[PRE REVIEW]: MIRTorch: A Differentiable Medical Image Reconstruction Toolbox #7253

editorialbot · 2024-09-20T15:00:46Z

Submitting author: @guanhuaw (Guanhua Wang)
Repository: https://github.com/guanhuaw/MIRTorch
Branch with paper.md (empty if default branch): feature/joss
Version: v0.1.2
Editor: @ymzayek
Reviewers: @paquiteau, @jonbmartin
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ab29a08651ff1a8da37b363bd6185820"><img src="https://joss.theoj.org/papers/ab29a08651ff1a8da37b363bd6185820/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ab29a08651ff1a8da37b363bd6185820/status.svg)](https://joss.theoj.org/papers/ab29a08651ff1a8da37b363bd6185820)

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editorialbot · 2024-09-20T15:00:48Z

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editorialbot · 2024-09-20T15:01:11Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (1306.8 files/s, 176821.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          44           1435           2496           6130
Jupyter Notebook                 6              0           2343            631
Markdown                         4            111              0            236
YAML                             6             27             18            187
reStructuredText                47            547            496            111
TeX                              1             10              0            104
TOML                             1              8              0             74
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           111           2150           5361           7508
-------------------------------------------------------------------------------

Commit count by author:

    39	m5520
    36	neelsh
    29	Guanhua
    29	guanhuaw
    18	Keyue Zhu
     5	quickstep
     4	SoniaMinseoKim
     3	Zongyu Li
     1	GuanhuaW
     1	Jeff Fessler
     1	nnmurthy
     1	ray@omni

editorialbot · 2024-09-20T15:01:15Z

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

✅ OK DOIs

- 10.1109/TMI.2018.2833635 is OK
- 10.1109/TMI.2018.2865356 is OK
- 10.1002/mrm.29645 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox
- No DOI given, and none found for title: SigPy: a python package for high performance itera...
- No DOI given, and none found for title: The BART toolbox for computational magnetic resona...

❌ MISSING DOIs

- 10.1201/9781351069397-24 may be a valid DOI for title: Methods of conjugate gradients for solving linear ...
- 10.1137/080716542 may be a valid DOI for title: A fast iterative shrinkage-thresholding algorithm ...
- 10.1007/s10851-010-0251-1 may be a valid DOI for title: A first-order primal-dual algorithm for convex pro...
- 10.1561/9781601987174 may be a valid DOI for title: Proximal algorithms
- 10.1002/mrm.24389 may be a valid DOI for title: Gadgetron: an open source framework for medical im...

❌ INVALID DOIs

- None

editorialbot · 2024-09-20T15:01:17Z

Paper file info:

📄 Wordcount for paper.md is 717

✅ The paper includes a Statement of need section

editorialbot · 2024-09-20T15:01:20Z

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot · 2024-09-20T15:02:26Z

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

editorialbot · 2024-09-20T15:03:11Z

Five most similar historical JOSS papers:

DIRECT: Deep Image REConstruction Toolkit
Submitting author: @georgeyiasemis
Handling editor: @osorensen (Active)
Reviewers: @estenhl, @sairamgeethanath
Similarity score: 0.7507

Radial Interstices Enable Speedy Low-volume Imaging
Submitting author: @spinicist
Handling editor: @emdupre (Active)
Reviewers: @uecker, @MartinK84
Similarity score: 0.7473

ivadomed: A Medical Imaging Deep Learning Toolbox
Submitting author: @charleygros
Handling editor: @cMadan (Retired)
Reviewers: @NMontanaBrown, @justusschock, @lbugnon
Similarity score: 0.7420

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.7300

elsa: an elegant framework for tomographic reconstruction
Submitting author: @ner0-m
Handling editor: @jbytecode (Active)
Reviewers: @uellue, @DanNixon
Similarity score: 0.7288

⚠️ 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.

Kevin-Mattheus-Moerman · 2024-09-23T14:24:23Z

@guanhuaw Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

Please study the above reference check ☝️ and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).

Kevin-Mattheus-Moerman · 2024-09-23T14:26:50Z

@guanhuaw I have just waitlisted this submission since many of the editors in this domain are currently handling other submissions. I aim to assign an editor as soon as possible.

Kevin-Mattheus-Moerman · 2024-09-23T14:27:23Z

@ymzayek I see you may be nearly done with one of you submissions. Do you think you could take on this one as editor once you are available?

Kevin-Mattheus-Moerman · 2024-09-26T15:53:39Z

@editorialbot invite @ymzayek as editor

editorialbot · 2024-09-26T15:53:42Z

Invitation to edit this submission sent!

ymzayek · 2024-09-26T16:32:01Z

Hi sorry for the late reply. Yes I'll take this

Kevin-Mattheus-Moerman · 2024-09-27T07:38:19Z

@editorialbot assign @ymzayek as editor

editorialbot · 2024-09-27T07:38:22Z

Assigned! @ymzayek is now the editor

ymzayek · 2024-09-28T09:58:05Z

@editorialbot generate pdf

ymzayek · 2024-09-28T09:58:13Z

@editorialbot check references

editorialbot · 2024-09-28T09:58:44Z

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

✅ OK DOIs

- 10.1109/TMI.2018.2833635 is OK
- 10.1109/TMI.2018.2865356 is OK
- 10.1002/mrm.29645 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox
- No DOI given, and none found for title: SigPy: a python package for high performance itera...
- No DOI given, and none found for title: The BART toolbox for computational magnetic resona...

❌ MISSING DOIs

- 10.1201/9781351069397-24 may be a valid DOI for title: Methods of conjugate gradients for solving linear ...
- 10.1137/080716542 may be a valid DOI for title: A fast iterative shrinkage-thresholding algorithm ...
- 10.1007/s10851-010-0251-1 may be a valid DOI for title: A first-order primal-dual algorithm for convex pro...
- 10.1561/9781601987174 may be a valid DOI for title: Proximal algorithms
- 10.1002/mrm.24389 may be a valid DOI for title: Gadgetron: an open source framework for medical im...

❌ INVALID DOIs

- None

editorialbot · 2024-09-28T09:59:54Z

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

editorialbot · 2024-09-28T10:00:38Z

Five most similar historical JOSS papers:

DIRECT: Deep Image REConstruction Toolkit
Submitting author: @georgeyiasemis
Handling editor: @osorensen (Active)
Reviewers: @estenhl, @sairamgeethanath
Similarity score: 0.7495

Radial Interstices Enable Speedy Low-volume Imaging
Submitting author: @spinicist
Handling editor: @emdupre (Active)
Reviewers: @uecker, @MartinK84
Similarity score: 0.7474

ivadomed: A Medical Imaging Deep Learning Toolbox
Submitting author: @charleygros
Handling editor: @cMadan (Retired)
Reviewers: @NMontanaBrown, @justusschock, @lbugnon
Similarity score: 0.7412

MRdataset : A unified and user-friendly interface to medical imaging datasets
Submitting author: @sinhaharsh
Handling editor: @mstimberg (Active)
Reviewers: @htwangtw, @djmannion
Similarity score: 0.7307

Scientific Computational Imaging Code (SCICO)
Submitting author: @bwohlberg
Handling editor: @danielskatz (Active)
Reviewers: @vitorsr, @DanNixon, @lucaferranti
Similarity score: 0.7276

⚠️ 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.

ymzayek · 2024-09-28T10:10:24Z

Hi @guanhuaw, I am the handling editor for this submission. Can you please check the reference summary for the skipped and missing DOIs in #7253 (comment) and update them or provide a reason for their omission?

Also let me know if you already have suggestions for reviewers. You can use the potential reviewers list provided at the top of this issue. You can also have a look at the authors in similar papers in JOSS #7253 (comment). If you have suggestions, please provide a list of potential reviewers here but do not use the @ character to avoid receiving unwanted notifications. Thank you in advance.

guanhuaw · 2024-09-29T22:51:54Z

Hi @ymzayek and @Kevin-Mattheus-Moerman,

Thank you both for your assistance with my submission. I apologize for not thoroughly checking the DOI and for directly using Zotero without careful review. We updated the paper.bib and added a contribution guideline as contribution.md. (in branch feature/joss)

Regarding potential reviewers, I believe individuals with expertise in inverse problems and medical imaging would be a good fit. From the list, the following may be suitable candidates: Pierre-Antoine Comby, Jonathan Bach Martin, Haykel Snoussi, Ajinkya Kadu, and sairamgeethanath.

Thanks again for your help!

Best,
Contributors of MIRTorch

ymzayek · 2024-10-03T14:25:14Z

@editorialbot check references

editorialbot · 2024-10-03T14:25:38Z

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

✅ OK DOIs

- 10.1109/TMI.2018.2833635 is OK
- 10.1109/TMI.2018.2865356 is OK
- 10.1137/080716542 is OK
- 10.1007/s10851-010-0251-1 is OK
- 10.1561/2400000003 is OK
- 10.1002/mrm.29645 is OK
- 10.1002/mrm.24389 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Michigan Image Reconstruction Toolbox
- No DOI given, and none found for title: SigPy: a python package for high performance itera...
- No DOI given, and none found for title: The BART toolbox for computational magnetic resona...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.6028/igres.049.044 is INVALID

ymzayek · 2024-10-03T14:28:58Z

Hello @paquiteau, @jonbmartin and @H-Snoussi,

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

MIRTorch: A Differentiable Medical Image Reconstruction Toolbox

You can find more information at the top of this Github issue.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer.

Thank you in advance!

paquiteau · 2024-10-03T14:43:06Z

Hello @ymzayek ¹

Yes I can review it :)

@guanhuaw: shameless plug, but you can check out our work on Non-Cartesian MRI https://github.com/mind-inria/mri-nufft, that should a nice addition for your MRI linear operators (with performance improvements compared to torchkbnufft ²)

(nice to see you here btw !) ↩
https://github.com/mind-inria/mri-nufft-benchmark ↩

jonbmartin · 2024-10-03T14:46:19Z

Hello Yasmin, Yes, this would be a very useful software tool for me - I'd be happy to review! Jonathan

…

On Thu, Oct 3, 2024 at 9:29 AM Yasmin ***@***.***> wrote: Hello @paquiteau <https://github.com/paquiteau>, @jonbmartin <https://github.com/jonbmartin> and @H-Snoussi <https://github.com/H-Snoussi>, Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)? JOSS publishes articles about open source research software. The submission I'd like you to review is titled: MIRTorch: A Differentiable Medical Image Reconstruction Toolbox You can find more information at the top of this Github issue. The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know. This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer. Thank you in advance! — Reply to this email directly, view it on GitHub <#7253 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKVCUT4DM6FO2BJQQH4UDPLZZVIEDAVCNFSM6AAAAABOSHB35CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJRGU3TAOBZGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

H-Snoussi · 2024-10-03T15:30:20Z

Hello Yasmin, Thank you for contacting me. Unfortunately, this is outside my expertise, so I won't be able to review it. Best regards, Haykel

…

On Thu, Oct 3, 2024 at 10:29 AM Yasmin ***@***.***> wrote: Hello @paquiteau <https://github.com/paquiteau>, @jonbmartin <https://github.com/jonbmartin> and @H-Snoussi <https://github.com/H-Snoussi>, Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)? JOSS publishes articles about open source research software. The submission I'd like you to review is titled: MIRTorch: A Differentiable Medical Image Reconstruction Toolbox You can find more information at the top of this Github issue. The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know. This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer. Thank you in advance! — Reply to this email directly, view it on GitHub <#7253 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEZIGBRBUFV5EMIXFAW3HOTZZVIEBAVCNFSM6AAAAABOSHB35CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJRGU3TAOBZGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

ymzayek · 2024-10-09T18:52:17Z

@paquiteau thanks for accepting. Good to hear from you as well :)

@jonbmartin thanks for agreeing to review this and I'm glad it if you can find it useful.

I think we can get this started then. The review will start in a separate thread.

@guanhuaw you can follow the review in the new review issue that will be opened.

ymzayek · 2024-10-09T18:52:35Z

@editorialbot start review

editorialbot · 2024-10-09T18:52:37Z

Can't start a review without reviewers

ymzayek · 2024-10-09T18:53:23Z

@editorialbot add @paquiteau as reviewer

editorialbot · 2024-10-09T18:53:26Z

@paquiteau added to the reviewers list!

ymzayek · 2024-10-09T18:53:50Z

@editorialbot add @jonbmartin as reviewer

editorialbot · 2024-10-09T18:53:53Z

@jonbmartin added to the reviewers list!

ymzayek · 2024-10-09T18:54:06Z

@editorialbot start review

editorialbot · 2024-10-09T18:54:10Z

OK, I've started the review over in #7340.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 20, 2024

editorialbot added Python TeX labels Sep 20, 2024

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Sep 23, 2024

Kevin-Mattheus-Moerman removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Sep 27, 2024

editorialbot assigned ymzayek Sep 27, 2024

editorialbot assigned paquiteau Oct 9, 2024

editorialbot assigned jonbmartin Oct 9, 2024

editorialbot closed this as completed Oct 9, 2024

[PRE REVIEW]: MIRTorch: A Differentiable Medical Image Reconstruction Toolbox #7253

[PRE REVIEW]: MIRTorch: A Differentiable Medical Image Reconstruction Toolbox #7253

Comments

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paquiteau commented Oct 3, 2024

Footnotes

jonbmartin commented Oct 3, 2024 via email

H-Snoussi commented Oct 3, 2024 via email

ymzayek commented Oct 9, 2024

ymzayek commented Oct 9, 2024

editorialbot commented Oct 9, 2024

ymzayek commented Oct 9, 2024

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