[REVIEW]: lys: interactive multi-dimensional data analysis and visualization platform

[editorialbot]

Submitting author: !--author-handle-->@lys-devel<!--end-author-handle-- (Asuka Nakamura) Repository: https://github.com/lys-devel/lys Branch with paper.md (empty if default branch): review Version: v0.3.3_zenodo Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @kuadrat, @ziatdinovmax, @pr4deepr Archive: 10.5281/zenodo.10241638

Status

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@kuadrat & @ziatdinovmax & @pr4deepr, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @emdupre know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @kuadrat

📝 Checklist for @pr4deepr

📝 Checklist for @ziatdinovmax

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.52 s (862.9 files/s, 243710.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           200           9160            600          57612
Python                         154           5336           4225          18475
JavaScript                      16           4511           4394          16122
SVG                              1              0              0           2671
reStructuredText                67            764            646           1000
CSS                              4            187             35            756
Markdown                         6            167              0            650
TeX                              1             16              0            204
DOS Batch                        1             23              1            166
make                             1             24              5            124
Bourne Shell                     1              8              3             34
YAML                             1              1              4             21
-------------------------------------------------------------------------------
SUM:                           453          20197           9913          97835
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/mcse.2011.35 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1294

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[emdupre]

👋 Hi @kuadrat, @ziatdinovmax, and @pr4deepr, and thank you again for agreeing to review this submission for lys !

The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @editorialbot generate my checklist.

In working through the checklist, you're likely to have specific feedback on lys. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

[pr4deepr]

Review checklist for @pr4deepr

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/lys-devel/lys?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@lys-devel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[pr4deepr]

Regarding "Contribution and authorship", I'm not sure how to judge this as there seems to be multiple accounts that have contributed to the code and I cannot ascertain who they belong to. Commit history.

There are multiple acccounts: @LabviewShare, @lys-devel which is the current account.

@emdupre, how do you suggest I proceed? @lys-devel

[lys-devel]

@pr4deepr , @emdupre I'm sorry for confusing commit history. "LabviewShare" is my private account. Since lys have been private repository in our lab, I used it until very recently. If it is needed, I will comment here from "LabviewShare" account for verification.

[pr4deepr]

Thanks @lys-devel . Perhaps that should be enough for now, unless anyone has other concerns..

[kuadrat]

Review checklist for @kuadrat

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/lys-devel/lys?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@lys-devel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[emdupre]

👋 Hi @ziatdinovmax, I noticed that you had not yet generated your reviewer checklist, so I wanted to check-in and make sure you weren't encountering any issues in doing so. Please let me know, and thank you again for agreeing to review lys !

[kuadrat]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[pr4deepr]

Hi @emdupre @kuadrat

I made 2 issues here:

https://github.com/lys-devel/lys/issues/14

https://github.com/lys-devel/lys/issues/13

Just wanted to make sure these are still in the scope of the review?

Cheers Pradeep

[ziatdinovmax]

Review checklist for @ziatdinovmax

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/lys-devel/lys?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@lys-devel) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[emdupre]

Just wanted to make sure these are still in the scope of the review?

Thanks for checking in on this, @pr4deepr ! I see https://github.com/lys-devel/lys/issues/13 and https://github.com/lys-devel/lys/issues/14 as in-scope for the review, targeting A statement of need: / State of the field: and Example usage:, respectively. If I've misunderstood your concern, though, please let me know !

And of course, if you have other questions, please don't hesitate to ask !

[lys-devel]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[emdupre]

👋 HI everyone, and happy Friday !

@ziatdinovmax I just wanted to follow-up and confirm if you're having any difficulties in working through your reviewer checklist, as I noticed you haven't yet been able to assess the "functionality", "documentation" or "software paper" categories -- which I know are more involved !

If you have any concerns, please let me know. And thank you again for agreeing to review lys !

[ziatdinovmax]

@lys-devel A minor suggestion re: automated tests. It is typically helpful to display the test coverage using e.g. codecov which is free. It also signals the maturity of the package and of maintenance effort which helps attract more users.

[ziatdinovmax]

For the statement of need, I feel it needs a further justification of why research scientists can't just rely on the already exisiting domain-specific software tools for data analysis and visualization.

[ziatdinovmax]

@lys-devel - my apologies if I missed this in the documentation, but I think currently it doesn't account for a pretty common situation when multi-dimensional data is in a proprietary format, and one needs to use some form of a translator to convert it to lys-readable format. This seems like the first and most important step without which one cannot use this package. I suggest mentioning it and perhaps providing links to some common translator packages.

[lys-devel]

@ziatdinovmax Thank you for your fruitful comments. For clarity, I opened the issues regarding the above points in the repository. I will respond all issues in a few days.

[lys-devel]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[emdupre]

👋 Hi everyone, just a small note that I will be out-of-office 30 October - 10 November. I will answer any comments or questions as soon as I'm back, though, so please don't hesitate to ping this thread.

[ziatdinovmax]

@lys-devel - thank you for addressing my questions/concerns! @emdupre - all my concerns have been now addressed and I'm happy to recommend this paper for publication.

[pr4deepr]

@lys-devel @emdupre Most of the concerns have been addressed. I've also tried going through most of the doc successfully. I really like the CUI/GUI architecture and the ability to run and use our own code quite flexibly.

I don't want to delay the review any longer as the software functions well. Although, I think the paper can benefit from some proofreading. @emdupre, is this something JOSS can assist with?

Examples of typo and grammar or sentence structure:

• Line 25: field
• Line 26 to 31: grammar and sentences can be condensed and made clearer.
• Line 52 to 54: unclear
• Line 57: Grammar. An example (not the best one): The philosophy of lys is to serve as a versatile data analysis and visualization platform, rather than a basic image viewer/analysis program. It is tailored to research scientists who would like to analyze and visualize their data with minimal coding.
• Line 62: significantly reduces the time
• Line 105: expansion capability -> you could use the term modularity maybe?
• Line 110: Users can verify the software and modify if needed

Other:

• Line 112. I would not say interactive GUI is lacking in the scientific ecosystem. napari can be used to visualize images and it also has an ipython console where you can enter code to process data interactively.
• Line 117. napari can be extended for data analysis. I think you should clarify and say lys is 'general purpose', i.e. it can handle different data types perhaps and not restricted to image data only. For example, napari has a massive ecosystem of plugins: https://www.napari-hub.org/

Cheers Pradeep

[lys-devel]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[lys-devel]

@pr4deepr , Thank you for the comments. I opened the issues in the repository because reply was long. In addition to the points above, I will proofread the manuscript with my colleagues before @emdupre comes back.

[lys-devel]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[emdupre]

Hi everyone,

I'm back in office ! Thank you for your patience.

@pr4deepr and @ziatdinovmax, thank you for your confirmation of your reviews ! @pr4deepr, I noted that https://github.com/lys-devel/lys/issues/20 was closed following your comments, so I believe these are now addressed. Please let me know, though, if this is not the case.

Otherwise, it looks like all three reviewer checklists are now completed ! @kuadrat could you please confirm that you are happy with this submission for lys in its current form ? I noted that you still have two open issues, but it looks like you've marked these as "not review-critical," so I wanted to confirm.

Once I have final confirmation, I'll perform a few additional editorial checks to help in processing this submission 🚀

[pr4deepr]

@emdupre , yup, happy with the manuscript.

[kuadrat]

Welcome back, @emdupre!

Indeed, I also think that the manuscript and the software fulfill the conditions for publication in JOSS. The remaining open issues are not review critical.

[emdupre]

Thank you both, @pr4deepr and @kuadrat !

I'll now perform a few additional editorial checks.

[emdupre]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[emdupre]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.25080/majora-7b98e3ed-013 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1109/mcse.2011.35 is OK
- 10.7567/APEX.11.092601 is OK
- 10.1021/acs.nanolett.0c01006 is OK
- 10.1063/4.0000059 is OK
- 10.1021/acs.nanolett.2c03938 is OK
- 10.1126/sciadv.abg1322 is OK
- 10.1063/5.0106517 is OK
- 10.1093/jmicro/dfad021 is OK
- 10.1039/D2FD00062H is OK
- 10.21105/joss.02969 is OK
- 10.1017/S1431927622006328 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[emdupre]

Thank you for your patience, @lys-devel ! I've reviewed and am also happy with the software 🎉 I have a few editorial requests on the software paper itself.

Major comments

• The summary currently points to several specific software packages and kinds of computing environments. While this is very useful for regular developers, it may be less familiar to non-specialist audiences. The JOSS guidelines for the Summary ask that this section focus on:

  describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.

  Could you thus please re-orient the Summary towards this non-specialist audience ? I would suggest to use similar language to e.g., L20-22 and L58-64.

• Figure 1. Can you please describe each of the figure panels directly in the figure caption, rather than in-text ?
• Figure 2. Similarly, can you please expand the figure caption ? I understand that it is not entirely possible to move the description into the caption given its length.

• napari and data-slicer are first mentioned on L37 as "sophisticated data analysis/visualization tools" ; however, a more direct comparison of lys with these tools is not provided until L115. It would be useful to have this discussion moved into the Statement of Need, to make the current state of the field clearer to the reader. Per the JOSS guidelines, the Statement of Need:

  clearly illustrates the research purpose of the software and places it in the context of related work.

  If desired, discussion of L47 - L57 could be moved into the Overview to focus each section's content.

Minor comments

• L9 : Please note that "GUI interface" is redundant. You can simply say 'GUI' or 'interface'
• L21 : Please remove 'the' before 'experimental and simulated data'
• L23 : Please capitalize Igor Pro as IGOR Pro
• L24 : Please capitalize Matlab as MATLAB
• L24 : Please add RRID for IGOR Pro and MATLAB.
• L33 : Please add spaces before each citation and its corresponding library
• L75 : preprocess --> preprocessing
• Figure 1. Could you please explicitly note that this GUI is the MultiCut interface referred to throughout the text ?

[lys-devel]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[lys-devel]

Thank you for you editorial effort, @emdupre. I also appreciate all reviewers for their kind comments. I modified the manuscript following your advice.

• Summary

  Could you thus please re-orient the Summary towards this non-specialist audience ?

Thank you for the comment. I modified the Summary towards non-specialist audience in Line 6-20.

• Figure captions

  Figure 1. Can you please describe each of the figure panels directly in the figure caption, rather than in-text ? Figure 2. Similarly, can you please expand the figure caption ? I understand that it is not entirely possible to move the description into the caption given its length.

I modified the figure captions of Fig. 1 and 2.

• Statement of need

  napari and data-slicer are first mentioned on L37 as "sophisticated data analysis/visualization tools" ; however, a more direct comparison of lys with these tools is not provided until L115. It would be useful to have this discussion moved into the Statement of Need, to make the current state of the field clearer to the reader

Thank you for the important comment. I added the sentences that describe the current state of the field in Line 46-54. I did not change the discussion in Line 117-133 because I consider the comparison between other software is also needed after describing what is lys.

• Other

  L24 : Please add RRID for IGOR Pro and MATLAB.

I could not find example of how to add RRID in JOSSS website, so I added RRID directly in Line 26. Could you confirm this style of RRID is suitable for JOSS?

Figure 1. Could you please explicitly note that this GUI is the MultiCut interface referred to throughout the text ?

Figure 1 is not the screenshot of MultiCut (there is no screenshot of MultiCut in the manuscript). So I did not modify the manuscript regarding this point.

I hope the manuscript has been modified suitably for JOSS, Thank you.

[emdupre]

Thank you, @lys-devel ! I appreciate you making these changes.

I could not find example of how to add RRID in JOSSS website, so I added RRID directly in Line 26. Could you confirm this style of RRID is suitable for JOSS?

Apologies for not providing this ; if you could please remove the space between RRID: and the SCR identifier, these would be in the correct format. Thus, MATLAB would be RRID:SCR_001622.

The only remaining concern I see is that the software are stylized as Igor Pro and Matlab on L120. Could you please correct the capitalization there as well ?

[emdupre]

After making these changes, could you then please:

• [x] Make a tagged release of your software, and list the version tag of the archived version here.
• [x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• [ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata (e.g., the JOSS paper and software archive have the same title and author listing)
• [x] List the DOI of the archived version here.

[lys-devel]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left: