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[REVIEW]: SMITE: Single Molecule Imaging Toolbox Extraordinaire (MATLAB) #5563

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editorialbot opened this issue Jun 15, 2023 · 87 comments
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accepted C++ Cuda Matlab published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Jun 15, 2023

Submitting author: @MJWester (Michael Wester)
Repository: https://github.com/LidkeLab/smite
Branch with paper.md (empty if default branch):
Version: 1.0.0
Editor: @jgostick
Reviewers: @bencardoen, @ajinkyakadu
Archive: 10.5281/zenodo.8327409

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bb7451e778d9a92cf9370903a6712ea0"><img src="https://joss.theoj.org/papers/bb7451e778d9a92cf9370903a6712ea0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bb7451e778d9a92cf9370903a6712ea0/status.svg)](https://joss.theoj.org/papers/bb7451e778d9a92cf9370903a6712ea0)

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

@bencardoen, 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 @jgostick 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 @bencardoen

📝 Checklist for @ajinkyakadu

@editorialbot editorialbot added C++ Cuda Matlab paused review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Jun 15, 2023
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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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.57 s (1055.7 files/s, 126688.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                         512           6742          20580          35129
Markdown                        62            610              0           4200
CUDA                             6            388            470           1489
C++                              5            255            148            860
TeX                              2             34              0            404
C/C++ Header                     5             40             52             96
YAML                             2              2              9             36
make                             3             27             33             36
-------------------------------------------------------------------------------
SUM:                           597           8098          21292          42250
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.1364/OPEX.13.007052 is OK
- 10.1126/science.1127344 is OK
- 10.1038/nmeth929 is OK
- 10.1126/science.1137395 is OK
- 10.1038/nprot.2011.336 is OK
- 10.1063/5.0069349 is OK
- 10.1021/acs.chemrev.6b00815 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1101/752287 is OK
- 10.1038/s41467-022-34894-2 is OK
- 10.1016/j.bpj.2018.11.1510 is OK
- 10.1016/j.bpj.2019.11.926 is OK
- 10.1101/2021.03.26.437196 is OK
- 10.1038/s41598-021-02850-7 is OK
- 10.3389/fbinf.2021.724325 is OK
- 10.7554/eLife.63678 is OK
- 10.1371/journal.pone.0246138 is OK
- 10.3791/63665 is OK
- 10.25827/CS2A-DH13 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.1038/s41592-020-0938-1 is OK
- 10.14440/jbm.2014.36 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Wordcount for paper.md is 813

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@MJWester
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I am not sure why there is an error. Is this our paper? The most recent artifact produced under issues in the main repository seems to be correct, so I am not sure where to begin.

@bencardoen
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bencardoen commented Jun 17, 2023

Review checklist for @bencardoen

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/LidkeLab/smite?
  • 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 (@MJWester) 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?

@bencardoen
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@MJWester when you check the output of the error, it seems it crashed on a missing affiliation

failure': Author (Eric A. Burns) is missing affiliation (Theoj::Error)

https://github.com/openjournals/joss-papers/actions/runs/5274452956/jobs/9538928136#step:3:93

@MJWester
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MJWester commented Jun 20, 2023

Thanks. I fixed the problem and pushed a corrected version of the repository. How do I (or do you) transfer this updated repo to the review chain?

@bencardoen
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@MJWester I think by

@editorialbot generate pdf

@jgostick
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@editorialbot add @ajinkyakadu as reviewer

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@ajinkyakadu added to the reviewers list!

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jgostick commented Jul 4, 2023

Hi @ajinkyakadu. Thanks for agreeing to review. To get started, you should generate your checklist using @editorialbot generate my checklist (while logged in as yourself, obvs). You'll then get a list of speific things to look for, and your job as reviewer is then straightforward.

@ajinkyakadu
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ajinkyakadu commented Jul 4, 2023

Review checklist for @ajinkyakadu

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/LidkeLab/smite?
  • 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 (@MJWester) 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?

@jgostick
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Hi @ajinkyakadu
I'm glad to see that you've made some good progress on your review. Hopefully you can finalize it in the week or so?

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

@MJWester
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Except for the JOSS DOI which I didn't expect to work until formally accepted, the article I downloaded looks great. Please let me know if I am specifically supposed to do anything else (I am assuming the editoriabotl comments above are for the editors).

@Kevin-Mattheus-Moerman
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@jgostick have you tried @editorialbot create post-review checklist to help remember these final steps? I'll run it now and you'll see it generates a helpful list.

@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Oct 1, 2023

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a PR)
  • Check the references in the paper for corrections (e.g. capitalization)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

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Kevin-Mattheus-Moerman commented Oct 1, 2023

@MJWester I am the AEiC on this track and here to help process final steps. I have checked this review, the paper, your repository, and the archive link, and most seems in other. I only have the below minor points that require your attention:

  • Check microscropy which should be microscopy
  • Check devloped which should read developed

@Kevin-Mattheus-Moerman
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Not sure which EiC will be looking at this one, but I would like to apologize in advanced that I always miss something in the final checks. In my last one I didn't notice that the version tag on github had a V, but I didn't include that...etc.

@jgostick well it looks like we're ticking all the boxes this time 😃

@MJWester
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MJWester commented Oct 1, 2023

@Kevin-Mattheus-Moerman I have made the fixes above and rereleased v1.0.0 with these changes.

@jgostick
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jgostick commented Oct 2, 2023

Hi @Kevin-Mattheus-Moerman, thanks for tidying this up. BTW, I was the person who suggested the 'post review checklist" features!

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@editorialbot generate pdf

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

@Kevin-Mattheus-Moerman
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@editorialbot accept

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

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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: Schodt
  given-names: David J.
  orcid: "https://orcid.org/0000-0002-8986-2736"
- family-names: Wester
  given-names: Michael J.
  orcid: "https://orcid.org/0000-0002-3520-7605"
- family-names: Fazel
  given-names: Mohamadreza
  orcid: "https://orcid.org/0000-0002-6215-1336"
- family-names: Khan
  given-names: Sajjad
  orcid: "https://orcid.org/0000-0002-6910-5199"
- family-names: Mazloom-Farsibaf
  given-names: Hanieh
  orcid: "https://orcid.org/0000-0002-2571-0418"
- family-names: Pallikkuth
  given-names: Sandeep
  orcid: "https://orcid.org/0009-0003-0400-6389"
- family-names: Meddens
  given-names: Marjolein B. M.
  orcid: "https://orcid.org/0000-0002-9965-1342"
- family-names: Farzam
  given-names: Farzin
  orcid: "https://orcid.org/0000-0002-9939-1923"
- family-names: Burns
  given-names: Eric A.
  orcid: "https://orcid.org/0000-0002-1625-2400"
- family-names: Kanagy
  given-names: William K.
  orcid: "https://orcid.org/0000-0002-5756-9965"
- family-names: Rinaldi
  given-names: Derek A.
  orcid: "https://orcid.org/0009-0000-8394-3626"
- family-names: Jhamba
  given-names: Elton
  orcid: "https://orcid.org/0000-0002-5272-6466"
- family-names: Liu
  given-names: Sheng
  orcid: "https://orcid.org/0000-0003-1225-0763"
- family-names: Relich
  given-names: Peter K.
  orcid: "https://orcid.org/0000-0002-6063-6233"
- family-names: Olah
  given-names: Mark J.
- family-names: Steinberg
  given-names: Stanly L.
- family-names: Lidke
  given-names: Keith A.
  orcid: "https://orcid.org/0000-0002-9328-4318"
contact:
- family-names: Lidke
  given-names: Keith A.
  orcid: "https://orcid.org/0000-0002-9328-4318"
doi: 10.5281/zenodo.8327409
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Schodt
    given-names: David J.
    orcid: "https://orcid.org/0000-0002-8986-2736"
  - family-names: Wester
    given-names: Michael J.
    orcid: "https://orcid.org/0000-0002-3520-7605"
  - family-names: Fazel
    given-names: Mohamadreza
    orcid: "https://orcid.org/0000-0002-6215-1336"
  - family-names: Khan
    given-names: Sajjad
    orcid: "https://orcid.org/0000-0002-6910-5199"
  - family-names: Mazloom-Farsibaf
    given-names: Hanieh
    orcid: "https://orcid.org/0000-0002-2571-0418"
  - family-names: Pallikkuth
    given-names: Sandeep
    orcid: "https://orcid.org/0009-0003-0400-6389"
  - family-names: Meddens
    given-names: Marjolein B. M.
    orcid: "https://orcid.org/0000-0002-9965-1342"
  - family-names: Farzam
    given-names: Farzin
    orcid: "https://orcid.org/0000-0002-9939-1923"
  - family-names: Burns
    given-names: Eric A.
    orcid: "https://orcid.org/0000-0002-1625-2400"
  - family-names: Kanagy
    given-names: William K.
    orcid: "https://orcid.org/0000-0002-5756-9965"
  - family-names: Rinaldi
    given-names: Derek A.
    orcid: "https://orcid.org/0009-0000-8394-3626"
  - family-names: Jhamba
    given-names: Elton
    orcid: "https://orcid.org/0000-0002-5272-6466"
  - family-names: Liu
    given-names: Sheng
    orcid: "https://orcid.org/0000-0003-1225-0763"
  - family-names: Relich
    given-names: Peter K.
    orcid: "https://orcid.org/0000-0002-6063-6233"
  - family-names: Olah
    given-names: Mark J.
  - family-names: Steinberg
    given-names: Stanly L.
  - family-names: Lidke
    given-names: Keith A.
    orcid: "https://orcid.org/0000-0002-9328-4318"
  date-published: 2023-10-02
  doi: 10.21105/joss.05563
  issn: 2475-9066
  issue: 90
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5563
  title: "SMITE: Single Molecule Imaging Toolbox Extraordinaire
    (MATLAB)"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05563"
  volume: 8
title: "SMITE: Single Molecule Imaging Toolbox Extraordinaire (MATLAB)"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05563 joss-papers#4640
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05563
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Oct 2, 2023
@Kevin-Mattheus-Moerman
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@MJWester one minor change, please can you add the country information for your affiliations? I.e. add United States of America. Thanks. Once done I'll re-accept to update the paper PDF.

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MJWester commented Oct 3, 2023

@Kevin-Mattheus-Moerman I added the city as well as the country information as that seemed reasonable.

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@editorialbot generate pdf

1 similar comment
@Kevin-Mattheus-Moerman
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@editorialbot generate pdf

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MJWester commented Oct 4, 2023

@Kevin-Mattheus-Moerman I don't see the revised affiliations when I look at the regenerated PDF via the JOSS DOI above. I didn't create a new GitHub version v1.0.0 this time with the changes as I have done for earlier modifications, which then creates a new Zenodo DOI. Should I do this or is the problem somewhere else (or the way I am looking at the paper)?

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@editorialbot reaccept

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Rebuilding paper!

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🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4654

@Kevin-Mattheus-Moerman
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@MJWester the above has updated the paper. No need for a new version or archive link. Congratulations on this publication in JOSS!

@Kevin-Mattheus-Moerman
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Thanks for editing @jgostick! And a special thank you to the reviewers: @bencardoen, @ajinkyakadu ! 🎉

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🎉🎉🎉 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.05563/status.svg)](https://doi.org/10.21105/joss.05563)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05563">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05563/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05563/status.svg
   :target: https://doi.org/10.21105/joss.05563

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@MJWester
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MJWester commented Oct 4, 2023

Thank. you everybody!!! This has been a very positive experience.

@jgostick
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jgostick commented Oct 4, 2023

It sure dragged on longer that normal so I am sorry for that...but I am glad it worked out in the end. Congrats!

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