[REVIEW]: SIAL: A simple image analysis library for wet-lab scientists

[whedon]

Submitting author: @d-tear (David Tyrpak)
Repository: https://github.com/d-tear/SIAL
Version: v1.0.1
Editor: @jni
Reviewer: @bogovicj, @haesleinhuepf
Archive: 10.5281/zenodo.4312250

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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

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

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Review checklist for @bogovicj

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 (@d-tear) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @haesleinhuepf

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 (@d-tear) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

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

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[whedon]

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

OK DOIs

- 10.1038/s41598-017-17204-5 is OK
- 10.1371/journal.pbio.2005970 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1038/nmeth.2019 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

[jni]

@bogovicj @haesleinhuepf thank you so much for agreeing to review this paper! You should have received a github invitation to join the joss-reviews repo which will allow you to tick items on your review checklist above. And, as mentioned in my email, the review process is also well-described in the JOSS documentation. If you have any questions at all, feel free to ping me here!

@d-tear as above, feel free to ask me if you have any questions.

[jni]

@haesleinhuepf you should have received an invite to this repo from GitHub, could you make sure you accept it? Let me know if you can't find it and I'll re-invite you.

[jni]

Hi everyone! Thank you for working on these reviews @bogovicj and @haesleinhuepf and thank you @d-tear for promptly addressing @haesleinhuepf's issues on the plugin repo! Can I get a status check from everyone on where things stand right now?

[bogovicj]

@jni

There is a bit more left for me to do, though I expect to finish up this weekend at the latest.

A question - is this thread the right place to include suggestions for the Software paper? Or should those go elsewhere, say the project repo?

[jni]

This thread is good!

[haesleinhuepf]

Hey @bogovicj, just FYI: I screwed up the checkboxes in your todo-list. I think I reverted everything. Just take little extra care ;-) Apologies.

[haesleinhuepf]

Hi @jni, @bogovicj and @d-tear,

I'll just summarize my review in case I get distracted again. ;-)

This project is a fantastic contribution to the ImageJ ecosystem. The three plugins for anonymisation (pseudonymisation?), phenotype-scoring and region-of-interest management are very useful, especiallly in the context of wet-lab imaging science. In many projects, automated image analysis is not at hand and programming experts not available. In such projects, manual annotation and phenotype scroring are state-of-the-art methods which are facilitated by the authors contribution in form a ImageJ/Fiji plugin. This eases the life of researchers and potentiallly reduces the likelihood of manual errors.
I would like to thank the authors that they made these tools available to the public and open source. The documentation is very well done, partly in form of youtube videos very nicely demonstrating and explaining the usage of the plugins. Very well done. I have minor last issues: I would like to ask the authors to add a statement about how to reach them in case someone needs support, potentially some links to other scientific software mentioned in the github-readme documentation and adding a short clarification of the difference between anonymization and pseudonymization.

Otherwise, very well done! Please let me know if there is anything else I can do to push this project forward. I'm happy to help spreading the word btw.

Thanks!

Best,
Robert

[bogovicj]

Hi @d-tear, @jni , @haesleinhuepf

Thanks David for your contribution!

Installation was easy and as described in the paper. The need for the software was well-motivated. For users, the tools are intuitive to use and quick to learn, especially given the video tutorials the authors provide.

As well, I quite like the logging mechanism that keeps track of what images users have already analyzed. That has the potential to be super useful for other developers. I'd like to check it out soon (tomorrow?) - I may ask for some clarification about how a tool-builder might use it.

Minor comments regarding the paper:
I feel the description of the ROI recorder in the text is a little too brief to understand (from the text alone. That is, the text describes the goal of the roi recorder more than its functionality / use. Consider adding a couple short sentences describing what the tools do in action.

A more significant (but easy to address) issue has to do with what versions of the code you distribute via the fiji update site. I'd ask that you release a 1.0.0 version when you're ready and avoid distributing snapshot versions in the future.

Nicely done,
John

[d-tear]

Hi @jni @haesleinhuepf @bogovicj , I really appreciate your time and effort in improving the quality of the paper and software! This was my first foray into an open source software project and it's really satisfying to see that this contribution would be beneficial to the community. I will incorporate your edits in the coming days, and address the issues in the repository. I'll also send an email out when I've addressed everything. John, I'd be happy to discuss the logging mechanism code. The relevant classes are the FileEditor and LogFile classes inside the repository. I'd be happy to discuss the details with you or any other developers, whether that's through email or zoom (note that I'm on the west coast PST). Cheers, David

…

On Sat, Oct 24, 2020 at 12:23 PM John Bogovic ***@***.***> wrote: Hi @d-tear <https://urldefense.com/v3/__https://github.com/d-tear__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2-emoyPHQ$>, @jni <https://urldefense.com/v3/__https://github.com/jni__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_mQLM5Fw$> , @haesleinhuepf <https://urldefense.com/v3/__https://github.com/haesleinhuepf__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_OP2FJRA$> Thanks David for your contribution! Installation was easy and as described in the paper. The need for the software was well-motivated. For users, the tools are intuitive to use and quick to learn, especially given the video tutorials the authors provide. As well, I quite like the logging mechanism that keeps track of what images users have already analyzed. That has the potential to be *super* useful for other developers. I'd like to check it out soon (tomorrow?) - I may ask for some clarification about how a tool-builder might use it. Minor comments regarding the paper: I feel the description of the ROI recorder in the text is a little too brief to understand (from the text alone. That is, the text describes the goal of the roi recorder more than its functionality / use. Consider adding a couple short sentences describing what the tools do in action. A more significant (but easy to address) issue has to do with what versions of the code you distribute via the fiji update site. I'd ask that you release a 1.0.0 version when you're ready and avoid distributing snapshot versions in the future. <https://urldefense.com/v3/__https://github.com/d-tear/SIAL/issues/6__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_V5yoPzQ$> Nicely done, John — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/openjournals/joss-reviews/issues/2689*issuecomment-716042846__;Iw!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf28aToiHpw$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AET7YN5RP3X7FCRA2JYOT4DSMMSRTANCNFSM4RVLICBA__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_h8IDDiw$> .

-- *David Tyrpak* PhD Pharmaceutical Sciences NIH Predoctoral Fellow, http://www.mackaylab.com University of Southern California School of Pharmacy 1985 Zonal Avenue, PSC 306A Los Angeles, California 90089 Tel: 323.442.4119

[d-tear]

Hi @jni , @bogovicj , and @haesleinhuepf ,

I believe I've addressed the open issues. If everything looks good, you can close them (or I can, either way).

(John, I went ahead closed the issue for the min number of phenotypes >=2. Let me know if that's OK. I also added some additional documentation for the ROI Recorder program.)

Please let me know if there's anything else to correct. I appreciate your valuable advice.

[d-tear]

@whedon generate pdf

[whedon]

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

[d-tear]

Hi @jni <https://urldefense.com/v3/__https://github.com/jni__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_mQLM5Fw$> , @haesleinhuepf <https://urldefense.com/v3/__https://github.com/haesleinhuepf__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_OP2FJRA$>, and @bogovicj <https://urldefense.com/v3/__https://github.com/bogovicj__;!!LIr3w8kk_Xxm!8_Sx2_UEdQ2GnjdLLT7MjlJ9A-o303ggvXymVKaKwk0DpfPqLHRH637LGEPh3w$> , I hope you are doing well! I believe I've addressed all of the open issues and concerns raised during the review process. If there is anything else that needs to be addressed, please let me know. Otherwise I will close the open issues in the repository. @jni <https://urldefense.com/v3/__https://github.com/jni__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_mQLM5Fw$> is there anything else that needs to be addressed before the manuscript can be published? I appreciate all of your effort! Best, David

…

On Mon, Oct 26, 2020 at 6:50 PM whedon ***@***.***> wrote: 👉📄 Download article proof <https://urldefense.com/v3/__https://raw.githubusercontent.com/openjournals/joss-papers/joss.02689/joss.02689/10.21105.joss.02689.pdf__;!!LIr3w8kk_Xxm!_-OgZ0giETWPuL1JNPfjyGGm6KO2zje9ItsB7adSwvgImvzkCNKYJsoQ5Yk4UA$> 📄 View article proof on GitHub <https://urldefense.com/v3/__https://github.com/openjournals/joss-papers/blob/joss.02689/joss.02689/10.21105.joss.02689.pdf__;!!LIr3w8kk_Xxm!_-OgZ0giETWPuL1JNPfjyGGm6KO2zje9ItsB7adSwvgImvzkCNKYJspAyNXQIg$> 📄 👈 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/openjournals/joss-reviews/issues/2689*issuecomment-716924667__;Iw!!LIr3w8kk_Xxm!_-OgZ0giETWPuL1JNPfjyGGm6KO2zje9ItsB7adSwvgImvzkCNKYJspdACSa8w$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AET7YN6GM7EUQ3JWAU4X4F3SMYRP5ANCNFSM4RVLICBA__;!!LIr3w8kk_Xxm!_-OgZ0giETWPuL1JNPfjyGGm6KO2zje9ItsB7adSwvgImvzkCNKYJsryc8AUrg$> .

-- *David Tyrpak* PhD Pharmaceutical Sciences NIH Predoctoral Fellow, http://www.mackaylab.com University of Southern California School of Pharmacy 1985 Zonal Avenue, PSC 306A Los Angeles, California 90089 Tel: 323.442.4119

[jni]

Hi everyone,

Apologies for the long silence, as it has been a very busy month for me. @bogovicj @haesleinhuepf thank you so much for your reviews so far. From the comments, it seems the paper is ready to be accepted, but I notice some unticked items in your reviewer checklists. Could you double check that everything is finished and confirm via comments that you are happy to accept the paper?

btw @d-tear it occurred to me this morning that for my very first paper, at USC, I scored confocal images (Fig 4 of this paper), blinded by hand by my co-author Beth. I find it quite amusing to be reviewing this plugin 15 years later! 😂

[d-tear]

@jni that is too funny. I actually have some friends that were in the Cannon lab. The world of science is so small!

[bogovicj]

Updated my checklist and happy to accept.

[haesleinhuepf]

I'm also happy to accept it.
@jni please press the button ;-)

[jni]

Awesome! Thank you all!

@d-tear the next step is for you to generate a new tagged release + Zenodo archive, and report the release number and archive DOI here. Then we can set those versions accept the paper! 🎉

[d-tear]

Hi @jni,

The new tagged release is v1.0.1 and the archive DOI is 10.5281/zenodo.4312250

[jni]

@whedon set 10.5281/zenodo.4312250 as archive

[whedon]

OK. 10.5281/zenodo.4312250 is the archive.

[jni]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.

[jni]

@whedon accept

🎉

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/nmeth.2019 is OK
- 10.1038/s41598-017-17204-5 is OK
- 10.1371/journal.pbio.2005970 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1970

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1970, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02689 joss-papers#1982
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02689
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...

[arfon]

@bogovicj, @haesleinhuepf - many thanks for your reviews here and to @jni for editing this submission. JOSS relies upon the efforts of volunteers like yourselves, and we simply wouldn't be able to do it without you ✨

@d-tear - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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

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HTML:
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</a>

reStructuredText:
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