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[PRE REVIEW]: SIAL: A simple image analysis library for wet-lab scientists #2683

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whedon opened this issue Sep 17, 2020 · 26 comments
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[PRE REVIEW]: SIAL: A simple image analysis library for wet-lab scientists #2683

whedon opened this issue Sep 17, 2020 · 26 comments
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@whedon
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whedon commented Sep 17, 2020 •
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Submitting author: @d-tear (David Tyrpak)
Repository: https://github.com/d-tear/SIAL
Version: v1.0.0
Editor: @jni
Reviewers: @bogovicj, @haesleinhuepf
Managing EiC: Kyle Niemeyer

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

Thanks for submitting your paper to JOSS @d-tear. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @jni.

@d-tear if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

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whedon commented Sep 17, 2020

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

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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

@whedon commands

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

@whedon generate pdf

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whedon commented Sep 17, 2020 

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.17 s (83.1 files/s, 16766.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                            10            981            411           1128
Maven                            1             23              0            150
Markdown                         2             36              0             71
TeX                              1              2              0             22
-------------------------------------------------------------------------------
SUM:                            14           1042            411           1371
-------------------------------------------------------------------------------


Statistical information for the repository '2683' was gathered on 2020/09/17.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
David Tyrpak                    46          2760            240          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
David Tyrpak               2520           91.3          1.0               16.75

@whedon
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whedon commented Sep 17, 2020 

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

OK DOIs

- 10.1038/s41598-017-17204-5 is OK
- 10.1371/journal.pbio.2005970 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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whedon commented Sep 17, 2020

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

@kyleniemeyer
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Hi @jni, the authors suggested you to edit this submission. Does this look like it would be a good fit, and do you have the bandwidth?

@kyleniemeyer
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@whedon invite @jni as editor

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whedon commented Sep 17, 2020

@jni has been invited to edit this submission.

@d-tear
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d-tear commented Sep 17, 2020 via email

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jni commented Sep 18, 2020

I don't have much bandwidth but progress is a bit stalled on my other reviews so, against my better judgment...

@whedon assign me as editor

😂

@d-tear Thank you for the contribution and for the youtube videos, they are clear and informative! At a minimum you should add a citation to Fiji btw! 😉 Also, I'm not a reviewer (I'll work on finding some), but to get you a head start, I would say that (a) the summary should include one-line sentences for each of the three functions that the plugin provides, not just a motivation, (b) the statement of need should work a bit harder to differentiate the specific functions that were missing from Fiji — since one would assume that Fiji itself would have functionality for "the most common tasks that fellow wet-lab researchers encounter", and perhaps (c) mention a bit more clearly (perhaps a YouTube video) how SIAL would be integrated with QuPath and CP, since that is not clear to me at all.

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jni commented Sep 18, 2020

Hmm I wonder if Whedon needs commands to be alone in a comment...

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jni commented Sep 18, 2020

@whedon assign me as editor

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whedon commented Sep 18, 2020

OK, the editor is @jni

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jni commented Sep 18, 2020

Yup.

@kyleniemeyer
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@jni thanks!

Also, regarding whedon, I think it works as long as the command is at the beginning of a longer comment.

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jni commented Sep 18, 2020

@whedon generate pdf

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whedon commented Sep 18, 2020

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

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d-tear commented Sep 18, 2020 via email

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d-tear commented Sep 19, 2020 via email

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d-tear commented Sep 19, 2020 via email

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whedon commented Sep 19, 2020

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

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jni commented Sep 22, 2020

@whedon assign @bogovicj as reviewer

@whedon whedon assigned jni and unassigned jni Sep 22, 2020
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whedon commented Sep 22, 2020

OK, @bogovicj is now a reviewer

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jni commented Sep 22, 2020

@whedon add @haesleinhuepf as reviewer

@whedon whedon unassigned jni Sep 22, 2020
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whedon commented Sep 22, 2020

OK, @haesleinhuepf is now a reviewer

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jni commented Sep 22, 2020

@whedon start review

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whedon commented Sep 22, 2020

OK, I've started the review over in #2689.

@whedon whedon closed this as completed Sep 22, 2020
@jni jni mentioned this issue Oct 19, 2020
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