[PRE REVIEW]: BrightEyes-MCS: a control suite for multichannel scanning microscopy

[editorialbot]

Submitting author: !--author-handle-->@VicidominiLab<!--end-author-handle-- (Mattia Donato) Repository: https://github.com/VicidominiLab/BrightEyes-MCS Branch with paper.md (empty if default branch): paper Version: v0.9.0 Editor: !--editor-->@adamltyson<!--end-editor-- Reviewers: @raacampbell, @jacopoabramo, @beniroquai Managing EiC: Kevin M. Moerman

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Author instructions

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.13 s (518.7 files/s, 218687.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          39           2789           1017          10753
Qt                               4              0              0           7135
SVG                              3              7              3           4870
Markdown                         3            317              0           1124
Cython                           3             84             31            394
HTML                             1              9              0            170
TeX                              1             16              0            152
DOS Batch                        7             17              0            115
XML                              7              0              0             82
Bourne Shell                     1              1              0              6
-------------------------------------------------------------------------------
SUM:                            69           3240           1051          24801
-------------------------------------------------------------------------------

Commit count by author:

    18  Developer (STED)
    10  Vicidomini Lab
     7  Mattia Donato
     6  Mattia D
     3  Developer FCS
     2  Developer ISMFLUX
     2  Mattia from Tracking PC
     1  Developer AO

[editorialbot]

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

OK DOIs

- 10.1103/PhysRevLett.104.198101 is OK
- 10.1088/1361-6420/accdc5 is OK
- 10.1016/j.bpr.2021.100025 is OK
- 10.21105/joss.03394 is OK
- 10.1002/0471142727.mb1420s92 is OK
- 10.1103/PhysRevResearch.5.023033 is OK

MISSING DOIs

- No DOI given, and none found for title: Super-resolution in confocal imaging
- No DOI given, and none found for title: Arkitekt : An open-source framework for modern bio...

INVALID DOIs

- 10.1038/s41592-018-0291-7 is INVALID
- 10.1038/s41467-022-31408-6 is INVALID
- 10.1038/s41467-023-15070-4 is INVALID
- 10.1038/s41566-023-01112-y is INVALID
- 10.1364/OPTICA.388600 is INVALID
- 10.1117/1.AP.6.1.015003 is INVALID
- 10.1038/s41467-022-35027-y is INVALID
- 10.1038/s41377-021-00515-w is INVALID

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2635

🔴 Failed to discover a Statement of need section in paper

[editorialbot]

License info:

🟡 License found: Other (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]

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⚠️ 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]

@VicidominiLab 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 :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.
• [ ] 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/).

Finally I see this work features hardware requirements. I need to point out that although we have successfully reviewed/published software works that link with specialised hardware in the past, we have also seen severe difficulties in finding reviewers or completing the reviews fully which in some cases has led to the papers ending up retracted. So, since this work appears to require particular NI FPGA's, I just want to add a word of warning that finding reviewers may take long or be unsuccessful altogether, and that the review process may take longer than usual. The success strongly depends on how clear and well documented your package is in terms of what the hardware requirements are and how to set everything up for testing. If you feel these aspects are in good shape that is great, if not, then pushing now for these to be extended would be a good idea. Further more, when asked by the editor, it would be really helpful if you could help suggest any potential reviewers (provided there is no conflict of interest). So in short, hardware related submissions in JOSS are possible, however they can be tricky, so keep that in mind. Thanks.

[Kevin-Mattheus-Moerman]

@VicidominiLab :wave:

[Kevin-Mattheus-Moerman]

@VicidominiLab responding to queries on this issue in a timely manor is important. Please respond to the above points by the end of this week. If we do not hear from you we'll proceed to reject this submission due to inactivity.

[Kevin-Mattheus-Moerman]

@VicidominiLab last reminder, please respond to the above points. Thanks.

[VicidominiLab]

Dear @Kevin-Mattheus-Moerman,

Thank you for your feedback on our submission and your patience. Thank you for the comment about the bibliography issues and the contributing guidelines. In the next commit I will fix the .bib file, the contributing.md and I will try to push more clearly hardware requirements and setup process.

We chose JOSS for our submission because it aligns with our project goals and audience. We've noticed similar projects microscopy-related, like ImSwitch, which also involve hardware components. I understand the complexities involved in reviewing hardware-dependent software but in scientific-paper revision it is rare that the reviewer has the hardware/complete system in hand. In our case, while the NIFPGA hardware mentioned in the paper is essential for running the BrightEyes-MCS acquisition, the additional hardware components (such as detectors, optics, optoelectronics, lasers, etc...) are not strictly required for testing the software.

Regarding the review process, I understand the potential challenges in finding suitable reviewers due to the hardware aspect. To assist, I would like to suggest two potential reviewers who they should have a system similar to ours.

• J. Abramo (GitHub: jacopoabramo) - the current maintainer of ImSwitch.
• B. Diederich (GitHub: beniroquai) - the founder of OpenUC2.

Thank you once again for your assistance. Please let me know if there's anything else I can do to support the process.

Kind regards,

Mattia

[Kevin-Mattheus-Moerman]

@editorialbot invite @adamltyson as editor

[editorialbot]

Invitation to edit this submission sent!

[adamltyson]

Thanks @Kevin-Mattheus-Moerman, happy to take this on.

[adamltyson]

@editorialbot assign @adamltyson as editor

[editorialbot]

Assigned! @adamltyson is now the editor

[Kevin-Mattheus-Moerman]

@adamltyson thanks! Please check all my comments above. Some work is still needed to proceed and I did raise the issue of hardware requirements. But, if we can find reviewers that can help, then I'm happy to proceed to review.

[adamltyson]

Hi @VicidominiLab, I'll take over the submission from now on.

As @Kevin-Mattheus-Moerman mentioned, it may be tricky, or even not possible for this to be reviewed, but we'll try our best! I will push ahead in finding reviewers, but in the mean time, can you make sure to address @Kevin-Mattheus-Moerman's comments about the references and the contributing guide?

Any questions, please let me know.

[adamltyson]

We have a bit of a head start, as @raacampbell has agreed offline to review.

[adamltyson]

@editorialbot add @raacampbell as reviewer

[editorialbot]

@raacampbell added to the reviewers list!

[adamltyson]

@jacopoabramo, @beniroquai, would you be able to review this submission to JOSS?

If you haven't reviewed for JOSS before, we carry out our checklist-driven reviews here in GitHub issues following these guidelines. If you have any questions, let me know.

[jacopoabramo]

Greetings @adamltyson, sorry for the late reply - I was on vacation until yesterday.

I'd be happy to review the paper. Since it's my first time reviewing for JOSS do you have any input on where I should start with the review? Any tip is appreciated. Thank you in advance.

[beniroquai]

Thanks @adamltyson, also sorry for the late reply. Same here. I'm in! :)

[adamltyson]

Hi @jacopoabramo, @beniroquai, thanks both for agreeing to review this. I will go ahead an start the review process. A new GitHub issue will be raised with information and links about how to go about the review, but feel free to ask me any questions.

[adamltyson]

@editorialbot add @jacopoabramo as reviewer

[editorialbot]

@jacopoabramo added to the reviewers list!

[adamltyson]

@editorialbot add @beniroquai as reviewer

[editorialbot]

@beniroquai added to the reviewers list!

[adamltyson]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7125.