[REVIEW]: Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow

[whedon]

Submitting author: @AlphonsG (Alphons Gwatimba)
Repository: https://github.com/AlphonsG/Rainbow-Optical-Flow-For-ALI
Branch with paper.md (empty if default branch): main
Version: v0.1.0
Editor: @jmschrei
Reviewers: @tpeulen, @Assistedevolution
Archive: 10.5281/zenodo.6355080

⚠️ 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.

Status

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Markdown: [![status](https://joss.theoj.org/papers/f1d97af6910c2dfffc3b1e396b70541f/status.svg)](https://joss.theoj.org/papers/f1d97af6910c2dfffc3b1e396b70541f)

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

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

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

Review checklist for @tpeulen

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@AlphonsG) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @Assistedevolution

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@AlphonsG) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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. @tpeulen, @Assistedevolution 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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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]

Wordcount for paper.md is 1005

[whedon]

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

OK DOIs

- 10.1007/978-3-030-32583-1_12 is OK
- 10.1088/1367-2630/14/11/115012 is OK
- 10.3389/fcell.2020.00021 is OK
- 10.1038/nmat4357 is OK
- 10.1038/s41467-020-18841-7 is OK
- 10.1038/s41467-020-15164-5 is OK
- 10.1038/s41598-017-17952-4 is OK
- 10.1016/S0065-2458(10)80007-5 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1111/cea.13097 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/rda.13481 is INVALID because of 'https://doi.org/' prefix

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.60 s (58.3 files/s, 32756.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             1           1778              2          13273
Python                          21            366            371           1013
TeX                              1             11              0            198
Jupyter Notebook                 4              0           2042            195
Markdown                         4             91              0            179
YAML                             3             18             48             84
JSON                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            35           2264           2463          14948
-------------------------------------------------------------------------------


Statistical information for the repository 'a01390c5a2187a51df2b5735' was
gathered on 2022/01/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alphons                        111          4434           1058          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Alphons                    1750           39.5          0.9                7.54

[jmschrei]

Howdy @tpeulen and @Assistedevolution

Thanks for agreeing to review this submission.

The process for conducting a review is outlined above in the checklist from @whedon. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.

Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
And here is a checklist, similar to above: https://joss.readthedocs.io/en/latest/review_checklist.html

Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!

[whedon]

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

[AlphonsG]

Hello @jmschrei, just want to confirm if these suggestions/questions should be there or in this issue page?

[jmschrei]

Either way, but it makes more sense to me for issues to be opened in that repo and resolved there, and high level remarks, such as saying that he review is done, are reported here.

[AlphonsG]

Alright no problem, thanks.

[whedon]

👋 @Assistedevolution, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @tpeulen, please update us on how your review is going (this is an automated reminder).

[Assistedevolution]

Provided author feedback following review of paper and repository.
Feedback requested providing clarity around what was being measured and why, More thought suggested into end use of the information. Requested more background (for the new reader) on the problem being solved.

Flagged in repo fixable package versioning issues with installation under Anaconda, (Note Miniconda is recommended, however I feel its more likely that people will try this with Anaconda).
Waiting on resolution of issues

[AlphonsG]

@whedon generate pdf from branch dev2

[whedon]

Attempting PDF compilation from custom branch dev2. Reticulating splines etc...

[whedon]

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

[Assistedevolution]

Successfully installed and ran code in the Dev2 branch.
Successfully Tested both in CLI and GUI mode.
Waiting on:
-Some notes on documentation
-Some notes on tests
-Improvements in readability of paper layout

[Assistedevolution]

Checklist complete on Dev2 branch.
Waiting for addition of instructions to run test added to the readme.
And suggestion of breaking up the paper text in smaller paragraphs

[AlphonsG]

@whedon generate pdf from branch dev2

[whedon]

Attempting PDF compilation from custom branch dev2. Reticulating splines etc...

[whedon]

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

[AlphonsG]

@whedon check references from branch dev2

[whedon]

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

OK DOIs

- 10.1007/978-3-030-32583-1_12 is OK
- 10.1088/1367-2630/14/11/115012 is OK
- 10.3389/fcell.2020.00021 is OK
- 10.1038/nmat4357 is OK
- 10.1038/s41467-020-18841-7 is OK
- 10.1038/s41467-020-15164-5 is OK
- 10.1038/s41598-017-17952-4 is OK
- 10.1016/S0065-2458(10)80007-5 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1111/cea.13097 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1111/rda.13481 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3051

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3051, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kthyng]

Can confirm 10.1109/iccv48922.2021.00963 is valid a DOI for Learning to Estimate Hidden Motions with Global Motion Aggregation, the Arxiv reference given in the paper accurate..

@AlphonsG, @YuliyaLab it seems one of your reviewers is going to the trouble of checking your missing DOIs for you! Can you please fix this now?

[kthyng]

Hi @tpeulen! Thank you for your effort reviewing this JOSS submission. We need to have a completed checklist from each reviewer. Can you run the following command and check off the boxes that you agree with? And if you are satisfied with the authors' work, please say so. It looked like you weren't sure earlier at least based on their manuscript, and of course we want to have everything fully complete before acceptance.

@editorialbot generate my checklist

[AlphonsG]

@editorialbot generate pdf

[editorialbot]

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

[AlphonsG]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/978-3-030-32583-1_12 is OK
- 10.1088/1367-2630/14/11/115012 is OK
- 10.3389/fcell.2020.00021 is OK
- 10.1038/nmat4357 is OK
- 10.1038/s41467-020-18841-7 is OK
- 10.1038/s41467-020-15164-5 is OK
- 10.1111/cea.13097 is OK
- 10.1038/s41598-017-17952-4 is OK
- 10.1016/S0065-2458(10)80007-5 is OK
- 10.1111/rda.13481 is OK
- 10.1109/ICCV48922.2021.00963 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.5281/zenodo.5517697 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.7717/peerj.453 is OK
- 10.1016/j.patcog.2021.107861 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[AlphonsG]

Can confirm 10.1109/iccv48922.2021.00963 is valid a DOI for Learning to Estimate Hidden Motions with Global Motion Aggregation, the Arxiv reference given in the paper accurate..

@AlphonsG, @YuliyaLab it seems one of your reviewers is going to the trouble of checking your missing DOIs for you! Can you please fix this now?

Hello, reference fixed now

[kthyng]

Hoping to hear back from @tpeulen after a follow up email.

[tpeulen]

Review checklist for @tpeulen

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 https://github.com/AlphonsG/Rainbow-Optical-Flow-For-ALI?
• 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 (@AlphonsG) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

[danielskatz]

@AlphonsG, @YuliyaLab - As the AEiC on duty this week, I'll now do a final proofread of the paper

[danielskatz]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3072

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3072, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

I'm suggesting some changes in AlphonsG/Rainbow-Optical-Flow-For-ALI#31. This hopefully will fix the missing mu character in the pdf.

In addition, the first sentence in the statement of need is not a sentence, but a phrase. This needs to be addressed.

[AlphonsG]

@editorialbot generate pdf

[editorialbot]

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

[AlphonsG]

Thanks for the suggestions @danielskatz, we've updated the paper accordingly.

[danielskatz]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 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.04080 joss-papers#3082
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04080
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...

[danielskatz]

Congratulations to @AlphonsG (Alphons Gwatimba) and co-authors!!

And thanks to @tpeulen and @Assistedevolution for reviewing, and @jmschrei for editing!
We couldn't do this without you!

[editorialbot]

🎉🎉🎉 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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04080/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04080/status.svg
   :target: https://doi.org/10.21105/joss.04080

This is how it will look in your documentation:

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[AlphonsG]

Thank you @danielskatz and all those involved for your efforts, this is great news!