[PRE REVIEW]: A MATLAB-based Instrument Control (MIC) package for fluorescence imaging

[editorialbot]

Submitting author: @sajjad88 (Sajjad Khan)
Repository: https://github.com/LidkeLab/matlab-instrument-control
Branch with paper.md (empty if default branch):
Version: v0.1.0
Editor: @adamltyson
Reviewers: @bencardoen, @raacampbell
Managing EiC: Kevin M. Moerman

Status

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Author instructions

Thanks for submitting your paper to JOSS @sajjad88. Currently, there isn't a JOSS editor assigned to your paper.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.31 s (1303.3 files/s, 183511.4 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
MATLAB                                 140           3471           6950          17329
XML                                     88              0              0          14990
C++                                     90           1049            856           3823
Markdown                                70            657              0           2489
C/C++ Header                             7            436            324           1599
Python                                   7            414            416           1574
Visual Studio Solution                   4              4              4           1006
TeX                                      1             16              0            179
Windows Module Definition                1              0              0              2
JSON                                     1              0              0              1
---------------------------------------------------------------------------------------
SUM:                                   409           6047           8550          42992
---------------------------------------------------------------------------------------

Commit count by author:

   580	dschodt
    91	Hanieh
    70	Sandeep
    48	sajjad88
    28	ellyse-taylor
    18	Michael Wester
    12	HMFarsibaf
    12	kiwibogo
    11	Keith Lidke
     8	Sandeep Pallikkuth
     8	TIRF
     7	Keith A. Lidke
     5	MohamadFazel
     3	kalidke
     2	Hanieh Mazloom Farsibaf
     2	Sajjad Khan
     2	Sheng Liu
     1	Ali
     1	Gert-Jan Bakker
     1	MJWester

[editorialbot]

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

✅ OK DOIs

- 10.1364/OPEX.13.007052 is OK
- 10.1126/science.1127344 is OK
- 10.1038/nmeth929 is OK
- 10.1126/science.1137395 is OK
- 10.1021/acs.chemrev.6b00815 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.21105/joss.05563 is OK
- 10.1371/journal.pone.0203291 is OK
- 10.1038/s41467-022-34894-2 is OK
- 10.1002/0471142727.mb1420s92 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The PYthon Microscopy Environment

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1016/j.celrep.2023.113603 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1124

✅ 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]

Five most similar historical JOSS papers:

ImSwitch: Generalizing microscope control in Python
Submitting author: @kasasxav
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @uellue, @beniroquai, @untzag
Similarity score: 0.7264

Madym: A C++ toolkit for quantitative DCE-MRI analysis
Submitting author: @michaelberks
Handling editor: @emdupre (Active)
Reviewers: @agahkarakuzu, @matteomancini
Similarity score: 0.7060

MAHOS: Measurement Automation Handling and Orchestration System
Submitting author: @ktahar
Handling editor: @arfon (Active)
Reviewers: @sidihamady, @aquilesC
Similarity score: 0.6887

qMRLab: Quantitative MRI analysis, under one umbrella
Submitting author: @agahkarakuzu
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mfroeling, @62442katieb
Similarity score: 0.6872

LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy
Submitting author: @uellue
Handling editor: @majensen (Active)
Reviewers: @alvarolopez, @fedorov
Similarity score: 0.6814

⚠️ 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]

@sajjad88, 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/).
• Does the project feature automated testing? If so I recommend adding links to this to your README.
• Does the project have dedicated documentation? I recommend adding links to this to your README.
• Can you please confirm if you feel the above code report (showing 17329 lines of MATLAB) is accurate? If so, can you clarify what proportion is truly your original contribution in terms of code? I ask this as MATLAB submission can sometimes feature large amounts of automatically generated code (e.g. for APP/GUI creation).

[sajjad88]

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[editorialbot]

Hello @sajjad88, here are the things you can ask me to do:

# List all available commands
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@editorialbot list editors

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@editorialbot check repository

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@editorialbot generate pdf

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@editorialbot generate preprint

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[sajjad88]

Names of potential reviewers:

1. Ben Cardoen (https://reviewers.joss.theoj.org/reviewers/2046).
2. caldarolamartin (https://reviewers.joss.theoj.org/reviewers/781).

[sajjad88]

@Kevin-Mattheus-Moerman thank you for helping in the initial steps. We have fixed the DOI issues, added documentation and contribution guidelines in main README.md.

When changes are made to the matlab-instrument-class, continuous integration tests are performed on the abstract classes, which are further inherited by the other instruments classes but cannot be applied to any instance class unless the corresponding instrument is actually hooked up.

There is no automatically generated code (e.g., .mlapp) included, such as code from MATLAB App Designer or other GUI creation tools. All of the MATLAB code, including any functions related to user interfaces or graphical components, has been manually written, ensuring that it reflects original contributions and not auto-generated templates or GUI elements. The 17,329 lines of MATLAB code in the report are entirely the result of manual development.

With these changes we created a new release: matlab-instrument-control v0.1.1.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[Kevin-Mattheus-Moerman]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1364/OPEX.13.007052 is OK
- 10.1126/science.1127344 is OK
- 10.1038/nmeth929 is OK
- 10.1126/science.1137395 is OK
- 10.1021/acs.chemrev.6b00815 is OK
- 10.1016/j.bpj.2017.11.2912 is OK
- 10.21105/joss.05563 is OK
- 10.1371/journal.pone.0203291 is OK
- 10.1016/j.celrep.2023.113603 is OK
- 10.1038/s41467-022-34894-2 is OK
- 10.1002/0471142727.mb1420s92 is OK
- 10.5281/zenodo.4289803 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot invite @adamltyson as editor

[editorialbot]

Invitation to edit this submission sent!

[editorialbot]

Five most similar historical JOSS papers:

ImSwitch: Generalizing microscope control in Python
Submitting author: @kasasxav
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @uellue, @beniroquai, @untzag
Similarity score: 0.7215

Madym: A C++ toolkit for quantitative DCE-MRI analysis
Submitting author: @michaelberks
Handling editor: @emdupre (Active)
Reviewers: @agahkarakuzu, @matteomancini
Similarity score: 0.7113

MAHOS: Measurement Automation Handling and Orchestration System
Submitting author: @ktahar
Handling editor: @arfon (Active)
Reviewers: @sidihamady, @aquilesC
Similarity score: 0.6886

qMRLab: Quantitative MRI analysis, under one umbrella
Submitting author: @agahkarakuzu
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @grlee77, @mfroeling, @62442katieb
Similarity score: 0.6884

LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy
Submitting author: @uellue
Handling editor: @majensen (Active)
Reviewers: @alvarolopez, @fedorov
Similarity score: 0.6854

⚠️ 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]

@adamltyson would you be able to help edit this one? It may be a tricky one in terms finding reviewers able to test the software that links to/needs particular hardware/instruments.

[adamltyson]

Hi @Kevin-Mattheus-Moerman, yes happy to take this on. I'll see what I can do.

[adamltyson]

@editorialbot assign @adamltyson as editor

[editorialbot]

Assigned! @adamltyson is now the editor

[adamltyson]

@bencardoen, @caldarolamartin, 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.

[bencardoen]

@adamltyson yes, I'd be happy to

[caldarolamartin]

Unfortunately I can't review this at this time. Best, Martin Martin Caldarola

…

On Mon, 16 Sept 2024, 17:19 Ben Cardoen, ***@***.***> wrote: @adamltyson <https://github.com/adamltyson> yes, I'd be happy to — Reply to this email directly, view it on GitHub <#7121 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAUGZKWSIFVA2PZ7D5HW52DZW3ZIJAVCNFSM6AAAAABMZ3DBFOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJTGIZDCMZXGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[adamltyson]

Thanks @bencardoen, and no problem at all @caldarolamartin.

@raacampbell has agreed offline to review.

[adamltyson]

@editorialbot add @bencardoen as reviewer

[editorialbot]

@bencardoen added to the reviewers list!

[adamltyson]

@editorialbot add @raacampbell as reviewer

[editorialbot]

@raacampbell added to the reviewers list!

[adamltyson]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7275.