[REVIEW]: SAMBA: A Trainable Segmentation Web-App with Smart Labelling

[editorialbot]

Submitting author: @rmdocherty (Ronan Docherty)
Repository: https://github.com/tldr-group/samba-web
Branch with paper.md (empty if default branch): paper
Version: v1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @pchlap, @jingpengw
Archive: 10.5281/zenodo.11307100

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/fddb3a679cbe8c6eb91d08509120f23f/status.svg)](https://joss.theoj.org/papers/fddb3a679cbe8c6eb91d08509120f23f)

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

@pchlap & @jingpengw, 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 @AJQuinn 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 @pchlap

📝 Checklist for @jingpengw

[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:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (652.1 files/s, 128472.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TypeScript                      14            360            222           2662
Python                           9            384            712           1546
JavaScript                       6            177            112           1492
Markdown                         4             65              0            228
TeX                              1             13              0            103
JSON                             2              0              0            102
YAML                             2              7              8             46
HTML                             2              8              1             21
CSS                              1              0              0              3
Sass                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            42           1014           1055           6206
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1233

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0582-9 is OK
- 10.1093/bioinformatics/btx180 is OK
- 10.1038/nmeth.2019 is OK
- 10.1101/2023.08.21.554208 is OK
- 10.7717/peerj.453 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[AJQuinn]

👋🏼 @rmdocherty, @pchlap and @jingpengw - this is the review thread for the paper. All of our communications will happen here from now on.

For @pchlap and @jingpengw - 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. Please can you do this soon as a confirmation that you've seen the review starting.

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. Summary conversation is great on this thread but try to avoid substantial discussion about the repository here, this should take place in issues on the source repository.

When discussing the submission on an issue thread, please mention #6159 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 (@AJQuinn) if you have any questions/concerns.

[pchlap]

Review checklist for @pchlap

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/tldr-group/samba-web?
• 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 (@rmdocherty) 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?

[rmdocherty]

@pchlap @jingpengw Hi all, happy to answer any questions you have!

[jingpengw]

Review checklist for @jingpengw

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/tldr-group/samba-web?
• 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 (@rmdocherty) 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?

[rmdocherty]

@pchlap @jingpengw is it possible to get an update on the review?

[jingpengw]

Sorry for the late response. I have completed the check list and have some other comments.

• the manual and video tutorial link in the web interface is not working. The manual markdown file does exist though.
• The reference is not complete. For example: https://github.com/haesleinhuepf/napari-accelerated-pixel-and-object-classification
  https://github.com/fractal-napari-plugins-collection/napari-feature-classifier

[AJQuinn]

Hi all - thanks @jingpengw for the comments - if there a detailed discussions required to resolve these points please continue using an issue on the source repo that includes a link to this thread in the description.

@pchlap - do you have a sense of when you would be able to finalise a review? please get in touch if you need any input from my side - happy to assist

[rmdocherty]

@jingpengw, thanks for the comments! I've fixed the links to manual but have yet to fix the video link - I'll edit that once the video is uploaded and will let you know when that happens. I've also added the references you listed to the paper.

[pchlap]

Hi @AJQuinn, @rmdocherty,
apologies for being slow to get on to this. I will block some time to work through this in the next few days. Thanks.

[rmdocherty]

@pchlap No worries!
@jingpengw the video tutorial link is now working

[pchlap]

@editorialbot generate pdf

[editorialbot]

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

[pchlap]

Congratulations on a great piece of work @rmdocherty. A really useful, well designed and well implemented tool.

@AJQuinn I have completed my review. All items in the checklist are satified in my opinion and I don't request any additional changes. This work certainly meets the criteria for inclusion in JOSS.

[AJQuinn]

Thanks for your time @pchlap , much appreciated.

@jingpengw - could we get an update on when you'll be able to take a look at the changes in response to the review? Let me know if you need any further input from us.

[rmdocherty]

Thanks for the kind words @pchlap! @jingpengw I've made the changes in the references and fixed the video link, do you need any more info from my side?

[jingpengw]

looks good to me.

[Kevin-Mattheus-Moerman]

@rmdocherty I am happy to proceed to process this work for acceptance in JOSS. Please check the above points for you for the post-review checklist. Are you able to work on those? Let me know if you have any questions.
In addition, please check the above reference check. If any of those potentially missing DOIs listed, have DOIs please add them. No problem if they truly do not have any. Thanks.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[rmdocherty]

Hi @Kevin-Mattheus-Moerman, thanks for getting this orgranised!

I've updated the paper to add orcid affiliations for each author, and have added two DOIs to paper.bib for the two arXiv preprints, the other works don't have an associated DOI. I have cited the preprints as @misc, unsure how or if this will affect whether these new DOIs are detected - should I cite them as a @article instead?

The release version is v1.0.0

The Zenodo DOI is 10.5281/zenodo.11307100 and is linked here

Let me know if there's anything else that needs doing

[Kevin-Mattheus-Moerman]

@editorialbot set 10.5281/zenodo.11307100 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11307100

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0582-9 is OK
- 10.1093/bioinformatics/btx180 is OK
- 10.5281/zenodo.8115575 is OK
- 10.5281/zenodo.10071078 is OK
- 10.1038/nmeth.2019 is OK
- 10.48550/arXiv.2304.02643 is OK
- 10.1101/2023.08.21.554208 is OK
- 10.48550/arXiv.2302.05442 is OK
- 10.7717/peerj.453 is OK

MISSING DOIs

- No DOI given, and none found for title: napari-feature-classifier: An interactive classifi...
- Errored finding suggestions for "ONNX: Open Neural Network Exchange", please try later
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@rmdocherty below I have two minor points in relation to the paper:

• Please add United Kingdom to your affiliation
• Check if generalizable should be generalisable to be consistent with the rest of the text which uses British English
• Can you check if you need to fix any of the DOI issues raised? (it is okay if some references actually do not have a DOI)

[rmdocherty]

@Kevin-Mattheus-Moerman

• I've added United Kingdom to the affiliations
• I've changed generalizable to generalisable, and have updated characterization to characterisation (also in the summary) following the same logic
• I have checked the last three DOI issues, and they don't have an associated DOI. The first two are software tools with no DOI/zenodo/associated paper on their homepage, github or citation instructions and the last is a JMLR paper which doesn't come with a DOI. I have slightly updated the .bib entry of the last citation to include the paper url and number in order to be more consistent

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@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

- 10.1038/s41592-019-0582-9 is OK
- 10.1093/bioinformatics/btx180 is OK
- 10.5281/zenodo.8115575 is OK
- 10.5281/zenodo.10071078 is OK
- 10.1038/nmeth.2019 is OK
- 10.48550/arXiv.2304.02643 is OK
- 10.1101/2023.08.21.554208 is OK
- 10.48550/arXiv.2302.05442 is OK
- 10.7717/peerj.453 is OK

MISSING DOIs

- No DOI given, and none found for title: napari-feature-classifier: An interactive classifi...
- No DOI given, and none found for title: ONNX: Open Neural Network Exchange
- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python

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#5451, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[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: Docherty
  given-names: Ronan
  orcid: "https://orcid.org/0000-0002-7332-0924"
- family-names: Squires
  given-names: Isaac
  orcid: "https://orcid.org/0000-0003-1919-061X"
- family-names: Vamvakeros
  given-names: Antonis
  orcid: "https://orcid.org/0000-0002-4745-0602"
- family-names: Cooper
  given-names: Samuel J.
  orcid: "https://orcid.org/0000-0003-4055-6903"
contact:
- family-names: Cooper
  given-names: Samuel J.
  orcid: "https://orcid.org/0000-0003-4055-6903"
doi: 10.5281/zenodo.11307100
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Docherty
    given-names: Ronan
    orcid: "https://orcid.org/0000-0002-7332-0924"
  - family-names: Squires
    given-names: Isaac
    orcid: "https://orcid.org/0000-0003-1919-061X"
  - family-names: Vamvakeros
    given-names: Antonis
    orcid: "https://orcid.org/0000-0002-4745-0602"
  - family-names: Cooper
    given-names: Samuel J.
    orcid: "https://orcid.org/0000-0003-4055-6903"
  date-published: 2024-06-05
  doi: 10.21105/joss.06159
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6159
  title: "SAMBA: A Trainable Segmentation Web-App with Smart Labelling"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06159"
  volume: 9
title: "SAMBA: A Trainable Segmentation Web-App with Smart Labelling"

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.06159 joss-papers#5452
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06159
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]

@rmdocherty congratulations on this JOSS publication!!!!

And a special thank you to the reviewers: @pchlap, @jingpengw !!!!

[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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06159/status.svg)](https://doi.org/10.21105/joss.06159)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06159">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06159/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06159/status.svg
   :target: https://doi.org/10.21105/joss.06159

This is how it will look in your documentation:

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[rmdocherty]

Thanks @pchlap and @jingpengw for the reviews and @Kevin-Mattheus-Moerman for all the help!