[PRE REVIEW]: Scanbot: An STM Automation Bot

[editorialbot]

Submitting author: !--author-handle-->@ceds92<!--end-author-handle-- (Julian Ceddia) Repository: https://github.com/New-Horizons-SPM/scanbot Branch with paper.md (empty if default branch): joss Version: v2.0.0 Editor: !--editor-->@zhubonan<!--end-editor-- Reviewers: @ziatdinovmax, @jagar2 Managing EiC: Kyle Niemeyer

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Thanks for submitting your paper to JOSS @ceds92. Currently, there isn't a JOSS editor assigned to your paper.

@ceds92 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).

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[editorialbot]

Wordcount for paper.md is 1074

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

OK DOIs

- 10.1088/2632-2153/ab42ec is OK
- 10.1021/acs.jpca.0c10731 is OK
- 10.1038/s42005-020-0317-3 is OK
- 10.5281/zenodo.7402665 is OK
- 10.1021/acsnano.8b02208 is OK

MISSING DOIs

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[editorialbot]

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

[kyleniemeyer]

@editorialbot set V2 as branch

[editorialbot]

Done! branch is now V2

[kyleniemeyer]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (192.2 files/s, 98737.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           5            719            442           2343
Markdown                         1             19              0             50
TOML                             1              2              0             21
-------------------------------------------------------------------------------
SUM:                             7            740            442           2414
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[kyleniemeyer]

@editorialbot set joss as branch

[editorialbot]

Done! branch is now joss

[kyleniemeyer]

@editorialbot invite @zhubonan as editor

Hi @zhubonan, could you edit this submission?

[editorialbot]

Invitation to edit this submission sent!

[zhubonan]

Thanks for the invitation @kyleniemeyer, happy to handle this one

[zhubonan]

@editorialbot assign @zhubonan as editor

[editorialbot]

Assigned! @zhubonan is now the editor

[zhubonan]

Hi @ceds92, thanks for the submission 🚀. I am wondering if you have any suggestions for the potential reviewers. I can see that the package requires installation of specific (propitiatory) software. Please do not directly @ any potential reviewer directly in the reply.

[ceds92]

Hey @zhubonan! Thanks for looking into this and apologies for my late reply - I've been away until now. I will look at this today/tomorrow and get back to you ASAP.

[ceds92]

Hi @zhubonan,

Testing this software requires Spec's Nanonis V5 which is a licensed product. Further, it may be challenging for reviewers to find time in their schedules to pause their research and test this software on a live system (STM). However, this Scanbot can be tested on the STM simulator V5 software provided by Specs here. All functionality except for Scanbot's control over the STM tip via the motors + camera feed can be tested using this simulator. For tracking the motion of the tip through the camera feed, I can upload a video recording of the STM tip moving, which can be used to replace the camera feed by running Scanbot in a 'demo' mode.

Some potential reviewers could be members of the following groups: Michael Crommie (UBC) Sarah Burke (UBC) Doug Bonn (UBC) Robert Wolkow (Alberta) Peter Liljeroth (Aalto) David Ecija (IMDEA) Willi Auwärter (TUM)

Let me know if there's anything else I can help with!

[zhubonan]

@ceds92 Great! Thanks for the suggestions.

[zhubonan]

Just a status update - I am still working on finding the referees.

[ceds92]

Thanks for the update, no worries!

[zhubonan]

@ceds92 Sorry for the delay. Unfortunately, I am still struggling to find reviewers. Could you please suggest more potential reviewers? Thanks PS, If you know any peers that are already on GitHub, usually they are more likely to respond.

[zhubonan]

Pinging @ceds92 - Please suggest some potential reviewers to help the pre-review process. Thanks a lot.

[ceds92]

Hi, apologies, I missed the your request for more potential reviewers!

Please try Peter Jacobson from University of Queensland. http://researchers.uq.edu.au/researcher/24423

[arfon]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

ampscan: A lightweight Python package for shape analysis of prosthetics and orthotics Submitting author: @JoshuaSteer Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @danasolav, @Kevin-Mattheus-Moerman Similarity score: 0.8229

Open Source Optical Coherence Tomography Software Submitting author: @spectralcode Handling editor: @arfon (Active) Reviewers: @jdavidli, @brandondube Similarity score: 0.8171

PiSCAT: A Python Package for Interferometric Scattering Microscopy Submitting author: @po60nani Handling editor: @emdupre (Active) Reviewers: @ziatdinovmax, @aquilesC Similarity score: 0.8109

InspectorCell: Finding Ground Truth in Multiplexed Microscopy Images Submitting author: @AndreGosselink Handling editor: @fboehm (Active) Reviewers: @suresh-lab, @cinnetcrash Similarity score: 0.8093

strucscan: A lightweight Python-based framework for high-throughput material simulation Submitting author: @thohamm Handling editor: @ppxasjsm (Active) Reviewers: @mturiansky, @wcwitt Similarity score: 0.8071

⚠️ 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 before considering asking the reviewers of these papers to review again for JOSS.

[arfon]

@zhubonan – this ☝️ list of similar papers might help when identifying possible reviewers for the paper (suggest starting with the past authors first).

[zhubonan]

Just an update - I have sent multiple review invitation but have not got any replies so far. Still looking..

[zhubonan]

Hi @AndreGosselink and @po60nani, would you be happy to review for this submission? If it is not in your area of expertise, could you please let me know you have any suggestions for the potential reviewers? Thanks.

[AndreGosselink]

Hi @zhubonan, as my expertise is outside this specific field, I must decline. The project looks well done, however!

Unfortunately, I cannot recommend alternative reviewers due to the rare use of scanning probe microscopy and reinforcement learning in biology.

Best

[po60nani]

Hello @zhubonan,

I appreciate the opportunity, but my expertise lies outside this field, so I respectfully decline.

I believe @ziatdinovmax could provide valuable assistance in this area.

Best regards,

[zhubonan]

Thanks for the suggestion @po60nani.

@ziatdinovmax is this work in your field of expertise? Your help is much appreciated.

[zhubonan]

Hi @emilikv, @ziatdinovmax would you be interested to review this JOSS submission? It is about automating scanning tunnelling microscope and help for things like tip preparation.

The manuscript can be viewed here 👉 View article proof on GitHub Software repository 👉 https://github.com/New-Horizons-SPM/scanbot The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

[ziatdinovmax]

Will be happy to review.

On Tue, Oct 24, 2023 at 7:37 AM Bonan Zhu @.***> wrote:

Hi @emilikv https://github.com/emilikv, @ziatdinovmax https://github.com/ziatdinovmax would you be interested to review this JOSS submission? It is about automating scanning tunnelling microscope and help for things like tip preparation.

The manuscript can be viewed here 👉 View article proof on GitHub https://github.com/openjournals/joss-papers/blob/joss.05432/joss.05432/10.21105.joss.05432.pdf Software repository 👉 https://github.com/New-Horizons-SPM/scanbot The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5432#issuecomment-1777037615, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIFIU23LDCCCY5DDQLSARV3YA6SATAVCNFSM6AAAAAAXUOUT3SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZXGAZTONRRGU . You are receiving this because you were mentioned.Message ID: @.***>

-- "Intelligence is the ability to adapt to change." - Stephen Hawking.

[zhubonan]

@editorialbot add @ziatdinovmax as reviewer

[editorialbot]

@ziatdinovmax added to the reviewers list!

[zhubonan]

@ziatdinovmax Thanks for agreeing to review. We are still one reviewer short. Do you know anyone who may be able to help review this package?

[ziatdinovmax]

@zhubonan - I recommend @jagar2 as a reviewer

[zhubonan]

Hi @jagar2 would you be interested to review this JOSS submission? It is about automating scanning tunnelling microscope and help for things like tip preparation.

The manuscript can be viewed here 👉 View article proof on GitHub Software repository 👉 https://github.com/New-Horizons-SPM/scanbot The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

[jagar2]

I would be, but I am not going to be able to get to it for the next 3 weeks. Is that okay?

---

Joshua C. Agar Assistant Professor, Department of Mechanical Engineering and Mechanics Drexel University Website: www.m3-learning.comhttp://www.m3-learning.com/ 3141 Chestnut Street Philadelphia, PA 19104 Phone: 203-919-2230 Email: @.**@.> Pronouns: he, him, his

[Text, logo Description automatically generated]

From: Bonan Zhu @.> Sent: Tuesday, October 31, 2023 10:29 PM To: openjournals/joss-reviews @.> Cc: Josh Agar @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: Scanbot: An STM Automation Bot (Issue #5432)

External.

Hi @jagar2https://github.com/jagar2 would you be interested to review this JOSS submission? It is about automating scanning tunnelling microscope and help for things like tip preparation.

The manuscript can be viewed here 👉 View article proof on GitHub Software repository 👉 https://github.com/New-Horizons-SPM/scanbot The JOSS reviewer policy and reviewer guideline for your reference 👉 Reviewer Guideline

Thanks!

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/5432#issuecomment-1788302650, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFRPV7EDRASGUOS3PVYFGYTYCGXXVAVCNFSM6AAAAAAXUOUT3SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOBYGMYDENRVGA. You are receiving this because you were mentioned.Message ID: @.**@.>>

[zhubonan]

@jagar2 Thanks that would be great! No problem if more time is needed. Would it be possible for you to give an ETA?

[ceds92]

Hi all,

@zhubonan thanks for sticking with this and finding reviewers, it is much appreciated! @jagar2 @ziatdinovmax, thanks for agreeing to review!!

Just a heads up... I have been doing some work on Scanbot over the few months since it was submitted. It has a GUI now which should make things easier when testing - this is available on the V3 branch. All core functionality is basically the same.

Also, given that STM time is generally precious, I've created ways to test Scanbot's functionality, without needing an STM, through introducing a demo mode (along with nanonis V5 simulator). For example, when tracking the motion of the STM tip in demo mode, the camera feed will be replaced by a recording of the tip moving. The other main example is when automated tip shaping is initiated, STM images of previously acquired tip imprints will be loaded from a pickled file instead of using images from the simulator.

The files for testing can be downloaded from this link. Just save and extract it in Scanbot's root directory.

If you have any questions, let me know!

Thanks!!

[zhubonan]

@editorialbot add @jagar2 as reviewer

[editorialbot]

@jagar2 added to the reviewers list!

[zhubonan]

Hi all,

@zhubonan thanks for sticking with this and finding reviewers, it is much appreciated! @jagar2 @ziatdinovmax, thanks for agreeing to review!!

Just a heads up... I have been doing some work on Scanbot over the few months since it was submitted. It has a GUI now which should make things easier when testing - this is available on the V3 branch. All core functionality is basically the same.

Also, given that STM time is generally precious, I've created ways to test Scanbot's functionality, without needing an STM, through introducing a demo mode (along with nanonis V5 simulator). For example, when tracking the motion of the STM tip in demo mode, the camera feed will be replaced by a recording of the tip moving. The other main example is when automated tip shaping is initiated, STM images of previously acquired tip imprints will be loaded from a pickled file instead of using images from the simulator.

The files for testing can be downloaded from this link. Just save and extract it in Scanbot's root directory.

If you have any questions, let me know!

Thanks!!

@ceds92 Thanks for the update. I think we can start the review.

[zhubonan]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6028.

[zhubonan]

Hi @kasasxav @jonatanalvelid @ianhi, would you be able to review this submission to JOSS? We need at least one more reviewer for this submission. Based on the reviewer record, you have background in microcopy automation and python. Please let me know. Thanks in advance!

[ianhi]

Am I correct in interpreting the below as saying that the free mimea substitutes for the nanonis V5?

Testing this software requires Spec's Nanonis V5 which is a licensed product. Further, it may be challenging for reviewers to find time in their schedules to pause their research and test this software on a live system (STM). However, this Scanbot can be tested on the STM simulator V5 software provided by Specs here. All functionality except for Scanbot's control over the STM tip via the motors + camera feed can be tested using this simulator.

I unfortunately have no experience with STM. That said if no one with expertise is available and it is possible to test without access to the licensed software/STM then I would be wiling to review. However, I would not be able to start until next week.