[PRE REVIEW]: scmorph: a Python package for analysing single-cell morphological profiles

[editorialbot]

Submitting author: @jeskowagner (Jesko Wagner)
Repository: https://github.com/edbiomedai/scmorph/
Branch with paper.md (empty if default branch): paper
Version: v0.3.1
Editor: @csoneson
Reviewers: @tushardave26
Managing EiC: Kevin M. Moerman

Status

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

✅ OK DOIs

- 10.1101/2021.03.09.433671 is OK
- 10.1016/j.cels.2019.03.010 is OK
- 10.1016/j.isci.2025.111871 is OK
- 10.1109/tkde.2022.3159580 is OK
- 10.48550/arxiv.2108.06828 is OK
- 10.1080/01621459.1952.10483441 is OK
- 10/gt2g9c is OK
- 10.1038/s41467-024-44823-0 is OK
- 10.1038/s41592-025-02611-8 is OK
- 10.1186/s12859-021-04344-9 is OK
- 10.1038/s41467-024-54264-4 is OK
- 10.1186/s12864-018-4772-0 is OK
- 10.21105/joss.04371 is OK
- 10.1186/s13059-017-1382-0 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.06 s (1328.5 files/s, 152864.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          34            965           1472           2444
Markdown                         9            117              1            372
YAML                            12             16             15            345
SVG                              3              3              3            333
TeX                              2             32              1            310
Jupyter Notebook                 3              0           1693            170
TOML                             1             16              3            139
reStructuredText                 8             56             78             86
R                                1             10             60             51
JSON                             1              0              0             30
INI                              1              3              0             12
make                             1              4              7              9
CSS                              1              0              1              3
-------------------------------------------------------------------------------
SUM:                            77           1222           3334           4304
-------------------------------------------------------------------------------

Commit count by author:

   161	Jesko Wagner
     7	jeskowagner
     2	s2221912

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 807

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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[tushardave26]

I can review this one.

[jeskowagner]

Thanks Tushar!

To editors: perhaps Pradeep Rajasekhar (pr4deepr), Virgile Andreani (Armavica), and James Kerns (jrkerns) could be additional suitable reviewers.

[jeskowagner]

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[Kevin-Mattheus-Moerman]

Dear authors, thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editors most appropriate for your area are all already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[csoneson]

@editorialbot assign @csoneson as editor

[editorialbot]

Assigned! @csoneson is now the editor

[csoneson]

👋🏻 @jeskowagner - I will handle your submission and start by finding at least two suitable reviewers. Thanks for the suggestions above!

[csoneson]

@tushardave26 - are you still interested and available for reviewing this submission? (I see that you are already engaged in several other JOSS reviews! 🙂)

[csoneson]

👋🏻 @pr4deepr, @Armavica, @jrkerns - would you be interested in reviewing this submission for JOSS?

scmorph: a Python package for analysing single-cell morphological profiles
#8005

Thanks in advance!

[tushardave26]

@tushardave26 - are you still interested and available for reviewing this submission? (I see that you are already engaged in several other JOSS reviews! 🙂)

@csoneson - Yes. I can review this one.

[csoneson]

Great, thanks @tushardave26 - I will assign you now, and I will open the review issue once we have secured one more reviewer.

[csoneson]

@editorialbot add @tushardave26 as reviewer

[editorialbot]

@tushardave26 added to the reviewers list!

[Armavica]

👋🏻 @pr4deepr, @Armavica, @jrkerns - would you be interested in reviewing this submission for JOSS?

scmorph: a Python package for analysing single-cell morphological profiles
#8005

Thanks in advance!

Hi, I would be happy to review this submission but I am a bit overwhelmed at the moment. I can try but I am not sure how much time I will have this month. I will definitely have more time in June, though.

[csoneson]

Thanks @Armavica - no worries, let me try to find another reviewer (no need to add additional stress 🙂).

[csoneson]

👋🏻 @emptymalei, @pr4deepr, @jrkerns, @bgailleton - would you be interested in reviewing this submission for the Journal of Open Source Software (JOSS)?

scmorph: a Python package for analysing single-cell morphological profiles
#8005

You can find more information about our checklist-driven review process here

Thanks in advance!

[jrkerns]

My apologies for the late reply. I don't currently have the bandwidth. Thank you for the consideration!

…

On Thu, May 15, 2025 at 3:03 PM Charlotte Soneson ***@***.***> wrote: *csoneson* left a comment (openjournals/joss-reviews#8005) <#8005 (comment)> 👋🏻 @emptymalei <https://github.com/emptymalei>, @pr4deepr <https://github.com/pr4deepr>, @jrkerns <https://github.com/jrkerns>, @bgailleton <https://github.com/bgailleton> - would you be interested in reviewing this submission for the Journal of Open Source Software (JOSS)? scmorph: a Python package for analysing single-cell morphological profiles #8005 <#8005> You can find more information about our checklist-driven review process here <https://joss.readthedocs.io/en/latest/reviewer_guidelines.html> Thanks in advance! — Reply to this email directly, view it on GitHub <#8005 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABEUWCEELK3OSSLUGCNUO4T26TXKLAVCNFSM6AAAAAB2RL6232VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQOBUHEZDSNBRGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[bgailleton]

Hi, thanks for the mention. I am happy to review the software side, I will not be able to provide insight on the science - as it's pretty far away from my own field.
Let me know if that's OK!

[csoneson]

Thanks @bgailleton - that sounds great.

@tushardave26 - do you feel comfortable commenting on the scientific aspect of the submission (to the extent covered by the JOSS review checklist)? I am also happy to look for a third reviewer.