[PRE REVIEW]: DL_Track: a python package to analyse muscle ultrasonography images

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@PaulRitsche@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @deepakri201, @GiacomoValliPhD Managing EiC: Kevin M. Moerman

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editorialbot commented 1 year ago

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (420.5 files/s, 92013.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Python                          15            864           3295           2682
reStructuredText                10            137            139            218
TeX                              1             12              0            213
Markdown                         3             48              0             83
YAML                             4              6             18             67
DOS Batch                        1              8              1             26
TOML                             1              2             16             22
make                             1              4              7              9
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SUM:                            36           1081           3476           3320
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gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 706

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/s40279-021-01436-7 is OK
- 10.1016/j.cmpb.2016.02.016 is OK
- 10.7717/peerj.7120 is OK
- 10.1109/CVPR.2009.5206848 is OK
- 10.1152/japplphysiol.00041.2022 is OK
- 10.1152/japplphysiol.00530.2011 is OK
- 10.1371/journal.pone.0229034 is OK
- 10.1016/j.jbiomech.2009.06.003 is OK
- 10.3390/jimaging4020029 is OK
- 10.1007/s00421-017-3769-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot assign me as editor

editorialbot commented 1 year ago

Assigned! @Kevin-Mattheus-Moerman is now the editor

Kevin-Mattheus-Moerman commented 1 year ago

@PaulRitsche thanks for this submission. I am the AEiC for this track and also the handling editor for your submission. I have a quick look at your repository and have the following points for you to work on for now:

[ ] The "user instructions" https://github.com/PaulRitsche/DLTrack/docs/usage produce a 404 error
[ ] The test instructions link on the readme produces a 404 error: https://github.com/PaulRitsche/DLTrack/tests
[ ] The documentation does not render properly for me (Firefox on Ubuntu) see screenshot: Given the above perhaps scan through your readme and make sure all links/instructions/documetation/testing are working.
[ ] I had a quick look at the paper. Since this submission features image processing, I recommend including some images of the software capabilities in the paper. Perhaps you could consider showing some of the ultrasound images, and some overlaid analysis, or graphs too for instance, or perhaps screenshots of the GUI. I would recommend adding some such images/visualizations to your readme too.

PaulRitsche commented 1 year ago

@Kevin-Mattheus-Moerman thanks for the suggestions.

We have fixed the links.
The documentation link for the code documentation now points directly to the docstrings not the overview of packages and modules. However, displaying the links to each module and not directly the docstrings was intentional, as we thought this is easier to navigate.
We have added a figure containig the image analysis process and a screenshot of the GUI to the paper and the Readme.md.
We have substituted figure 1 (Workflow) in the paper with the figure of the image analysis process.

Please let us know in case we need to adapt something else or if our changes were unsufficient.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Kevin-Mattheus-Moerman commented 1 year ago

@modenaxe @BKillen05 @MaartenAfschrift @VDB-Bram @mh-skjelvareid @lassoan @thewtex @wspr @antoinevacavant @deepakri201 @PaulT95 @luuleitner would you be interested in reviewing this submission _DLTrack: a python package to analyse muscle ultrasonography images for JOSS (the Journal of Open Source Software)?

JOSS reviews focus on the evaluation of the software and the review of a short paper.

This is a pre-review issue where reviewers are assigned. Once we have sufficient reviewers we will open a review issue, so the review will take place on GitHub. Here is an example of a complete review if you are curious as to what the process is like: https://github.com/openjournals/joss-reviews/issues/4859 As you can see, a checklist guides each reviewer through the process.

Let me know if you can help or if you have any more questions. Note we can be quite flexible regarding the time needed to complete the review. Thanks!

modenaxe commented 1 year ago

sorry @Kevin-Mattheus-Moerman I wouldn't be able to work on this at least until next year. I will think about alternative reviewers if you have problems finding reviewers though.

Kevin-Mattheus-Moerman commented 1 year ago

@modenaxe January next year is okay. Most reviewers will likely tell me that. So if you're interested and can start early next year that's fine.

VDB-Bram commented 1 year ago

Thanks for the invitation to review this code, @Kevin-Mattheus-Moerman. Though, I will not be able to review it, my apologies. Ultra sound is outside my field of expertise.

PaulT95 commented 1 year ago

Thanks for the invitation to review this code, however, I am sorry @Kevin-Mattheus-Moerman but I am a little rusty regarding python and CNN.

Kind regards

Paolo Tecchio

Il giorno mar 6 dic 2022 alle ore 17:22 Bram Van Den Bosch < @.***> ha scritto:

Thanks for the invitation to review this code, @Kevin-Mattheus-Moerman https://github.com/Kevin-Mattheus-Moerman. Though, I will not be able to review it, my apologies. Ultra sound is outside my field of expertise.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4948#issuecomment-1339628282, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARN3LCU4I44HLE4YL73VCT3WL5R27ANCNFSM6AAAAAASEV6T5I . You are receiving this because you were mentioned.Message ID: @.***>

Kevin-Mattheus-Moerman commented 1 year ago

@modenaxe would you reconsider if we say you can pick this up in the new year?

Kevin-Mattheus-Moerman commented 1 year ago

@BKillen05 @MaartenAfschrift @mh-skjelvareid @lassoan @thewtex @wspr @antoinevacavant @deepakri201 @luuleitner would you be interested in reviewing this submission _DLTrack: a python package to analyse muscle ultrasonography images for JOSS (the Journal of Open Source Software)?

JOSS reviews focus on the evaluation of the software and the review of a short paper.

This is a pre-review issue where reviewers are assigned. Once we have sufficient reviewers we will open a review issue, so the review will take place on GitHub. Here is an example of a complete review if you are curious as to what the process is like: https://github.com/openjournals/joss-reviews/issues/4859 As you can see, a checklist guides each reviewer through the process.

Let me know if you can help or if you have any more questions. Note we can be quite flexible regarding the time needed to complete the review. Thanks!

mh-skjelvareid commented 1 year ago

@Kevin-Mattheus-Moerman I'm very sorry, but I have so many other work-related obligations right now that I don't have time to do a review.

deepakri201 commented 1 year ago

@Kevin-Mattheus-Moerman I would be able to do a review of this submission. Thanks!

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot add @deepakri201 as reviewer

editorialbot commented 1 year ago

@deepakri201 added to the reviewers list!

Kevin-Mattheus-Moerman commented 1 year ago

@emmanuelle @BKillen05 @MaartenAfschrift @lassoan @thewtex @wspr @antoinevacavant @luuleitner @jcfr @waltsims would you be interested in reviewing this submission _DLTrack: a python package to analyse muscle ultrasonography images for JOSS (the Journal of Open Source Software)?

JOSS reviews focus on the evaluation of the software and the review of a short paper.

This is a pre-review issue where reviewers are assigned. Once we have sufficient reviewers we will open a review issue, so the review will take place on GitHub. Here is an example of a complete review if you are curious as to what the process is like: https://github.com/openjournals/joss-reviews/issues/4859 As you can see, a checklist guides each reviewer through the process.

Let me know if you can help or if you have any more questions. Note we can be quite flexible regarding the time needed to complete the review. Thanks!

BKillen05 commented 1 year ago

Hi Kevin, Sorry for the dealy on this: A postdoc from my lab is willing it review – CC’d and github a/c WannesSwinnen Bryce A Killen, BExSc Hons PhDPostdoctoral Research FellowHuman Movement Biomechanics Research GroupKU Leuven, Leuven, BelgiumTwitter: @bryce_killen From: Kevin Mattheus MoermanSent: dinsdag 10 januari 2023 12:21To: openjournals/joss-reviewsCc: BKillen05; MentionSubject: Re: [openjournals/joss-reviews] [PRE REVIEW]: DL_Track: a python package to analyse muscle ultrasonography images (Issue ***@***.*** @BKillen05 @MaartenAfschrift @lassoan @thewtex @wspr @antoinevacavant @luuleitner @jcfr @waltsims would you be interested in reviewing this submission DL_Track: a python package to analyse muscle ultrasonography images for JOSS (the Journal of Open Source Software)?JOSS reviews focus on the evaluation of the software and the review of a short paper.This is a pre-review issue where reviewers are assigned. Once we have sufficient reviewers we will open a review issue, so the review will take place on GitHub. Here is an example of a complete review if you are curious as to what the process is like:#4859As you can see, a checklist guides each reviewer through the process.Let me know if you can help or if you have any more questions. Note we can be quite flexible regarding the time needed to complete the review. Thanks!—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

Kevin-Mattheus-Moerman commented 1 year ago

Thanks @WannesSwinnen for being able to review for JOSS. Could you please share your full name and affiliation please? Also I would recommend adding this information to your GitHub profile. Thanks.

WannesSwinnen commented 1 year ago

Hi Kevin,

Sorry for my late reply, but I feel that I had some miscommunication with Bryce. I thought he was looking for someone with ultrasound data who was willing to compare the new algorithm with results obtained from published algorithms. Unfortunately, I have little experience with either GitHub nor Python and hence I'm afraid I won't have very useful contributions to improve the algorithm/method or review the manuscript.

I'm sorry for that, Wannes

On Wed, Jan 11, 2023 at 1:11 PM Kevin Mattheus Moerman < @.***> wrote:

Thanks @WannesSwinnen https://github.com/WannesSwinnen for being able to review for JOSS. Could you please share your full name and affiliation please? Also I would recommend adding this information to your GitHub profile. Thanks.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4948#issuecomment-1378656513, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP5ASGTZKUPSWHIRQIS6X5TWR2PNZANCNFSM6AAAAAASEV6T5I . You are receiving this because you were mentioned.Message ID: @.***>

modenaxe commented 1 year ago

@modenaxe would you reconsider if we say you can pick this up in the new year?

Hi @Kevin-Mattheus-Moerman I am afraid I am not able to do this, unfortunately. Ultrasonography is not exactly my field so I am not able to suggest an alternative reviewer either...sorry about that!

waltsims commented 1 year ago

Hi all, I'm currently not available to review.

Thanks! Walter

PaulRitsche commented 1 year ago

@Kevin-Mattheus-Moerman Would it be appropriate to suggest some reviewers ourselves?

Thanks and best wishes, Paul

Kevin-Mattheus-Moerman commented 1 year ago

@PaulRitsche you may suggest them and mention their GitHub handle, but please leave out the @ symbol so they are not tagged. Thanks. Apologies for the delay encountered here so far. I will resume my search again in the coming week.

Kevin-Mattheus-Moerman commented 1 year ago

@joshrbaxter @luuleitner @haripen @rlkrup @soleym @u0078867 @bishesh @emmanuelle @MaartenAfschrift @lassoan @thewtex @wspr @antoinevacavant @jcfr would you be interested in reviewing this submission _DLTrack: a python package to analyse muscle ultrasonography images for JOSS (the Journal of Open Source Software)?

JOSS reviews focus on the evaluation of the software and the review of a short paper.

This is a pre-review issue where reviewers are assigned. Once we have sufficient reviewers we will open a review issue, so the review will take place on GitHub. Here is an example of a complete review if you are curious as to what the process is like: https://github.com/openjournals/joss-reviews/issues/4859 As you can see, a checklist guides each reviewer through the process.

Let me know if you can help or if you have any more questions. Note we can be quite flexible regarding the time needed to complete the review. Thanks!

PaulRitsche commented 1 year ago

@PaulRitsche you may suggest them and mention their GitHub handle, but please leave out the @ symbol so they are not tagged. Thanks. Apologies for the delay encountered here so far. I will resume my search again in the coming week.

Thanks @Kevin-Mattheus-Moerman for the information and don't worry about the delay. Here are the names and Github handles:

Philipp Wirth: philippmwirth
Giacomo Valli: GiacomoValliPhD
Antonio Morales: ajmoralesa
Tim van der Zee: timvanderzee

Kevin-Mattheus-Moerman commented 1 year ago

@GiacomoValliPhD @ajmoralesa @timvanderzee @joshrbaxter @luuleitner @haripen @rlkrup @soleym @u0078867 @bishesh @emmanuelle @MaartenAfschrift @lassoan @thewtex @wspr @antoinevacavant @jcfr would you be interested in reviewing this submission _DLTrack: a python package to analyse muscle ultrasonography images for JOSS (the Journal of Open Source Software)?

JOSS reviews focus on the evaluation of the software and the review of a short paper.

This is a pre-review issue where reviewers are assigned. Once we have sufficient reviewers we will open a review issue, so the review will take place on GitHub. Here is an example of a complete review if you are curious as to what the process is like: https://github.com/openjournals/joss-reviews/issues/4859 As you can see, a checklist guides each reviewer through the process.

Let me know if you can help or if you have any more questions. Note we can be quite flexible regarding the time needed to complete the review. Thanks!

GiacomoValliPhD commented 1 year ago

Hi @Kevin-Mattheus-Moerman I would like to review this article and the code. I should state, however, that I personally know @PaulRitsche. Although I know him I was not aware about the existence of this article until I received the invitation to review it and I have no direct interest in the acceptance of this manuscript. I am willing to perform a honest revision if you perceive this appropriate.

Kevin-Mattheus-Moerman commented 1 year ago

@GiacomoValliPhD thanks for the comments. I'm unsure about whether this would be a conflict of interest. Are you able to clarify how you know him? Or how that might be (or be perceived as) a conflict of interest? Thanks

GiacomoValliPhD commented 1 year ago

@Kevin-Mattheus-Moerman I met @PaulRitsche when he came to my university more than a year ago to collaborate with some colleagues that were working on ultrasound imaging for the development of DeepACSA. I was not working with ultrasound so I was not included in the development and publication of DeepACSA. However, we remained in touch to exchange feedback and support on coding.

I have been reviewing the JOSS COIs "As a reviewer (or editor), COIs are your present or previous association with any authors of a submission: recent (past four years) collaborators in funded research or work that is published; and lifetime for the family members, business partners, and thesis student/advisor or mentor. In addition, your recent (past year) association with the same organization of a submitter is a COI, for example, being employed at the same institution" and I don't perceive to fit in any of them.

However, I await your opinion on that.

Best

Kevin-Mattheus-Moerman commented 1 year ago

@GiacomoValliPhD thanks for clarifying this. I think I am happy to have you join as a reviewer.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot add @GiacomoValliPhD as reviewer

editorialbot commented 1 year ago

@GiacomoValliPhD added to the reviewers list!

PaulRitsche commented 1 year ago

Good morning @Kevin-Mattheus-Moerman I was wondering how the revision is supposed to proceed? Is there anything else you need from us or do we just need to wait for the issue to change from pre-review to review? Or, in case we need to suggest more reviewers, just let me know. Best wishes, Paul

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot start review

editorialbot commented 1 year ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5206.

Kevin-Mattheus-Moerman commented 1 year ago

@PaulRitsche apologies for the delay. I was hoping to find one more reviewer, but we'll proceed now with two.

PaulRitsche commented 1 year ago

@Kevin-Mattheus-Moerman no worries and thanks for proceeding with the review process!

openjournals / joss-reviews

[PRE REVIEW]: DL_Track: a python package to analyse muscle ultrasonography images #4948

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