[PRE REVIEW]: ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing

[editorialbot]

Submitting author: !--author-handle-->@mkuczyns<!--end-author-handle-- (Michael Tadeusz Kuczynski) Repository: https://github.com/SpectraCollab/ORMIR_XCT Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@prashjha<!--end-editor-- Reviewers: @codeling, @zhangjy-ge Managing EiC: Kevin M. Moerman

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Author instructions

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

@mkuczyns if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (353.0 files/s, 50048.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          43           1162           1496           3223
Jupyter Notebook                 5              0           1693            339
TeX                              1             10              0            118
Markdown                         7             20              0            115
YAML                             2              1              0             47
-------------------------------------------------------------------------------
SUM:                            58           1193           3189           3842
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1854

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.21203/rs.2.14575/v1 may be a valid DOI for title: The utility of multi-stack alignment and 3D longitudinal image registration to assess bone remodeling in rheumatoid arthritis patients from second generation HR-pQCT scans
- 10.1002/jbmr.2873 may be a valid DOI for title: Sex- and Site-Specific Normative Data Curves for HR-pQCT
- 10.1080/03009742.2020.1869303 may be a valid DOI for title: Heterogenous bone response to biologic DMARD therapies in rheumatoid arthritis patients and their relationship to functional indices
- 10.1016/j.bone.2010.05.034 may be a valid DOI for title: Reproducibility of direct quantitative measures of cortical bone microarchitecture of the distal radius and tibia by HR-pQCT
- 10.3389/fninf.2013.00045 may be a valid DOI for title: The Design of SimpleITK
- 10.21037/qims.2019.12.11 may be a valid DOI for title: Consensus approach for 3D joint space width of metacarpophalangeal joints of rheumatoid arthritis patients using high-resolution peripheral quantitative computed tomography

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot invite @mstimberg as editor

[editorialbot]

Invitation to edit this submission sent!

[mstimberg]

As mentioned in the other issue: apologies, I am at capacity at the moment and have to decline.

[Kevin-Mattheus-Moerman]

@editorialbot invite @danasolav as editor

[editorialbot]

Invitation to edit this submission sent!

[danasolav]

Sorry, I'm also at capacity and have to decline this time.

[Kevin-Mattheus-Moerman]

@prashjha looks like you are also at capacity at the moment. However, do you think you could handle this submission once you are available? Thanks

[prashjha]

@Kevin-Mattheus-Moerman thanks for the invite. I can handle this one. In one of my submissions, author wishes to withdraw and I have pinged the editor. Another submission is almost done with review.

[prashjha]

@editorialbot assign me as editor

[editorialbot]

Assigned! @prashjha is now the editor

[mkuczyns]

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Hello @mkuczyns, here are the things you can ask me to do:

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@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

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@editorialbot check repository

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@editorialbot generate my checklist

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@editorialbot generate pdf

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@editorialbot generate preprint

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[mkuczyns]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1186/s12880-020-00437-8 is OK
- 10.1002/jbmr.2873 is OK
- 10.1080/03009742.2020.1869303 is OK
- 10.1046/j.1365-2818.1997.1340694.x is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK
- 10.3389/fninf.2013.00045 is OK
- 10.7717/peerj.453 is OK
- 10.21037/qims.2019.12.11 is OK
- 10.5281/zenodo.8155738 is OK

MISSING DOIs

- None

INVALID DOIs

- 0.1016/j.bone.2010.05.034 is INVALID

[mkuczyns]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1186/s12880-020-00437-8 is OK
- 10.1002/jbmr.2873 is OK
- 10.1080/03009742.2020.1869303 is OK
- 10.1016/j.bone.2010.05.034 is OK
- 10.1046/j.1365-2818.1997.1340694.x is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1145/2833157.2833162 is OK
- 10.3389/fninf.2013.00045 is OK
- 10.7717/peerj.453 is OK
- 10.21037/qims.2019.12.11 is OK
- 10.5281/zenodo.8155738 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mkuczyns]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@prashjha thanks again for handling this submission. Do you think you can start looking for reviewers at this point?

[prashjha]

@Kevin-Mattheus-Moerman, sure, I will speed up the review. Sorry about the delay. I am currently in the process of relocating.

[prashjha]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

QUIT: QUantitative Imaging Tools Submitting author: @spinicist Handling editor: @cMadan (Active) Reviewers: @oesteban Similarity score: 0.8291

Open Source Optical Coherence Tomography Software Submitting author: @spectralcode Handling editor: @arfon (Active) Reviewers: @jdavidli, @brandondube Similarity score: 0.8260

open_iA: A tool for processing and visual analysis of industrial computed tomography datasets Submitting author: @codeling Handling editor: @katyhuff (Retired) Reviewers: @trallard, @behollister Similarity score: 0.8224

PiSCAT: A Python Package for Interferometric Scattering Microscopy Submitting author: @po60nani Handling editor: @emdupre (Active) Reviewers: @ziatdinovmax, @aquilesC Similarity score: 0.8211

PoreSpy: A Python Toolkit for Quantitative Analysis of Porous Media Images Submitting author: @jgostick Handling editor: @usethedata (Retired) Reviewers: @yxqd, @cr458 Similarity score: 0.8207

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before before considering asking the reviewers of these papers to review again for JOSS.

[prashjha]

Howdy @spinicist, I am looking for reviewers for this JOSS submission. Due to the relevance of this submission with your area of expertise and experience as the author of the JOSS paper, I am wondering if you will be interested in reviewing this work for JOSS. Please let me know.

[prashjha]

Hi @codeling, I am looking for the reviewers for this JOSS submission. Due to the relevance of this work with your work and your experience as a JOSS author, I am wondering if you would be interested in reviewing this submission. Please let me know. I can help with further details.

[codeling]

Yes I can review the submission!

[spinicist]

Apologies, I am too busy at the moment. Also I'm very surprised my paper/repo came top of the similarity list. It's an MRI project, not CT. But I guess the generic name might not help.

[prashjha]

Hi @codeling, thank you for agreeing to review the submission. Adding you as a reviewer now.

[prashjha]

@editorialbot add @codeling as reviewer

[editorialbot]

@codeling added to the reviewers list!

[prashjha]

Hi @spinicist, no worries. Yes, the similarity check is the new feature JOSS introduced, and there is a scope for improvement.

[prashjha]

Hi @po60nani, I am looking for one more reviewer for this JOSS submission. As per the JOSS similarity check, it appears this submission is relevant to your previous JOSS publication. You can read more about this work by following the pdf link and software link.

Please let me know if you will be interested in reviewing this work. Thanks!!

[mkuczyns]

@prashjha, thanks for your help finding reviewers so far. If it helps, I've taken a look at the list of reviewers and here are the GitHub usernames of a few that I think might fit this work:

• NMontanaBrown
• michaelberks
• zhangjy-ge
• ajinkyakadu

Please let me know if there is anything else I can help with. Thanks!

[prashjha]

@mkuczyns, thanks for the list. Let me try a couple of more people.

[prashjha]

Hello @NMontanaBrown, would you be interested in reviewing this JOSS submission? The corresponding software is at this link. This link covers pretty much everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

[prashjha]

Hello @michaelberks, would you be interested in reviewing this JOSS submission? The corresponding software is at this link. This link covers pretty much everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

[NMontanaBrown]

Hi @prashjha, thanks for the invite. Unfortunately I'm at capacity for the minute, so cannot help this time around. Apologies!

[prashjha]

@NMontanaBrown, thanks for letting me know.

[prashjha]

Hi @ajinkyakadu, would you be interested in reviewing this JOSS submission? The corresponding software is at this link. This link covers pretty much everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

[prashjha]

Howdy @zhangjy-ge, would you be interested in reviewing this JOSS submission? The corresponding software is at this link. This link covers pretty much everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

[zhangjy-ge]

Howdy @zhangjy-ge, would you be interested in reviewing this JOSS submission? The corresponding software is at this link. This link covers pretty much everything about the review process; I will be happy to help with more information.

Please let me know if you are interested. Thank you!

Hi @prashjha I am happy to review it

[prashjha]

Thank you, @zhangjy-ge! Adding you as a reviewer now.

[prashjha]

@editorialbot add @zhangjy-ge as reviewer

[editorialbot]

@zhangjy-ge added to the reviewers list!