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

Closed editorialbot closed 2 months ago

editorialbot commented 3 months 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: !--editor-->@adamltyson<!--end-editor-- Reviewers: @bencardoen, @raacampbell Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/145f04b4b9a1d7dcb68f8e7d5bbe665b/status.svg)](https://joss.theoj.org/papers/145f04b4b9a1d7dcb68f8e7d5bbe665b)

Author instructions

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

@sajjad88 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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editorialbot commented 3 months ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 3 months 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 months 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 months ago

Paper file info:

📄 Wordcount for paper.md is 1124

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

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

editorialbot commented 3 months 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 months 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 months 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:

sajjad88 commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

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


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
sajjad88 commented 3 months ago

Names of potential reviewers:

  1. Ben Cardoen (https://reviewers.joss.theoj.org/reviewers/2046).
  2. caldarolamartin (https://reviewers.joss.theoj.org/reviewers/781).
sajjad88 commented 3 months 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.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot generate pdf

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot check references

editorialbot commented 2 months 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
- 10.1016/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 commented 2 months ago

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

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot invite @adamltyson as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

editorialbot commented 2 months 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: 0.7215

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 commented 2 months ago

@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 commented 2 months ago

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

adamltyson commented 2 months ago

@editorialbot assign @adamltyson as editor

editorialbot commented 2 months ago

Assigned! @adamltyson is now the editor

adamltyson commented 2 months ago

@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 commented 2 months ago

@adamltyson yes, I'd be happy to

caldarolamartin commented 2 months ago

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 https://github.com/openjournals/joss-reviews/issues/7121#issuecomment-2353221371, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAUGZKWSIFVA2PZ7D5HW52DZW3ZIJAVCNFSM6AAAAABMZ3DBFOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNJTGIZDCMZXGE . You are receiving this because you were mentioned.Message ID: @.***>

adamltyson commented 2 months ago

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

@raacampbell has agreed offline to review.

adamltyson commented 2 months ago

@editorialbot add @bencardoen as reviewer

editorialbot commented 2 months ago

@bencardoen added to the reviewers list!

adamltyson commented 2 months ago

@editorialbot add @raacampbell as reviewer

editorialbot commented 2 months ago

@raacampbell added to the reviewers list!

adamltyson commented 2 months ago

@editorialbot start review

editorialbot commented 2 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7275.