[PRE REVIEW]: The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images

[whedon]

Submitting author: @antoinevacavant (Antoine Vacavant) Repository: https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation Version: 1.0.0 Editor: @Kevin-Mattheus-Moerman Reviewers: @lassoan, @deepakri201 Managing EiC: Kyle Niemeyer

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Author instructions

Thanks for submitting your paper to JOSS @antoinevacavant. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @Kevin-Mattheus-Moerman.

@antoinevacavant if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

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[whedon]

Wordcount for paper.md is 888

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.1007/978-1-4614-7657-3_19 may be a valid DOI for title: 3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support
- 10.1007/s11517-008-0420-1 may be a valid DOI for title: An image-based modeling framework for patient-specific computational hemodynamics
- 10.1109/ipta50016.2020.9286658 may be a valid DOI for title: A Time-dependent joint segmentation and registration model: Applications to longitudinal registration of hepatic DCE-MRI sequences
- 10.3390/app11114895 may be a valid DOI for title: Segmentation of liver anatomy by combining 3-D U-Net approaches
- 10.1109/icpr48806.2021.9412362 may be a valid DOI for title: Vesselness filters: A survey with benchmarks applied to liver imaging

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.33 s (81.8 files/s, 20933.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          21           1251           1711           3540
Markdown                         2             74              0            174
TeX                              1              8              0             64
CMake                            3             11             14             61
-------------------------------------------------------------------------------
SUM:                            27           1344           1725           3839
-------------------------------------------------------------------------------

Statistical information for the repository 'e072d3e0148fa6896b236ba9' was
gathered on 2021/10/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Lucie Macron                     2           305             14            1.59
Thibault Pelletier             109         12976           6765           98.41

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Lucie Macron                 47           15.4          4.7                8.51
Thibault Pelletier         6455           49.7         17.6               13.90

[kyleniemeyer]

Hi @antoinevacavant, because of the nature of this submission we are going to review it to ensure it is in scope for us to review. We will get back to you within a week or two max, thank you for your patience.

[kyleniemeyer]

@whedon query scope

[whedon]

Submission flagged for editorial review.

[whedon]

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

[arfon]

@whedon invite @Kevin-Mattheus-Moerman as editor

:wave: @Kevin-Mattheus-Moerman – would you be willing to edit this submission for JOSS?

[whedon]

@Kevin-Mattheus-Moerman has been invited to edit this submission.

[Kevin-Mattheus-Moerman]

@whedon assign me as editor

[whedon]

OK, the editor is @Kevin-Mattheus-Moerman

[Kevin-Mattheus-Moerman]

@antoinevacavant apologies for the delay. I will now be looking for reviewers. If you like to suggest any let me know. You can mention their github handles but please omit the @ symbol for now. Thanks.

[Kevin-Mattheus-Moerman]

@thewtex @lassoan @fedorov @ljod @daniellepace would you be interested in reviewing this work for JOSS (the Journal of Open Source Software): "The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images"? The JOSS review process focuses on the software as well as a short paper.

If you haven't reviewed for JOSS before, below is an example of our GitHub based review process, where you can see that sets of check-boxes guide the reviewers through the process: https://github.com/openjournals/joss-reviews/issues/2969

[fedorov]

Sorry, I am completely swamped at the moment, and have to decline.

[Kevin-Mattheus-Moerman]

@fedorov no problem, thanks for letting us know. Let us know if you might have a colleague in mind that could help. Thanks

[daniellepace]

Sorry, I'm on maternity leave and can't do any reviews at this time.

Best,

Danielle

On Tue, Oct 26, 2021, 11:38 AM Kevin Mattheus Moerman < @.***> wrote:

@fedorov https://github.com/fedorov no problem, thanks for letting us know. Let us know if you might have a colleague in mind that could help. Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3807#issuecomment-952064146, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACTAYJPN3BC5L6CI3P5R2DUI3KQHANCNFSM5FRXXJ7Q . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[lassoan]

I can review this.

[fedorov]

Let us know if you might have a colleague in mind that could help.

I do! I would like to nominate Deepa Krishnaswamy (@deepakri201), she is a new postdoc working with me.

[Kevin-Mattheus-Moerman]

Sorry, I'm on maternity leave and can't do any reviews at this time.

@daniellepace no worries and congratulations!

[Kevin-Mattheus-Moerman]

@whedon assign @lassoan as reviewer

[whedon]

OK, @lassoan is now a reviewer

[antoinevacavant]

Hi, thanks a lot for the update. As a reviewer (and with an active Github account), I could recommend Filip Malmberg (Uppsala, SW). Best, Antoine

[Kevin-Mattheus-Moerman]

@antoinevacavant can you please share their github account (you can leave out the @ symbol for now)?

[Kevin-Mattheus-Moerman]

@deepakri201 would you be able to help review this work for JOSS?

[antoinevacavant]

@Kevin-Mattheus-Moerman here it is: FMalmberg

[deepakri201]

@Kevin-Mattheus-Moerman Yes, I'd be happy to help review this work

[Kevin-Mattheus-Moerman]

@whedon add @deepakri201 as reviewer

[whedon]

OK, @deepakri201 is now a reviewer

[Kevin-Mattheus-Moerman]

@thewtex @ljod @FMalmberg would you be interested in reviewing this work for JOSS (the Journal of Open Source Software): "The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images"? The JOSS review process focuses on the software as well as a short paper.

If you haven't reviewed for JOSS before, below is an example of our GitHub based review process, where you can see that sets of check-boxes guide the reviewers through the process: https://github.com/openjournals/joss-reviews/issues/2969

[fedorov]

@Kevin-Mattheus-Moerman, I am assuming you will make a separate [REVIEW] issue for the assigned reviewers, right (like you did for the submission I reviewed in the past here)?

I am just not sure if the process is the same as before, considering you assigned @deepakri201 19 days ago, but she has not received any instructions.

[Kevin-Mattheus-Moerman]

@thewtex @ljod @FMalmberg would you be interested in reviewing this work for JOSS (the Journal of Open Source Software): "The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images"? The JOSS review process focuses on the software as well as a short paper.

If you haven't reviewed for JOSS before, below is an example of our GitHub based review process, where you can see that sets of check-boxes guide the reviewers through the process: https://github.com/openjournals/joss-reviews/issues/2969

[Kevin-Mattheus-Moerman]

@fedorov thanks for your message. The process has not changed, and I will initiate the review now to avoid further delay. I was hoping to attract an additional reviewer but will proceed with two for now. We can also add a 3rd if needed at a later stage.

[Kevin-Mattheus-Moerman]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3920.

[Kevin-Mattheus-Moerman]

@thewtex @ljod @FMalmberg if you are able to review for us I can still add you over at https://github.com/openjournals/joss-reviews/issues/3920.