[REVIEW]: SLIX: A Python package for fully automated evaluation of Scattered Light Imaging measurements on brain tissue

[whedon]

Submitting author: @Thyre (Jan André Reuter)
Repository: https://github.com/3d-pli/SLIX
Version: v1.2.1
Editor: @oliviaguest
Reviewers: @matteomancini, @rly, @alexrockhill
Archive: 10.5281/zenodo.4121953

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/2fc15b63a406c1087f188af400743fe2/status.svg)](https://joss.theoj.org/papers/2fc15b63a406c1087f188af400743fe2)

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

@matteomancini & @rly, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @matteomancini

Conflict of interest

• 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

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

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Thyre) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

Review checklist for @rly

Conflict of interest

• 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

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

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Thyre) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

Review checklist for @alexrockhill

Conflict of interest

• 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

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

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@Thyre) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @matteomancini, @rly it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1103/PhysRevX.10.021002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[oliviaguest]

Hey 👋 @matteomancini, @rly: this is where the review will take place. Please make sure to read the instructions above.

For any and all things worthy of discussion or comment, use this issue right here — so drop comments or questions for me, the author, etc., here. For any very code-specific things please feel free to start an issue on the repo of the code itself (if appropriate!) and link back to it from here. For an example of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

[oliviaguest]

Hey @matteomancini, @rly — when you get a chance can you give me an ETA for your reviews, please?

[matteomancini]

Apologies for the delayed reply, I should be able to provide a review by Friday the 16th of October.

[rly]

@oliviaguest I'll have this done by October 8.

[oliviaguest]

@whedon remind @rly in 1 week

[whedon]

Reminder set for @rly in 1 week

[alexrockhill]

I take it I'm no longer needed to review, if so best of luck with the review process

[oliviaguest]

@alexrockhill I would appreciate your input here — are you free/able to review this?

[alexrockhill]

Sure, I can have this done in a week

[oliviaguest]

@whedon add @alexrockhill as reviewer

[whedon]

OK, @alexrockhill is now a reviewer

[whedon]

👋 @rly, please update us on how your review is going.

[miriammenzel]

@oliviaguest We were not aware that the repository on zenodo needs to have the same title as the paper. We thought it should have the same title as the software and the documentation. Is this a problem? (I'm not sure if we can change this without changing the DOI.)
We have added the missing DOIs to the paper.

[oliviaguest]

@miriammenzel see: https://help.zenodo.org/

I only want to change the title of my upload, do I still get a new DOI?

No, as before you can continue to edit the metadata of your upload without creating a new version of a record. You should only create a new version if you want to update the files of your record.

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1103/PhysRevX.10.021002 is OK
- 10.1016/j.neuroimage.2010.08.075 is OK
- 10.3389/fninf.2011.00034 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1852

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1852, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[miriammenzel]

@oliviaguest I have changed the title of the repository on zenodo accordingly. Everything should be all set now. Thanks again for the review.

[kyleniemeyer]

Hi @miriammenzel, I'm the EIC on duty this week doing final checks before publishing. Could you address these issues?

• The article is missing a Statement of Need section, which we have begun requiring for articles. You can likely use text that is already present in the article.
• There are a few citations that appear to use the incorrect command, such as in the first paragraph, and end up with nested parentheses. I think you should use the [@author:2001] command for those instead. For reference, the options are:

- `@author:2001`  ->  "Author et al. (2001)"
- `[@author:2001]` -> "(Author et al., 2001)"
- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"

Thanks!

[miriammenzel]

@kyleniemeyer: Thanks for letting me know. I have added a Statement of Need section at the end of our paper and corrected the citations in the first paragraph. Please let me know if everything is OK now.

[Thyre]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[oliviaguest]

@Thyre can you merge and compile the PDF again with this change, please? 3d-pli/SLIX#16

[miriammenzel]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[oliviaguest]

Oh, I think that "M." is errant in like "M. Axer, Amunts, et al., 2011", but maybe I'm wrong ? Either way that didn't fix it.

[kyleniemeyer]

@oliviaguest @miriammenzel I have seen behavior like that with combined citations that include the same surname, so I think it is ok and probably not (easily) changeable

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1103/PhysRevX.10.021002 is OK
- 10.1016/j.neuroimage.2010.08.075 is OK
- 10.3389/fninf.2011.00034 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1858

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1858, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02675 joss-papers#1859
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02675
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congrats @Thyre on your article's publication in JOSS!

Many thanks to @matteomancini, @rly, and @alexrockhill for reviewing this, and @oliviaguest for editing.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02675/status.svg)](https://doi.org/10.21105/joss.02675)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02675/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02675/status.svg
   :target: https://doi.org/10.21105/joss.02675

This is how it will look in your documentation:

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