to have a table of words usage, the source for the word-cloud images. I t can be a supplement table. 6. Also, it will be very helpful to organize all the relevant factual numbers in one table: number of journals, number of articles in each one. Also add N=… to the figures or figure captions [Note: HTML markup is below. Please do not edit.] [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. https://doi.org/10.1371/journal.pone.0245795.r003
Revision 2
5 Jan 2021 Author Response Dear Dr. Yuval Garini, I submitted the manuscript entitled "A comparative study on the use of microscopy in pharmacology and cell biology research" (PONE-D-20-26569R1) for publication in PLOS ONE. After careful consideration, it was considered that the manuscript has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands, pending minor revisions. Therefore, I made the modifications in the manuscript and in its figures and I included a point-by-point response to the reviewer’s comments, which were very useful to improve the data presentation and interpretation. New figures were added. I thank the Editor for his careful and appropriate analysis. Editor comments: The manuscript is now improved according to all the comments and requests by the reviewers. There are still few issues to be refined as listed below. 1 - PNAS was one of the journals that was evaluated. Note however, that PNAS is a general journal that publish articles in many subjects that are outside the scope of cell biology, or even biology. Consider how to take this into account (i.e. when quoting in page 8 the percentage of OM, the value is lower, 32%, but I believe that if this will be normalized by the percentage of bio-related publications from all publications, the number will become more similar to that of the cell-bio journals). Author’s response – We thank the editor for this important comment. We now analyzed the percentage of OM use in bio-related (biological sciences section of the journal) articles from PNAS. In fact, the percentage of OM in all PNAS’s articles was 32%, whereas the percentage of OM only in bio-related articles is 47%. So, we incorporated this new analysis in the new version of the manuscript. 2 - Page 8: “Optical microscopy (OM) was much more used than electron microscopy (EM), probably because EM is more labor-intensive than OM”. There are many reasons for the broader use of optical microscopy rather than EM, except for the labor issue. It is also because it is faster, possible to label multiple probes simultaneously, works on live cells, the structure is not damaged during the preparation, it is fully quantitative, and even though the resolution is not as good, it is still good enough to provide sub-cellular information. Most likely, it is more accurate to claim that EM is used only where very high resolution is needed, and OM cannot provide that resolution. Author’s response – We agree with the editor that there are many reasons for the broader use of optical microscopy rather than EM, except for the labor issue. So, we changed this sentence accordingly. 3 - Page 9: “and an image of the object of study should be almost a requirement for these studies”. It is not clear where is this fact coming from? Please check the argument, and if necessary, please provide a reference. Author’s response – We rephrased this sentence since it was not clear. 4 - Page 10 lines 222: Cryo-EM is most likely being used for basic-science studies, which explains the low-percentage use. Author’s response – We added this sentence to our manuscript, and we thank the editor for this suggestion. 5 - I may have missed it, but it will be useful to have a table of words usage, the source for the word-cloud images. I t can be a supplement table. Author’s response – We now included a new Table (supplementary Table 2) in the manuscript with all the words and their frequencies used for the generation of the word clouds. 6 - Also, it will be very helpful to organize all the relevant factual numbers in one table: number of journals, number of articles in each one. Also add N=… to the figures or figure captions. Author’s response – We now included a new Table in the manuscript containing all the study’s relevant factual numbers (number of journals, journal’s abbreviations, number of articles in each one) and we also added to all the figure captions the number of articles (N) used for each journal. We hope that the modifications made in the new version of the manuscript have properly addressed the criticism and suggestions made by the referee, and that the improvements made in the manuscript will be sufficient for its publication in PLOS ONE. I would like to state that all listed authors qualify for authorship and agreed in the submission of the manuscript. The final version of the manuscript has been seen and approved by all coauthors. The authors declare that they have no conflict of interest. With kind regards, Claudia Mermelstein Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0245795.r004
8 Jan 2021 Decision Letter - Yuval Garini, Editor A comparative study on the use of microscopy in pharmacology and cell biology research PONE-D-20-26569R2 Dear Dr. Mermelstein, 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, Yuval Garini, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): The authors have answered all the comments, and the manuscript is now ready for publication. Well done! https://doi.org/10.1371/journal.pone.0245795.r005
Formally Accepted
12 Jan 2021 Acceptance Letter - Yuval Garini, Editor PONE-D-20-26569R2 A comparative study on the use of microscopy in pharmacology and cell biology research Dear Dr. Mermelstein: 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 Prof. Yuval Garini Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0245795.r006

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