[PRE REVIEW]: SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software #4023

whedon · 2021-12-21T17:10:40Z

Submitting author: @jiahecui (Jiahe Cui)
Repository: https://github.com/jiahecui/SenAOReFoc
Version: v1.0.0
Editor: @diehlpk
Reviewers: @abhilash12iec002 , @JackTyson, @alvesjnr
Managing EiC: Arfon Smith

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Status

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Markdown: [![status](https://joss.theoj.org/papers/c0c5c8e06b379c4ac5374b261241068d/status.svg)](https://joss.theoj.org/papers/c0c5c8e06b379c4ac5374b261241068d)

Author instructions

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

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

@jiahecui 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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The text was updated successfully, but these errors were encountered:

whedon · 2021-12-21T17:10:43Z

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

whedon · 2021-12-21T17:11:26Z

Wordcount for paper.md is 1615

whedon · 2021-12-21T17:11:39Z

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

OK DOIs

- 10.1038/lsa.2014.46 is OK
- 10.1038/nn.4358 is OK
- 10.1364/OE.401117 is OK
- 10.1364/OE.27.031316 is OK
- 10.1364/OE.25.004368 is OK
- 10.1364/OE.26.001655 is OK
- 10.1364/OE.23.026208 is OK
- 10.5281/zenodo.3885508 is OK
- 10.1364/OE.442025 is OK
- 10.1364/BOE.8.004369 is OK
- 10.1364/AOPT.2005.AThB4 is OK
- 10.1111/j.1365-2966.2004.08524.x is OK
- 10.1364/OL.26.000746 is OK
- 10.1097/OPX.0b013e3181ff9a8b is OK
- 10.1098/rsta.2007.0013 is OK
- 10.1038/nmeth.4218 is OK
- 10.3928/1081-597X-20010901-13 is OK

MISSING DOIs

- 10.1364/boda.2021.dth2a.2 may be a valid DOI for title: Remote-Focussing for Volumetric Imaging in a Contactless and Label-Free Neurosurgical Microscope
- 10.1117/12.2054470 may be a valid DOI for title: Object-oriented Matlab adaptive optics toolbox
- 10.1146/annurev.aa.31.090193.000305 may be a valid DOI for title: Adaptive optics for astronomy: principles, performance, and applications

INVALID DOIs

- None

whedon · 2021-12-21T17:11:44Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.24 s (210.3 files/s, 81868.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          43           3134           4702           8803
Qt                               2              0              0           1474
Markdown                         2            165              0            763
TeX                              1             21              0            241
YAML                             1             12              0             82
JSON                             1              0              0             70
-------------------------------------------------------------------------------
SUM:                            50           3332           4702          11433
-------------------------------------------------------------------------------


Statistical information for the repository 'cf2651fd48f43136d981d7e9' was
gathered on 2021/12/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jiahe Cui                      203       1380249        1369584           99.68
jiahecui                        55          7430           1470            0.32

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
Jiahe Cui                 16639            1.2          9.7               10.30

whedon · 2021-12-21T17:12:12Z

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

jiahecui · 2021-12-21T21:09:50Z

Suggestion for potential reviewers: caldarolamartin, jonatanalvelid

arfon · 2021-12-29T08:25:08Z

👋 @jiahecui – many thanks for your submission to JOSS. While I look for an editor to handle your submission if you want to fix the DOIs (noting that Whedon's suggestions are not always right), you can, then use the following commands (one at a time, as the first line of a new comment) to regenerate the PDF and check the references.

@whedon generate pdf
@whedon check references

arfon · 2021-12-29T08:25:37Z

@whedon invite @jni as editor

👋 @jni – would you be able to edit this submission for JOSS? Many thanks!

whedon · 2021-12-29T08:25:39Z

@jni has been invited to edit this submission.

jiahecui · 2022-01-04T08:56:09Z

@whedon generate pdf

whedon · 2022-01-04T08:58:08Z

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

jiahecui · 2022-01-04T09:11:41Z

@whedon check references

whedon · 2022-01-04T09:13:17Z

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

OK DOIs

- 10.1038/lsa.2014.46 is OK
- 10.1038/nn.4358 is OK
- 10.1364/OE.401117 is OK
- 10.1364/OE.27.031316 is OK
- 10.1364/OE.25.004368 is OK
- 10.1364/OE.26.001655 is OK
- 10.1364/OE.23.026208 is OK
- 10.5281/zenodo.3885508 is OK
- 10.1364/boda.2021.dth2a.2 is OK
- 10.1364/OE.442025 is OK
- 10.1364/BOE.8.004369 is OK
- 10.1364/AOPT.2005.AThB4 is OK
- 10.1111/j.1365-2966.2004.08524.x is OK
- 10.1117/12.2054470 is OK
- 10.1364/OL.26.000746 is OK
- 10.1146/annurev.aa.31.090193.000305 is OK
- 10.1097/OPX.0b013e3181ff9a8b is OK
- 10.1098/rsta.2007.0013 is OK
- 10.1038/nmeth.4218 is OK
- 10.3928/1081-597X-20010901-13 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kthyng · 2022-01-06T22:44:09Z

@whedon assign @diehlpk as editor

whedon · 2022-01-06T22:44:13Z

OK, the editor is @diehlpk

diehlpk · 2022-01-07T15:32:54Z

@jiahecui would be great if you could recommend some reviewers?

jiahecui · 2022-01-07T16:27:59Z

Hello and thank you for agreeing to be editor! Suggestion for potential reviewers: caldarolamartin, jonatanalvelid.

diehlpk · 2022-01-07T17:06:55Z

Hi @caldarolamartin and @jonatanalvelid would you be interested in reviewing this paper?

diehlpk · 2022-01-10T21:44:15Z

Hi @dvanic or @sfuxy or @jodemaey or @abhilash12iec002 would you be interested in reviewing this paper?

dvanic · 2022-01-10T22:59:36Z

@diehlpk: sorry, it's too far outside my area of expertise 😓

jonatanalvelid · 2022-01-11T07:59:15Z

Hi @diehlpk, thank you for considering me, but I am unfortunately not available to review currently.
I hope I will be considered again in the future and will happily review then, and thanks for your understanding.

Best,
Jonatan

abhilash12iec002 · 2022-01-11T08:15:29Z

Yes, I can review the said paper. Best, Abhilash Singh PhD Scholar, 1810302 Fluvial Geomorphology and Remote Sensing Lab, Department of EES, AB-2, Lab-10, Indian Institute of Science Education and Research Bhopal mobile: +91-9990674147 ***@***.*** www.abhilashsingh.net ***@***.***>

…

On Tue, Jan 11, 2022 at 1:29 PM Jonatan Alvelid ***@***.***> wrote: Hi @diehlpk <https://github.com/diehlpk>, thank you for considering me, but I am unfortunately not available to review currently. I hope I will be considered again in the future and will happily review then, and thanks for your understanding. Best, Jonatan — Reply to this email directly, view it on GitHub <#4023 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALFVGVBVTTS67XANNVAWWGDUVPPN7ANCNFSM5KQVAYHA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

jodemaey · 2022-01-11T08:49:02Z

Hi,

Same as @dvanic comment for me, it is way outside of my area of expertise.

Sorry,

Jonathan

diehlpk · 2022-01-11T15:56:38Z

@whedon assign @abhilash12iec002 as reviewer

whedon · 2022-01-11T15:56:43Z

OK, @abhilash12iec002 is now a reviewer

diehlpk · 2022-01-19T17:13:01Z

@jiahecui would be great if you could recommend more reviewers?

abhilash12iec002 · 2022-01-19T17:17:22Z

@jiahecui Please find my comments below;
I have read the complete article, “SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software” with full consideration. The title is short and sufficient. The summary part is nicely written in a very concise way. In the statement of need section, there exists a scope of improvement. For example; “The functionality of the software has also been tested on different operating systems (Windows/macOS/Linux) for sake of generality.” For this line, a concluding remark on the performance on each platform must be added. Also, the lines from 71 to 73 must be explained in detail. I think these two points are very crucial points and a good set of motivation for this software. I am very much satisfied with the Example usage section. Apart from reading the article, I have spent a good chunk of time using the SenAOReFoc package in the due course of this review. I am satisfied with the functionality of this software.

Overall, the submitted manuscript is well written, and ably demonstrates the community requirement for this open-source tool. I recommend publication after incorporating the suggestions discussed above.

diehlpk · 2022-01-19T17:35:45Z

@whedon start review

whedon · 2022-01-19T17:35:49Z

OK, I've started the review over in #4075.

diehlpk · 2022-01-19T17:36:48Z

@abhilash12iec002 That was quick. I started the review in #4075, and please check the checkboxes there.

jiahecui · 2022-01-20T09:23:54Z

@diehlpk Sure no problem, I suggest JackTyson, caldarolamartin, alvesjnr, aquilesC. Thank you very much!

jiahecui · 2022-01-20T09:28:24Z

@jiahecui Please find my comments below; I have read the complete article, “SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software” with full consideration. The title is short and sufficient. The summary part is nicely written in a very concise way. In the statement of need section, there exists a scope of improvement. For example; “The functionality of the software has also been tested on different operating systems (Windows/macOS/Linux) for sake of generality.” For this line, a concluding remark on the performance on each platform must be added. Also, the lines from 71 to 73 must be explained in detail. I think these two points are very crucial points and a good set of motivation for this software. I am very much satisfied with the Example usage section. Apart from reading the article, I have spent a good chunk of time using the SenAOReFoc package in the due course of this review. I am satisfied with the functionality of this software.

Overall, the submitted manuscript is well written, and ably demonstrates the community requirement for this open-source tool. I recommend publication after incorporating the suggestions discussed above.

@abhilash12iec002 Thank you very much for the thorough review and detailed comments. Your time is greatly appreciated! We will make the revisions as soon as possible!

abhilash12iec002 · 2022-01-20T09:32:31Z

@jiahecui Thanks and Good luck!

diehlpk · 2022-01-20T16:29:24Z

Hi @JackTyson, @caldarolamartin, @alvesjnr, @aquilesC would you be interested in reviewing this paper?

aquilesC · 2022-01-20T17:47:04Z

Thanks for the invite! I am wrapping up another review here on JOSS and with zero bandwidth to take up another one.

JackTyson · 2022-01-20T19:27:44Z

Hi @diehlpk, yes, this area sits within my expertise and I would be happy to review.

diehlpk · 2022-01-20T19:38:35Z

@whedon add @JackTyson as reviewer

whedon · 2022-01-20T19:38:40Z

OK, @JackTyson is now a reviewer

alvesjnr · 2022-01-20T19:46:42Z

Hi, I would be happy to review.

…

On Thu, Jan 20, 2022, 17:29 Patrick Diehl ***@***.***> wrote: Hi @JackTyson <https://github.com/JackTyson>, @caldarolamartin <https://github.com/caldarolamartin>, @alvesjnr <https://github.com/alvesjnr>, @aquilesC <https://github.com/aquilesC> would you be interested in reviewing this paper? — Reply to this email directly, view it on GitHub <#4023 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABXQCAZAPX6DXXZ3LCIE6LUXAZ7BANCNFSM5KQVAYHA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

diehlpk · 2022-01-21T17:08:34Z

@whedon add @alvesjnr as reviewer

whedon · 2022-01-21T17:08:41Z

OK, @alvesjnr is now a reviewer

whedon added the pre-review label Dec 21, 2021

whedon added Python TeX labels Dec 21, 2021

whedon assigned diehlpk Jan 6, 2022

whedon assigned abhilash12iec002 and unassigned diehlpk Jan 11, 2022

whedon assigned diehlpk Jan 11, 2022

whedon closed this as completed Jan 19, 2022

whedon assigned abhilash12iec002, diehlpk and JackTyson and unassigned diehlpk and abhilash12iec002 Jan 20, 2022

whedon assigned abhilash12iec002, diehlpk and JackTyson and unassigned JackTyson, diehlpk and abhilash12iec002 Jan 21, 2022

[PRE REVIEW]: SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software #4023

[PRE REVIEW]: SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software #4023

Comments

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diehlpk commented Jan 7, 2022

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diehlpk commented Jan 10, 2022

dvanic commented Jan 10, 2022

jonatanalvelid commented Jan 11, 2022

abhilash12iec002 commented Jan 11, 2022 via email

jodemaey commented Jan 11, 2022

diehlpk commented Jan 11, 2022

whedon commented Jan 11, 2022

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abhilash12iec002 commented Jan 19, 2022

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jiahecui commented Jan 20, 2022 • edited Loading

jiahecui commented Jan 20, 2022

abhilash12iec002 commented Jan 20, 2022

diehlpk commented Jan 20, 2022

aquilesC commented Jan 20, 2022

JackTyson commented Jan 20, 2022

diehlpk commented Jan 20, 2022

whedon commented Jan 20, 2022

alvesjnr commented Jan 20, 2022 via email

diehlpk commented Jan 21, 2022

whedon commented Jan 21, 2022

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