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

editorialbot commented 3 weeks ago

Submitting author: !--author-handle-->@sajjad88<!--end-author-handle-- (Sajjad Khan) Repository: https://github.com/LidkeLab/matlab-instrument-control Branch with paper.md (empty if default branch): Version: v0.1.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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editorialbot commented 3 weeks ago

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editorialbot commented 3 weeks ago

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 commented 3 weeks ago

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 commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1124

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago

License info:

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

editorialbot commented 3 weeks ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 3 weeks ago

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 commented 3 weeks ago

@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 :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/).
[ ] 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 commented 3 weeks ago

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editorialbot commented 3 weeks ago

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


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sajjad88 commented 3 weeks ago

Names of potential reviewers:

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

sajjad88 commented 3 weeks ago

@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.

openjournals / joss-reviews

[PRE REVIEW]: A MATLAB-based Instrument Control (MIC) package for fluorescence imaging #7121

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