[PRE REVIEW]: Fundus Image Toolbox: A Python package for fundus image processing

[editorialbot]

Submitting author: !--author-handle-->@juliusge<!--end-author-handle-- (Julius Gervelmeyer) Repository: https://github.com/berenslab/fundus_image_toolbox Branch with paper.md (empty if default branch): paper Version: v0.0.1 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @saeedahmadicp, @sashakolpakov, @ojasiiitd Managing EiC: Chris Vernon

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (1028.5 files/s, 148364.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Python                          63           1365           1017           4563
CSV                              1              0              0           1582
Jupyter Notebook                15              0           3789            829
Markdown                        12            153              0            582
SVG                              2              1              1            254
TeX                              1             14              0            158
YAML                             4             19              5             74
TOML                             1              3              0             10
INI                              1              1              0              5
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SUM:                           100           1556           4812           8057
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Commit count by author:

    66  juliusge

[editorialbot]

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

OK DOIs

- 10.1007/978-3-031-19803-8_35 is OK
- 10.1007/978-3-030-32239-7_6 is OK
- 10.3390/diagnostics13101664 is OK
- 10.1167/tvst.11.7.12 is OK
- 10.1109/tmi.2022.3172773 is OK
- 10.1016/j.media.2019.101570 is OK
- 10.1016/j.media.2019.101561 is OK
- 10.1016/j.patter.2022.100512 is OK
- 10.1117/1.JBO.19.4.046006 is OK
- 10.1038/s41597-022-01564-3 is OK
- 10.35119/maio.v1i4.42 is OK
- 10.3390/diagnostics13040622 is OK

MISSING DOIs

- No DOI given, and none found for title: Efficiently correcting patch-based segmentation er...

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 890

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[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:

ivadomed: A Medical Imaging Deep Learning Toolbox Submitting author: @charleygros Handling editor: @cMadan (Active) Reviewers: @NMontanaBrown, @justusschock, @lbugnon Similarity score: 0.6912

Brainchop: In-browser MRI volumetric segmentation and rendering Submitting author: @Mmasoud1 Handling editor: @samhforbes (Active) Reviewers: @mwegrzyn, @62442katieb, @richford Similarity score: 0.6881

The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images Submitting author: @antoinevacavant Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @lassoan, @deepakri201 Similarity score: 0.6862

COVID-19 Lung Segmentation Submitting author: @RiccardoBiondi Handling editor: @jmschrei (Active) Reviewers: @pps121, @amtseng Similarity score: 0.6810

Pylinac: Image analysis for routine quality assurance in radiotherapy Submitting author: @jrkerns Handling editor: @kellyrowland (Active) Reviewers: @ProfLeao, @SimonBiggs Similarity score: 0.6752

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

[juliusge]

From the list of people reviewing for JOSS, I think

• NMontanaBrown
• pchlap
• saeedahmadicp

could be a good fit as they mention Python, Medial Image Analysis and Deep Learning.

[crvernon]

@editorialbot invite @osorensen as editor

:wave: @osorensen - are you ready to take on submissions again? Let me know if not and I'll shift this one around. Thanks!

[editorialbot]

Invitation to edit this submission sent!

[osorensen]

@crvernon I am ready

[osorensen]

@editorialbot add @osorensen as editor

[editorialbot]

Assigned! @osorensen is now the editor

[osorensen]

@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:

ivadomed: A Medical Imaging Deep Learning Toolbox Submitting author: @charleygros Handling editor: @cMadan (Active) Reviewers: @NMontanaBrown, @justusschock, @lbugnon Similarity score: 0.6926

Brainchop: In-browser MRI volumetric segmentation and rendering Submitting author: @Mmasoud1 Handling editor: @samhforbes (Active) Reviewers: @mwegrzyn, @62442katieb, @richford Similarity score: 0.6872

The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images Submitting author: @antoinevacavant Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @lassoan, @deepakri201 Similarity score: 0.6870

COVID-19 Lung Segmentation Submitting author: @RiccardoBiondi Handling editor: @jmschrei (Active) Reviewers: @pps121, @amtseng Similarity score: 0.6816

Pylinac: Image analysis for routine quality assurance in radiotherapy Submitting author: @jrkerns Handling editor: @kellyrowland (Active) Reviewers: @ProfLeao, @SimonBiggs Similarity score: 0.6746

⚠️ 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 considering asking the reviewers of these papers to review again for JOSS.

[osorensen]

👋 @charleygros @antoinevacavant @haoxue-fan @vahid-sb would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[vahid-sb]

Hi @osorensen. Thanks for the invite. Normally, I would be happy to help with the review, but these days I am way over my head with various commitments. So, have to respectfully decline the invitation.

[osorensen]

Thanks a lot for your quick response, @vahid-sb.

[osorensen]

@NMontanaBrown, @pchlap, @saeedahmadicp, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[saeedahmadicp]

@osorensen Yes, I am ready to review the paper. Thanks for considering.

[osorensen]

@editorialbot add @saeedahmadicp as reviewer

[editorialbot]

@saeedahmadicp added to the reviewers list!

[NMontanaBrown]

Hi @osorensen - thanks for the invite but unfortunately I'm at capacity right now.

[pchlap]

@osorensen, unfortunately I am also currently unable to commit to this so I'll have to pass on the invitation to review this time.

[osorensen]

:wave: @ojasiiitd, @sashakolpakov, @RafaelPalomar, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[sashakolpakov]

Sure @osorensen, please ask @editorialbot to add @sashakolpakov as reviewer

[editorialbot]

I'm sorry @sashakolpakov, I'm afraid I can't do that. That's something only editors are allowed to do.

[osorensen]

Thanks for agreeing to review @sashakolpakov!

[osorensen]

@editorialbot add @sashakolpakov as reviewer

[editorialbot]

@sashakolpakov added to the reviewers list!

[RafaelPalomar]

@osorensen, I'm sorry I don't have capacity for this review right now

[ojasiiitd]

@osorensen I'm happy to review this, but I would require some guidance as it is my first review. I've just signed up on the platform.

[osorensen]

Thanks @ojasiiitd, that's fine. Once I start the review issue you will find a detailed guide, and you're always welcome to reach out to me if you have questions.

[osorensen]

@editorialbot add @ojasiiitd as reviewer

[editorialbot]

@ojasiiitd added to the reviewers list!

[osorensen]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7101.

[ojasiiitd]

@editorialbot generate my checklist

[editorialbot]

Checklists can only be created once the review has started in the review issue