[REVIEW]: DeepReg: a deep learning toolkit for medical image registration #2705

whedon · 2020-09-28T20:31:20Z

Submitting author: @mathpluscode (Yunguan Fu)
Repository: https://github.com/DeepRegNet/DeepReg
Version: v0.1.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @ethanwharris, @lbrea, @zhangfanmark
Archive: 10.5281/zenodo.4210215

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Markdown: [![status](https://joss.theoj.org/papers/7e6de472bc82a70d7618e23f618960b3/status.svg)](https://joss.theoj.org/papers/7e6de472bc82a70d7618e23f618960b3)

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✨ 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 ✨

Review checklist for @ethanwharris

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 (@mathpluscode) 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 @lbrea

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 (@mathpluscode) 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 @zhangfanmark

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 (@mathpluscode) 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?

The text was updated successfully, but these errors were encountered:

whedon · 2020-09-28T20:31:23Z

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

⚠️ JOSS reduced service mode ⚠️

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon · 2020-09-28T20:31:59Z

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

OK DOIs

- 10.1007/978-3-030-32245-8_45 is OK
- 10.1016/j.media.2018.07.002 is OK
- 10.1109/ISBI.2018.8363756 is OK
- 10.1016/j.media.2018.11.010 is OK
- 10.1109/TMI.2019.2897538 is OK
- 10.1016/j.media.2019.07.006 is OK
- 10.1016/j.cmpb.2018.01.025 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1016/j.neuroimage.2007.07.007 is OK
- 10.1016/j.neuroimage.2008.10.040 is OK
- 10.1088/0031-9155/46/3/201 is OK
- 10.1007/s00138-020-01066-5 is OK
- 10.1088/1361-6560/ab843e is OK
- 10.1007/978-3-658-29267-6_53 is OK
- 10.1109/42.796284 is OK
- 10.5281/zenodo.3835682 is OK
- 10.1002/mp.12268 is OK
- 10.5281/zenodo.3715652 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2020-09-28T20:32:22Z

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

Kevin-Mattheus-Moerman · 2020-09-29T08:55:09Z

@ethanwharris, @lbrea, @zhangfanmark, this is where the review takes place. There are instructions, and a set of checkboxes for each of you at the top of this issue which will guide you through the process. We would appreciate it if you could complete the review within about 2-3 weeks. Please let me know if you have any questions.

Let the reviewing begin! 🎉

Kevin-Mattheus-Moerman · 2020-09-29T08:57:08Z

@lbrea, @zhangfanmark, could you please consider updating your GitHub profile with your full name, and preferably a link to a professional (e.g. university) profile, ORCID, or equivalent.

Kevin-Mattheus-Moerman · 2020-10-04T10:52:39Z

@ethanwharris, @lbrea, @zhangfanmark, this is where the review takes place. I hope you are able to get started if you haven't already. Let me know if you have questions.

mathpluscode · 2020-10-05T23:56:32Z

@whedon generate pdf

whedon · 2020-10-05T23:57:24Z

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

mathpluscode · 2020-10-05T23:59:44Z

@whedon check references

whedon · 2020-10-06T00:00:39Z

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

OK DOIs

- 10.1007/978-3-030-32245-8_45 is OK
- 10.1016/j.media.2018.07.002 is OK
- 10.1109/ISBI.2018.8363756 is OK
- 10.1016/j.media.2018.11.010 is OK
- 10.1109/TMI.2019.2897538 is OK
- 10.1016/j.media.2019.07.006 is OK
- 10.1016/j.cmpb.2018.01.025 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1016/j.neuroimage.2007.07.007 is OK
- 10.1016/j.neuroimage.2008.10.040 is OK
- 10.1088/0031-9155/46/3/201 is OK
- 10.1007/s00138-020-01066-5 is OK
- 10.1088/1361-6560/ab843e is OK
- 10.1007/978-3-658-29267-6_53 is OK
- 10.1109/42.796284 is OK
- 10.5281/zenodo.3835682 is OK
- 10.1002/mp.12268 is OK
- 10.5281/zenodo.3715652 is OK
- 10.1016/j.cmpb.2009.09.002 is OK
- 10.1109/CVPRW.2016.78 is OK

MISSING DOIs

- 10.1007/978-3-030-59716-0_24 may be a valid DOI for title: Longitudinal Image Registration with Temporal-order and Subject-specificity Discrimination
- 10.1007/978-3-030-59716-0_15 may be a valid DOI for title: MvMM-RegNet: A new image registration framework based on multivariate mixture model and neural network estimation

INVALID DOIs

- None

mathpluscode · 2020-10-08T18:12:38Z

@whedon check references

whedon · 2020-10-08T18:13:10Z

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

OK DOIs

- 10.1007/978-3-030-32245-8_45 is OK
- 10.1016/j.media.2018.07.002 is OK
- 10.1109/ISBI.2018.8363756 is OK
- 10.1016/j.media.2018.11.010 is OK
- 10.1109/TMI.2019.2897538 is OK
- 10.1016/j.media.2019.07.006 is OK
- 10.1007/978-3-030-59716-0_24 is OK
- 10.1016/j.cmpb.2018.01.025 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1016/j.neuroimage.2007.07.007 is OK
- 10.1016/j.neuroimage.2008.10.040 is OK
- 10.1088/0031-9155/46/3/201 is OK
- 10.1007/s00138-020-01066-5 is OK
- 10.1088/1361-6560/ab843e is OK
- 10.1007/978-3-030-59716-0_15 is OK
- 10.1007/978-3-658-29267-6_53 is OK
- 10.1109/42.796284 is OK
- 10.5281/zenodo.3835682 is OK
- 10.1002/mp.12268 is OK
- 10.5281/zenodo.3715652 is OK
- 10.1016/j.cmpb.2009.09.002 is OK
- 10.1109/CVPRW.2016.78 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ethanwharris · 2020-10-17T14:54:17Z

@Kevin-Mattheus-Moerman I have now finished my review. The authors have responded to my breif comments on the paper and the code base / documentation is in good shape (installation works and the demos run as expected etc.) so I recommend acceptance 😃

Kevin-Mattheus-Moerman · 2020-10-21T20:03:08Z

Thanks for your help @ethanwharris !

Kevin-Mattheus-Moerman · 2020-10-21T20:04:07Z

@lbrea, @zhangfanmark thanks again for agreeing to review this work. Can you let me know if you have started and when you expect to complete this review? Let me know if you have questions.

lbrea · 2020-10-23T07:27:05Z

Hi, sorry for the late reply. I am now working now on the review, and I expect to complete it by Monday 26 at the latest.

…

On Wed, Oct 21, 2020 at 10:04 PM Kevin Mattheus Moerman < ***@***.***> wrote: @lbrea <https://github.com/lbrea>, @zhangfanmark <https://github.com/zhangfanmark> thanks again for agreeing to review this work. Can you let me know if you have started and when you expect to complete this review? Let me know if you have questions. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2705 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMAQ7BR53KURSTGPDPQD5GDSL45ERANCNFSM4R46NN5A> .

zhangfanmark · 2020-10-23T17:18:37Z

Sorry for the delay. I will perform the review and get it back early next week.

lbrea · 2020-10-26T08:40:37Z

@Kevin-Mattheus-Moerman I've finished my review (see further comments above). The package looks great to me, and I would recommend acceptance.

mathpluscode · 2020-10-28T14:04:59Z

Hi @zhangfanmark @lbrea, thank you so much for your reviews. We've addressed all the mentioned issues and please feel free to try again ;)

mathpluscode · 2020-10-28T14:05:12Z

@whedon generate pdf

whedon · 2020-10-28T14:06:08Z

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

Kevin-Mattheus-Moerman · 2020-11-02T10:33:37Z

@ethanwharris, @zhangfanmark looks like you've ticked all boxes above. Can you review the latest changes and/or confirm you are happy to recommend acceptance of this work?

zhangfanmark · 2020-11-02T12:22:52Z

Hi @Kevin-Mattheus-Moerman , the code and the paper look good to me. I recommend acceptance of the work. Thank you!

ethanwharris · 2020-11-02T20:27:14Z

Hi @Kevin-Mattheus-Moerman , all looks good to me, happy to recommend acceptance :)

Kevin-Mattheus-Moerman · 2020-11-02T21:08:35Z

@whedon check references

whedon · 2020-11-02T21:09:01Z

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

OK DOIs

- 10.1007/978-3-030-32245-8_45 is OK
- 10.1016/j.media.2018.07.002 is OK
- 10.1109/ISBI.2018.8363756 is OK
- 10.1016/j.media.2018.11.010 is OK
- 10.1109/TMI.2019.2897538 is OK
- 10.1016/j.media.2019.07.006 is OK
- 10.1007/978-3-030-59716-0_24 is OK
- 10.1016/j.cmpb.2018.01.025 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1016/j.neuroimage.2007.07.007 is OK
- 10.1016/j.neuroimage.2008.10.040 is OK
- 10.1088/0031-9155/46/3/201 is OK
- 10.1007/s00138-020-01066-5 is OK
- 10.1088/1361-6560/ab843e is OK
- 10.1007/978-3-030-59716-0_15 is OK
- 10.1007/978-3-658-29267-6_53 is OK
- 10.1109/42.796284 is OK
- 10.5281/zenodo.3835682 is OK
- 10.1002/mp.12268 is OK
- 10.5281/zenodo.3715652 is OK
- 10.1016/j.cmpb.2009.09.002 is OK
- 10.1109/CVPRW.2016.78 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2020-11-02T21:20:01Z

@mathpluscode this looks like it is ready to process for acceptance. At this point can you do the following:

Can you archive a copy of the reviewed software on Zenodo and report back here with the DOI? (some find this approach useful: https://guides.github.com/activities/citable-code/).
Please check that the Zenodo archive metadata like the title, authors, and version matches that of the paper. You may need to ammend/edit this information manually.
Can you confirm if v0.1.0 is the most appropriate version tag for this work, or has the version moved on?

Thanks

mathpluscode · 2020-11-02T23:58:55Z

@mathpluscode this looks like it is ready to process for acceptance. At this point can you do the following:

Can you archive a copy of the reviewed software on Zenodo and report back here with the DOI? (some find this approach useful: https://guides.github.com/activities/citable-code/).

Please check that the Zenodo archive metadata like the title, authors, and version matches that of the paper. You may need to ammend/edit this information manually.

Can you confirm if v0.1.0 is the most appropriate version tag for this work, or has the version moved on?

Thanks

Hi @Kevin-Mattheus-Moerman,

Here is the archive of DeepReg v0.1.0
Yes we've corrected the title, authors and version
Yes we confirm v0.1.0 is the correct version tag.

Thanks!

Kevin-Mattheus-Moerman · 2020-11-04T21:27:14Z

@whedon set 10.5281/zenodo.4210215 as archive

whedon · 2020-11-04T21:27:18Z

OK. 10.5281/zenodo.4210215 is the archive.

Kevin-Mattheus-Moerman · 2020-11-04T21:28:37Z

@whedon accept

whedon · 2020-11-04T21:28:40Z

Attempting dry run of processing paper acceptance...

whedon · 2020-11-04T21:29:39Z

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

OK DOIs

- 10.1007/978-3-030-32245-8_45 is OK
- 10.1016/j.media.2018.07.002 is OK
- 10.1109/ISBI.2018.8363756 is OK
- 10.1016/j.media.2018.11.010 is OK
- 10.1109/TMI.2019.2897538 is OK
- 10.1016/j.media.2019.07.006 is OK
- 10.1007/978-3-030-59716-0_24 is OK
- 10.1016/j.cmpb.2018.01.025 is OK
- 10.1109/CVPR.2016.90 is OK
- 10.1016/j.neuroimage.2007.07.007 is OK
- 10.1016/j.neuroimage.2008.10.040 is OK
- 10.1088/0031-9155/46/3/201 is OK
- 10.1007/s00138-020-01066-5 is OK
- 10.1088/1361-6560/ab843e is OK
- 10.1007/978-3-030-59716-0_15 is OK
- 10.1007/978-3-658-29267-6_53 is OK
- 10.1109/42.796284 is OK
- 10.5281/zenodo.3835682 is OK
- 10.1002/mp.12268 is OK
- 10.5281/zenodo.3715652 is OK
- 10.1016/j.cmpb.2009.09.002 is OK
- 10.1109/CVPRW.2016.78 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2020-11-04T21:30:26Z

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

Check final proof 👉 openjournals/joss-papers#1892

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1892, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman · 2020-11-04T21:33:29Z

@whedon accept deposit=true

whedon · 2020-11-04T21:33:32Z

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

whedon · 2020-11-04T21:35:13Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2020-11-04T21:35:14Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02705 joss-papers#1893
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02705
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

mathpluscode · 2020-11-04T21:54:54Z

Hi, @Kevin-Mattheus-Moerman @ethanwharris @zhangfanmark @lbrea, thank you a lot for the edit and review!

YipengHu · 2020-11-04T21:56:54Z

Hi, @Kevin-Mattheus-Moerman @ethanwharris @zhangfanmark @lbrea, thank you a lot for the edit and review!

Great editorial service - will recommend to colleagues 👍

whedon · 2020-11-04T22:06:25Z

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

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reStructuredText:
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   :target: https://doi.org/10.21105/joss.02705

This is how it will look in your documentation:

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whedon added Python review labels Sep 28, 2020

whedon assigned Kevin-Mattheus-Moerman Sep 28, 2020

whedon mentioned this issue Sep 28, 2020

[PRE REVIEW]: DeepReg: a deep learning toolkit for medical image registration #2633

Closed

whedon assigned ethanwharris and zhangfanmark Sep 29, 2020

arfon changed the title ~~[REVIEW]: https://joss.theoj.org/papers/new~~ [REVIEW]: DeepReg: a deep learning toolkit for medical image registration Sep 29, 2020

whedon assigned lbrea Oct 3, 2020

This was referenced Oct 4, 2020

[JOSS Review] State of the field DeepRegNet/DeepReg#429

Closed

[JOSS Review] Referencing TensorFlow DeepRegNet/DeepReg#430

Closed

This was referenced Oct 23, 2020

[JOSS Review] Demo testing DeepRegNet/DeepReg#478

Closed

[JOSS Review] Code Review Summary DeepRegNet/DeepReg#479

Closed

[JOSS Review] Paper Review Summary DeepRegNet/DeepReg#480

Closed

mathpluscode mentioned this issue Nov 2, 2020

Release v0.1.0 DeepRegNet/DeepReg#499

Closed

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 4, 2020

whedon added accepted published Papers published in JOSS labels Nov 4, 2020

Kevin-Mattheus-Moerman closed this as completed Nov 4, 2020

editorialbot mentioned this issue Sep 26, 2023

[PRE REVIEW]: DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning #5878

Closed

[REVIEW]: DeepReg: a deep learning toolkit for medical image registration #2705

[REVIEW]: DeepReg: a deep learning toolkit for medical image registration #2705

Comments

whedon commented Sep 28, 2020 • edited Loading

Status

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