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

Created on 22 Sep 2020  ยท  16Comments  ยท  Source: openjournals/joss-reviews

Submitting author: @d-tear (David Tyrpak)
Repository: https://github.com/d-tear/SIAL
Version: v1.0.0
Editor: @jni
Reviewer: @bogovicj, @haesleinhuepf
Archive: Pending

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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:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

โœจ 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 โœจ

Review checklist for @bogovicj

Conflict of interest

  • [x] 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

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] 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

  • [x] Installation: Does installation proceed as outlined in the documentation?
  • [x] Functionality: Have the functional claims of the software been confirmed?
  • [x] 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

  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • [x] 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)?
  • [x] 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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] 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?
  • [x] 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

  • [x] 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

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] 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?
  • [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

  • [x] Installation: Does installation proceed as outlined in the documentation?
  • [x] Functionality: Have the functional claims of the software been confirmed?
  • [x] 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

  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • [x] 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)?
  • [x] 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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] 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?
Java TeX review

Most helpful comment

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

All 16 comments

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 :tada:.

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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

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

@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.

@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.

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?

@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?

This thread is good!

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

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

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

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 notifications@github.com
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

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--

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

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.

@whedon generate pdf

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Hi @jni
https://urldefense.com/v3/__https://github.com/jni__;!!LIr3w8kk_Xxm!_U7Nbabchvz-kBYleZmBizKicTUJQCQ1SmDnNak-HLRVjh5Jo0_mf2_mQLM5Fw$
, @haesleinhuepf
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and @bogovicj
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,

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

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--

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

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