[REVIEW]: Thresholdmann: A Web tool for interactively creating adaptive thresholds to segment MRI data.

[editorialbot]

Submitting author: @katjaq (Katja Heuer)
Repository: https://github.com/neuroanatomy/thresholdmann
Branch with paper.md (empty if default branch): joss-paper-branch
Version: v.1.0.0
Editor: @adamltyson
Reviewers: @sneakers-the-rat, @62442katieb, @anibalsolon
Archive: 10.5281/zenodo.11080336

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6a44256339696ac6d33df13deacd3771"><img src="https://joss.theoj.org/papers/6a44256339696ac6d33df13deacd3771/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6a44256339696ac6d33df13deacd3771/status.svg)](https://joss.theoj.org/papers/6a44256339696ac6d33df13deacd3771)

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

@sneakers-the-rat & @62442katieb & @anibalsolon, 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 @adamltyson 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 @sneakers-the-rat

📝 Checklist for @anibalsolon

📝 Checklist for @62442katieb

[editorialbot]

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

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

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (529.1 files/s, 211173.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             2              0              0           7232
JavaScript                       8            415            160           2476
HTML                             3             43             13            426
CSS                              1              8              3            285
SVG                              7              3              3            207
TeX                              1              9              0            109
Markdown                         5             42              0            102
YAML                             2              1              4             33
-------------------------------------------------------------------------------
SUM:                            29            521            183          10870
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1016/j.cortex.2019.04.011 is OK
- 10.1038/s42003-023-05553-z is OK
- 10.3897/rio.2.e9113 is OK
- 10.21105/joss.02670 is OK
- 10.1016/j.neuroimage.2006.01.015 is OK
- 10.1016/j.neuron.2019.12.023 is OK
- 10.1016/j.neuron.2021.10.015 is OK
- 10.1016/j.neuroimage.2020.117519 is OK
- 10.5281/ZENODO.3402456 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1109

[editorialbot]

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

[adamltyson]

👋🏼 @katjaq @sneakers-the-rat @62442katieb @anibalsolon, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6336 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@adamltyson) if you have any questions/concerns.

[sneakers-the-rat]

Review checklist for @sneakers-the-rat

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/neuroanatomy/thresholdmann?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@katjaq) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

Issues and PRs

• [joss][nice to have] Provide demo data? neuroanatomy/thresholdmann#16
• [joss][docs] Developer docs neuroanatomy/thresholdmann#17
• [joss][tests] Test run failure - before hook times out neuroanatomy/thresholdmann#18
• [joss][tests] Use playwright for testing multiple browsers neuroanatomy/thresholdmann#19
• [joss][tests] Add test cases for listed functionality neuroanatomy/thresholdmann#20
• [joss][package structure][nice to have] Refactor into src-like directory structure? neuroanatomy/thresholdmann#21
• [joss][question] Size of $\epsilon$ term? neuroanatomy/thresholdmann#22
• [joss][packaging][question] CDN vs. webpacking? neuroanatomy/thresholdmann#23
• [joss] Handling non-8bit images? neuroanatomy/thresholdmann#24
• [joss][chore] Remove unused and old code :) neuroanatomy/thresholdmann#25
• [joss][ui] Restrict control points to be within the borders of the image neuroanatomy/thresholdmann#26
• Example of using webpack and js modules alongside vanilla js :) neuroanatomy/thresholdmann#33
• [joss][docs] Performance limits? neuroanatomy/thresholdmann#34

Review Comments

If there is one thing you can always say about @katjaq , @r03ert0 , and @ntraut 's code it's that it does exactly what it says it does with style, simplicity, and solidity. Thanks to the authors for this lovely tool. I am only familiar with working with fMRI data being a huge hassle of gigantic packages and cumbersome GUIs, and so this tool that you can hold in the palm of your hand and run anywhere is an absolute treat. I am a huge fan of the author's small web, single purpose tool philosophy, and this is another great entry in that saga.

I have said this a number of times in the issues, but I think this kind of web development is especially lovely to see in an era of increasingly bloated javascript frameworks that are difficult to maintain and reverse engineer. for this tool to literally be deployed as is from a static web server - not even a build stage! - shows how much more legroom the web browser as programming environment has. The code is capable, concise, and correct. very well done. Docs are good, tests are good, all claims made in the paper easily validated, fundamentals are sound.

The area of growth i have suggested for the authors is to use some of those tools to extend the functional modularity of their work into a bit more fluid programmatic modularity. They make excellent use of their prior work with mriviewer and muijs, but the use of global page state does put a little bit of a cap on how the excellent work they have done here can be reused. One of the virtues of their very modular approach is that it naturally lends itself to compositionality - it's already possible to mix and match their tools as part of a researcher's workflow, the next level would be to be able to mix and match them in downstream tools. I have written a skeleton draft of a transitional path there in an above linked PR for the authors to take or leave. Even without tools like webpack, ES6 modules are well supported by browsers, so the authors can keep the dream of the low-fi but high-function read/write web alive and make a lovely little ecosystem that builds and builds and builds on itself!

I don't have much more to say since the work speaks for itself. Thanks again to the authors for their work, i will continue to jump at the chance to use and look at any work y'all do - always a treat. They have addressed all my suggestions and i wholeheartedly endorse this for JOSS!

[anibalsolon]

Review checklist for @anibalsolon

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/neuroanatomy/thresholdmann?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@katjaq) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

Issues and PRs

• [joss][ui] control points contrast neuroanatomy/thresholdmann#35
• [joss][ui] controls become unusable upon text selection neuroanatomy/thresholdmann#36
• [joss][ui] easier point moving neuroanatomy/thresholdmann#37
• [joss][ui] numeric input neuroanatomy/thresholdmann#38
• [joss][sec] possible injection and data leakage neuroanatomy/thresholdmann#39
• [joss][feature] negative selection & flood fill neuroanatomy/thresholdmann#40

[62442katieb]

Review checklist for @62442katieb

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/neuroanatomy/thresholdmann?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@katjaq) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

[adamltyson]

Hi @sneakers-the-rat, @anibalsolon, @62442katieb it looks like you've all started your reviews. Please let me know if I can be of any assistance!

[adamltyson]

👋 @anibalsolon, @62442katieb,

Just a quick remidner that we aim to have reviews completed within 2-4 weeks. Do you have an idea when you'll have time to look into this?

@sneakers-the-rat it looks like you've raised issues on the software repo (thanks!) and are awaiting a response. Let me know if I can help with anything.

Thanks!
Adam

[editorialbot]

Done! archive is now 10.5281/zenodo.11080336

[adamltyson]

@editorialbot generate pdf

[editorialbot]

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

[adamltyson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.cortex.2019.04.011 is OK
- 10.1038/s42003-023-05553-z is OK
- 10.3897/rio.2.e9113 is OK
- 10.21105/joss.02670 is OK
- 10.1016/j.neuroimage.2006.01.015 is OK
- 10.1016/j.neuron.2019.12.023 is OK
- 10.1016/j.neuron.2021.10.015 is OK
- 10.1016/j.neuroimage.2020.117519 is OK
- 10.5281/ZENODO.3402456 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

No declaration for attribute displaystyle of element mfrac
No declaration for attribute displaystyle of element mfrac

[adamltyson]

Hi @katjaq, based on this and this comment, it seems as if setting a fraction in displaystyle using \dfrac is not supported by the JOSS compilation tool. Could you change it to \frac and see if that fixes the problem?

[katjaq]

Hello @adamltyson . Yeyyyyy, thank you so much for setting publication in motion 😍
I changed it to \dfrac and it seems to look like before from what I can see in the GitHub actions :). So, 🤞 . Sorry for the hiccup.

[adamltyson]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.cortex.2019.04.011 is OK
- 10.1038/s42003-023-05553-z is OK
- 10.3897/rio.2.e9113 is OK
- 10.21105/joss.02670 is OK
- 10.1016/j.neuroimage.2006.01.015 is OK
- 10.1016/j.neuron.2019.12.023 is OK
- 10.1016/j.neuron.2021.10.015 is OK
- 10.1016/j.neuroimage.2020.117519 is OK
- 10.5281/ZENODO.3402456 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5285, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[adamltyson]

Thanks @katjaq, that seems to have fixed it!

I'll hand this over to the EiC for the final checks.

[Kevin-Mattheus-Moerman]

@katjaq as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Everything seems to be in order, the only thing I've noticed is that your archive page does not list the license. Can you check (but attempting to manually edit the listing) if you can add your software license? Here is one for a different project, and as you can see it will be listed under "Rights": https://zenodo.org/records/10278296.

[katjaq]

Hello @Kevin-Mattheus-Moerman . Thank you very much for your feedback. Sorry for my misunderstanding. I thought it was enough that the license appears in the archive.

The license is now listed in our Zenodo entry.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Heuer
  given-names: Katja
  orcid: "https://orcid.org/0000-0002-7237-0196"
- family-names: Traut
  given-names: Nicolas
  orcid: "https://orcid.org/0000-0003-3277-6316"
- family-names: Toro
  given-names: Roberto
  orcid: "https://orcid.org/0000-0002-6671-858X"
doi: 10.5281/zenodo.11080336
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Heuer
    given-names: Katja
    orcid: "https://orcid.org/0000-0002-7237-0196"
  - family-names: Traut
    given-names: Nicolas
    orcid: "https://orcid.org/0000-0003-3277-6316"
  - family-names: Toro
    given-names: Roberto
    orcid: "https://orcid.org/0000-0002-6671-858X"
  date-published: 2024-05-03
  doi: 10.21105/joss.06336
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6336
  title: "Thresholdmann: A Web tool for interactively creating adaptive
    thresholds to segment MRI data."
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06336"
  volume: 9
title: "Thresholdmann: A Web tool for interactively creating adaptive
  thresholds to segment MRI data."

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot 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.06336 joss-papers#5302
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06336
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...

[Kevin-Mattheus-Moerman]

@katjaq congratulations on this JOSS publication!

Thanks for editing this work @adamltyson

Also a special thank you to the reviewers: @sneakers-the-rat, @62442katieb, @anibalsolon !!!

[editorialbot]

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.06336/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06336/status.svg
   :target: https://doi.org/10.21105/joss.06336

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[adamltyson]

Thanks @Kevin-Mattheus-Moerman.

Congratulations @katjaq, and thank you @sneakers-the-rat, @anibalsolon @62442katieb!

[katjaq]

Wouuuhouuuu! Thank you @adamltyson and @Kevin-Mattheus-Moerman ! 😍 That was a fantastic review experience! Thank you so much @sneakers-the-rat , @anibalsolon and @62442katieb 🌟
❤️

[r03ert0]

Thank you everyone for your work! Our tool is much better now thanks to your help :D

…

On May 3 2024, at 10:09 am, katja heuer ***@***.***> wrote: Wouuuhouuuu! Thank you @adamltyson (https://github.com/adamltyson) and @Kevin-Mattheus-Moerman (https://github.com/Kevin-Mattheus-Moerman) ! 😍 That was a fantastic review experience! Thank you so much @sneakers-the-rat (https://github.com/sneakers-the-rat) , @anibalsolon (https://github.com/anibalsolon) and @62442katieb (https://github.com/62442katieb) 🌟 ❤️ — Reply to this email directly, view it on GitHub (#6336 (comment)), or unsubscribe (https://github.com/notifications/unsubscribe-auth/AARUETCGPX4NXSWUMGX2GSDZANA4JAVCNFSM6AAAAABC7PNGUKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJSGUZDCMBWGQ). You are receiving this because you were mentioned.