[PRE REVIEW]: PyStack3D: A python package for fast image stack correction

[editorialbot]

Submitting author: !--author-handle-->@patquem<!--end-author-handle-- (Patrick Quéméré) Repository: https://github.com/CEA-MetroCarac/pystack3d Branch with paper.md (empty if default branch): Version: v2024.1 Editor: !--editor-->@mstimberg<!--end-editor-- Reviewers: @kasasxav, @xiuliren, @sklumpe Managing EiC: Kevin M. Moerman

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

@patquem 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 1.90  T=0.04 s (1086.3 files/s, 168468.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            755           1194           2168
XML                              1              0              0           1016
reStructuredText                13            310            164            359
TOML                             5             42             42            218
DOS Batch                        1             21              1            134
Markdown                         2             65              0            128
make                             1             22              4            108
TeX                              1              3              0             47
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            44           1219           1409           4196
-------------------------------------------------------------------------------

Commit count by author:

   137  patquem
     8  TomDavFr

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.10623640 is OK

MISSING DOIs

- 10.1038/nmeth.2019 may be a valid DOI for title: Fiji: an open-source platform for biological-image...
- 10.1109/83.650848 may be a valid DOI for title: A Pyramid Approach to Subpixel Registration Based ...
- No DOI given, and none found for title: Variational algorithms to remove stationary noise....

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 767

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[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:

PyQMRI: An accelerated Python based Quantitative MRI toolbox Submitting author: @maieroli2010 Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @grlee77, @agahkarakuzu, @DARSakthi Similarity score: 0.7197

PoreSpy: A Python Toolkit for Quantitative Analysis of Porous Media Images Submitting author: @jgostick Handling editor: @usethedata (Retired) Reviewers: @yxqd, @cr458 Similarity score: 0.7176

AXITOM: A Python package for reconstruction of axisymmetric tomograms acquired by a conical beam Submitting author: @PolymerGuy Handling editor: @katyhuff (Retired) Reviewers: @PingjunChen, @dgursoy Similarity score: 0.7168

OrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networks Submitting author: @Marcdh3 Handling editor: @akeshavan (Retired) Reviewers: @serine, @vc1492a Similarity score: 0.7131

CleanX: A Python library for data cleaning of large sets of radiology images Submitting author: @drcandacemakedamoore Handling editor: @cMadan (Active) Reviewers: @henrykironde, @anki-xyz Similarity score: 0.7120

⚠️ 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]

@patquem, thanks for this submission. I am the AEiC on this track and here to help process the initial steps and will look for a handling editor for this submission. As you may have noticed I have just applied the waitlisted label, this is because all editors in this domain are currently preoccupied with other submission. I will assign an editor once one becomes available.

While we wait, and before we can proceed, these are some points that require your attention:

• [x] Please study the above reference check :point_up: 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.
• [x] 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/).

[patquem]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/nmeth.2019 is OK
- 10.1109/83.650848 is OK
- 10.5281/zenodo.10623640 is OK
- 10.1109/TIP.2012.2206037 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[patquem]

Hi @Kevin-Mattheus-Moerman ,

Thank you very much for the registration in the JOSS reviewing process and for your comments.

• The DOIs have been updated.

• The contributing section is now included in the README and links to the documentation (hoping this is okay with you).

Regarding the "Five most similar historical JOSS papers," they seem quite different from pyStack3D, but I will let the editor form their own opinion. I understand that they are quite busy at the moment and I hope that one will soon be available to start the reviewing process.

Regarding the reviewers, among the list of people likely to review for JOSS in connection with this paper, I had noted: Sklumpe , pr4deepr and two other people who are not currently JOSS reviewers but work on processes similar to those proposed in pystack3d: gleb-shtengel, kleinerELM.

[Kevin-Mattheus-Moerman]

@editorialbot invite @mstimberg as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/nmeth.2019 is OK
- 10.1109/83.650848 is OK
- 10.5281/zenodo.10623640 is OK
- 10.1109/TIP.2012.2206037 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mstimberg]

@Kevin-Mattheus-Moerman happy to review the submission, but please note that I will be away for a long (4-week) summer break starting on August 5th.

[ritika-giri]

@Kevin-Mattheus-Moerman - also happy to review this submission.

[Kevin-Mattheus-Moerman]

@editorialbot assign @mstimberg as editor

[editorialbot]

Assigned! @mstimberg is now the editor

[Kevin-Mattheus-Moerman]

@ritika-giri thanks for offering to review. However, the handling editor (@mstimberg) is responsible for looking for reviewers.

[patquem]

Thank you @mstimberg for accepting to be the editor and thanks to @ritika-giri for volunteering to review the paper.

[mstimberg]

👋 @patquem, I will be the editor for your submission, looking forward to working with you.

The first step is to look for reviewers. I will do this mostly over email, so don't be surprised if you won't see much activity here. 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.

[mstimberg]

@editorialbot add @kasasxav as reviewer

Thanks for joining us!

[editorialbot]

@kasasxav added to the reviewers list!

[patquem]

@mstimberg

If you have any suggestions for potential reviewers ...

I made some suggestions at the the end of my message https://github.com/openjournals/joss-reviews/issues/6954#issuecomment-2208724619

[mstimberg]

I made some suggestions at the the end of my message #6954 (comment)

Ah, I overlooked this, thanks!

[mstimberg]

@editorialbot add @xiuliren as reviewer

Thanks for helping us out!

[editorialbot]

@xiuliren added to the reviewers list!

[mstimberg]

@editorialbot add @sklumpe as reviewer

Thanks for joining us!

[editorialbot]

@sklumpe added to the reviewers list!

[mstimberg]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7079.