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[PRE REVIEW]: pySegmentationUpsampler: Resampling segmented medical image data for treatment planning in ultrasound therapy #7463

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editorialbot opened this issue Nov 12, 2024 · 35 comments
Open

[PRE REVIEW]: pySegmentationUpsampler: Resampling segmented medical image data for treatment planning in ultrasound therapy #7463

editorialbot opened this issue Nov 12, 2024 · 35 comments
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Matlab pre-review Python query-scope Submissions of uncertain scope for JOSS TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Nov 12, 2024 •
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Submitting author: @Donny-bla (Liangpu Liu)
Repository: https://github.com/Donny-bla/segmentation-upsampler.git
Branch with paper.md (empty if default branch): joss-paper
Version: v1.0.0
Editor: Pending
Reviewers: Pending
Managing EiC: Arfon Smith

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3de30d409117bd4b6e6637bc526ad52c"><img src="https://joss.theoj.org/papers/3de30d409117bd4b6e6637bc526ad52c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3de30d409117bd4b6e6637bc526ad52c/status.svg)](https://joss.theoj.org/papers/3de30d409117bd4b6e6637bc526ad52c)

Author instructions

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

@Donny-bla 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Nov 12, 2024
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Hello human, 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

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (739.9 files/s, 219328.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              7              1              3           7134
MATLAB                          13            136            454            700
Python                           8            201            644            381
TeX                              1             15              0            129
Markdown                         2             60              0             92
YAML                             3             15             35             79
-------------------------------------------------------------------------------
SUM:                            34            428           1136           8515
-------------------------------------------------------------------------------

Commit count by author:

   195	Donny-bla
    38	Rui Xu
     1	Donny

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Paper file info:

📄 Wordcount for paper.md is 1573

✅ The paper includes a Statement of need section

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License info:

🔴 Failed to discover a valid open source license

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: The Visualization Toolkit
- No DOI given, and none found for title: Scipy 1.0: Fundamental algorithms for scientific c...

❌ MISSING DOIs

- 10.1080/02656736.2022.2112309 may be a valid DOI for title: First-in-man histotripsy of hepatic tumors: the TH...
- 10.1101/2024.06.08.597305 may be a valid DOI for title: Ultrasound system for precise neuromodulation of h...
- 10.1121/10.0013426 may be a valid DOI for title: Benchmark problems for transcranial ultrasound sim...
- 10.1088/1361-6560/ad506f may be a valid DOI for title: Strategies and safety simulations for ultrasonic c...
- 10.1103/physrevapplied.12.014016 may be a valid DOI for title: Holograms to focus arbitrary ultrasonic fields thr...
- 10.1121/1.4976339 may be a valid DOI for title: Accurate simulation of transcranial ultrasound pro...
- 10.1109/embc.2016.7591443 may be a valid DOI for title: ITK-SNAP: An interactive tool for semi-automatic s...
- 10.1109/3dv.2016.79 may be a valid DOI for title: V-net: Fully convolutional neural networks for vol...
- 10.1162/089976603321891855 may be a valid DOI for title: Asymptotic behaviors of support vector machines wi...
- 10.1109/ldav.2015.7348069 may be a valid DOI for title: Flying edges: A high-performance scalable isoconto...
- 10.54294/216g01 may be a valid DOI for title: Boolean operations on surfaces in vtk without exte...
- 10.1117/1.3360308 may be a valid DOI for title: k-Wave: MATLAB toolbox for the simulation and reco...
- 10.1038/s41597-021-01060-0 may be a valid DOI for title: A computed tomography vertebral segmentation datas...
- 10.1109/embc.2016.7591444 may be a valid DOI for title: AustinMan and AustinWoman: High-fidelity, anatomic...

❌ INVALID DOIs

- None

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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Five most similar historical JOSS papers:

DICaugment: A Python Package for 3D Medical Imaging Augmentation
Submitting author: @jjmcintosh
Handling editor: @osorensen (Active)
Reviewers: @MaierOli2010, @kuadrat
Similarity score: 0.6570

Nanomesh: A Python workflow tool for generating meshes from image data
Submitting author: @stefsmeets
Handling editor: @prashjha (Active)
Reviewers: @jameshgrn, @vijaysm
Similarity score: 0.6387

SAMBA: A Trainable Segmentation Web-App with Smart Labelling
Submitting author: @rmdocherty
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @pchlap, @jingpengw
Similarity score: 0.6375

Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning
Models
Submitting author: @OllyK
Handling editor: @osorensen (Active)
Reviewers: @jingpengw, @estenhl
Similarity score: 0.6239

Disimpy: A massively parallel Monte Carlo simulator for generating diffusion-weighted MRI data in Python
Submitting author: @kerkelae
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @DARSakthi, @grlee77, @ritagnunes
Similarity score: 0.6203

⚠️ 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.

@arfon
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arfon commented Nov 12, 2024 •
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@editorialbot query scope

@Donny-bla – thanks for your submission to JOSS. I'm querying this submission as it looks to not meet our required standards to head out for review. In particular, it's on the smaller side of what we typically publish, there does not appear to be an open source license, and the Python code does appear to be appropriately packaged.

Per our submission guidelines:

In addition, JOSS requires that software should be feature-complete (i.e., no half-baked solutions), packaged appropriately according to common community standards for the programming language being used (e.g., Python, R), and designed for maintainable extension (not one-off modifications of existing tools). “Minor utility” packages, including “thin” API clients, and single-function packages are not acceptable.

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Submission flagged for editorial review.

@editorialbot editorialbot added the query-scope Submissions of uncertain scope for JOSS label Nov 12, 2024
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Donny-bla commented Nov 15, 2024 via email

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Hello @Donny-bla, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

@Donny-bla
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Donny-bla commented Nov 16, 2024 via email

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

@Donny-bla
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Donny-bla commented Nov 16, 2024 via email

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Done! branch is now joss-paper

@Donny-bla
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Donny-bla commented Nov 16, 2024 via email

@Donny-bla
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Donny-bla commented Nov 16, 2024 via email

@editorialbot
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⚠️ An error happened when generating the pdf.

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⚠️ An error happened when generating the pdf.

@Donny-bla
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@editorialbot generate pdf

@editorialbot
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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@editorialbot
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Five most similar historical JOSS papers:

DICaugment: A Python Package for 3D Medical Imaging Augmentation
Submitting author: @jjmcintosh
Handling editor: @osorensen (Active)
Reviewers: @MaierOli2010, @kuadrat
Similarity score: 0.6855

Nanomesh: A Python workflow tool for generating meshes from image data
Submitting author: @stefsmeets
Handling editor: @prashjha (Active)
Reviewers: @jameshgrn, @vijaysm
Similarity score: 0.6765

SAMBA: A Trainable Segmentation Web-App with Smart Labelling
Submitting author: @rmdocherty
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @pchlap, @jingpengw
Similarity score: 0.6643

Disimpy: A massively parallel Monte Carlo simulator for generating diffusion-weighted MRI data in Python
Submitting author: @kerkelae
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @DARSakthi, @grlee77, @ritagnunes
Similarity score: 0.6540

Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning
Models
Submitting author: @OllyK
Handling editor: @osorensen (Active)
Reviewers: @jingpengw, @estenhl
Similarity score: 0.6513

⚠️ 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.

@Donny-bla
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@editorialbot check references

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

✅ OK DOIs

- 10.1080/02656736.2022.2112309 is OK
- 10.1101/2024.06.08.597305 is OK
- 10.1121/10.0013426 is OK
- 10.1088/1361-6560/ad506f is OK
- 10.1103/PhysRevApplied.12.014016 is OK
- 10.1121/1.4976339 is OK
- 10.1109/EMBC.2016.7591443 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1162/089976603321891855 is OK
- 10.1109/LDAV.2015.7348069 is OK
- 10.54294/216g01 is OK
- 10.1117/1.3360308 is OK
- 10.48550/arXiv.2103.06360 is OK
- 10.1109/EMBC.2016.7591444 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The Visualization Toolkit

❌ MISSING DOIs

- 10.1109/3dv.2016.79 may be a valid DOI for title: V-Net: Fully Convolutional Neural Networks for Vol...

❌ INVALID DOIs

- None

@Donny-bla
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@editorialbot check reference

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

@editorialbot commands

@Donny-bla
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@editorialbot check references

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

✅ OK DOIs

- 10.1080/02656736.2022.2112309 is OK
- 10.1101/2024.06.08.597305 is OK
- 10.1121/10.0013426 is OK
- 10.1088/1361-6560/ad506f is OK
- 10.1103/PhysRevApplied.12.014016 is OK
- 10.1121/1.4976339 is OK
- 10.1109/EMBC.2016.7591443 is OK
- 10.48550/arXiv.1606.04797 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1162/089976603321891855 is OK
- 10.1109/LDAV.2015.7348069 is OK
- 10.54294/216g01 is OK
- 10.1117/1.3360308 is OK
- 10.48550/arXiv.2103.06360 is OK
- 10.1109/EMBC.2016.7591444 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The Visualization Toolkit

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@Donny-bla
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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (787.0 files/s, 222871.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              7              1              3           7134
MATLAB                          13            136            454            708
Python                           9            202            645            390
TeX                              1             16              0            200
Markdown                         2             60              0             92
YAML                             3             15             35             75
TOML                             1              2              1             26
-------------------------------------------------------------------------------
SUM:                            36            432           1138           8625
-------------------------------------------------------------------------------

Commit count by author:

   254	Donny-bla
    38	Rui Xu
     1	Donny

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Paper file info:

📄 Wordcount for paper.md is 1573

✅ The paper includes a Statement of need section

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License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

@Donny-bla
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Donny-bla commented Nov 19, 2024 •
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@arfon I believe I have made the necessary update - the DOIs are fixed, the python code is packaged and can be installed with pip, and I have added a license. Can you please clarify on whether the paper is on the short side, or whether the code is on the short side? We welcome your guidance on next steps.

@Kevin-Mattheus-Moerman
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@Donny-bla you can address me as the AEiC on this track from now on for this submission.

The editorial board is currently reviewing if this work is in scope for JOSS. The review should hopefully be complete by the end of this week. We will inform you once we are done.

@Donny-bla
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@Kevin-Mattheus-Moerman Hi Kevin, may I kindly ask the reviewing progress? Are there feedback for me?

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