[REVIEW]: Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning Models

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@OllyK@osorensen<!--end-editor-- Reviewers: @jingpengw, @estenhl Archive: 10.5281/zenodo.7143363

Status

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Markdown: [![status](https://joss.theoj.org/papers/cb6e86a01006b487a09e41a9fc5b4e5e/status.svg)](https://joss.theoj.org/papers/cb6e86a01006b487a09e41a9fc5b4e5e)

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

@jingpengw & @estenhl, 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 @osorensen 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 @estenhl

📝 Checklist for @jingpengw

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (558.2 files/s, 85401.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             5            551              0           3284
Python                          36            602            517           2555
Markdown                         6            140              0            471
YAML                             6             12             27            198
TeX                              1              7              0            103
TOML                             1              5              0             50
JavaScript                       1              3              3             40
-------------------------------------------------------------------------------
SUM:                            56           1320            547           6701
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 989

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

osorensen commented 2 years ago

👋 @jingpengw, @estenhl, could you please update us on how it's going with your reviews?

estenhl commented 2 years ago

👋 @jingpengw, @estenhl, could you please update us on how it's going with your reviews?

Will finish it sometime next week

estenhl commented 2 years ago

Review checklist for @estenhl

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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/DiamondLightSource/volume-segmantics?
[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 (@OllyK) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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).
[x] 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?
[x] 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: 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?
[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)?
[x] 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?

xiuliren commented 2 years ago

Review checklist for @jingpengw

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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/DiamondLightSource/volume-segmantics?
[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 (@OllyK) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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).
[x] 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?
[x] 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: 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?
[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)?
[x] 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?

xiuliren commented 2 years ago

@osorensen @OllyK It seems that the State of the field is missing. It would be better to compare with existing tools including my own: https://github.com/flatironinstitute/neutorch

I have also listed some others in the README of my repo. DeepEM DataProvider3 PyTorchUtils pytorch_connectomics

As such, the reference list is not complete from this perspective.

OllyK commented 2 years ago

Hi @jingpengw Thank you for taking the time to look at this. Sure, good point, I'll add this section next week and let you know when it's ready.

OllyK commented 2 years ago

Hi @jingpengw I've made some changes to the paper now as requested. I'll ask editorialbot to regenerate the PDF and check references again, just in case. Best wishes OllyK

OllyK commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

OllyK commented 2 years ago

@editorialbot check repository

editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (562.2 files/s, 87155.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             5            551              0           3284
Python                          36            602            517           2555
Markdown                         6            145              0            475
TeX                              1             17              0            198
YAML                             6             12             27            198
TOML                             1              5              0             50
JavaScript                       1              3              3             40
-------------------------------------------------------------------------------
SUM:                            56           1335            547           6800
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1216

OllyK commented 2 years ago

Hi @osorensen , according to the docs, only editors can run the editorialbot check references command. Would it be possible for you to run it? - I updated the references last week. Kind regards

osorensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.1038/s41598-019-55431-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 2 years ago

@jingpengw, could you please let us now if the last edits by the authors address the remaining issues on your checklist?

osorensen commented 2 years ago

@estenhl, thanks for your review!

Is the missing check in the Reproducibility section related to the results reported in this section of the paper?

xiuliren commented 2 years ago

thank you! I think it is good to go!

OllyK commented 2 years ago

@estenhl Feel free to ask if there's anything that needs clarifying or updating. The paper doesn't contain any original results, it references studies where we've used earlier versions of the code to segment data. Best Wishes.

estenhl commented 2 years ago

Sorry for the late reply @osorensen, the missing check was purely due to a mistake on my part. @OllyK, great work, and thanks for the detailed replies to @jinpengw's questions, both here and in the pre-review thread

osorensen commented 2 years ago

@OllyK, I will now read through the manuscript a final time, and let you know if I have any suggested changes. Meanwhile, could you

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

OllyK commented 2 years ago

Thanks very much @osorensen ! And once again many thanks to @jingpengw and @estenhl for taking the time to review

@OllyK, I will now read through the manuscript a final time, and let you know if I have any suggested changes. Meanwhile, could you

[x ] Make a tagged release of your software, and list the version tag of the archived version here.
[x ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x ] Please list the DOI of the archived version here. The DOI of the archive is https://doi.org/10.5281/zenodo.7143363

Please let me know if there's anything else you need. Best Wishes,

OllyK

osorensen commented 2 years ago

@editorialbot generate pdf

osorensen commented 2 years ago

@editorialbot check references

osorensen commented 2 years ago

@editorialbot set 10.5281/zenodo.7143363 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7143363

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.1038/s41598-019-55431-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

osorensen commented 2 years ago

@editorialbot v0.2.7 as version

editorialbot commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

osorensen commented 2 years ago

@editorialbot set v0.2.7 as version

editorialbot commented 2 years ago

Done! version is now v0.2.7

editorialbot commented 2 years ago

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

osorensen commented 2 years ago

@OllyK, I think the paper is clear and well written. As you see, I have opened some rather small issues in the source repository. Please let me know when they are fixed (or if you disagree with my suggestions, which is absolutely fine), and I can move forward with accepting the submission.

OllyK commented 2 years ago

That's brilliant, thanks @osorensen ! I hope to resolve those issues today and will update you.

OllyK commented 2 years ago

@osorensen Have updated the paper with the requested changes and closed the issues as you may have seen. Best wishes, OllyK

osorensen commented 2 years ago

@editorialbot generate pdf

osorensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.48550/arXiv.2112.05754 is OK
- 10.1038/s41598-019-55431-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

osorensen commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1007/s11263-015-0816-y is OK
- 10.1007/978-3-030-32245-8_4 is OK
- 10.3390/info11020125 is OK
- 10.1002/essoar.10506807.2 is OK
- 10.1098/rsif.2021.0140 is OK
- 10.3389/fcell.2022.842342 is OK
- 10.48550/arXiv.1706.05587 is OK
- 10.48550/arXiv.2112.05754 is OK
- 10.1038/s41598-019-55431-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3581, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

OllyK commented 2 years ago

🎉 Thanks again @estenhl @jingpengw @osorensen . It's been a pleasure.

arfon commented 2 years ago

@editorialbot accept

openjournals / joss-reviews