[REVIEW]: SpmImage Tycoon: Organize and analyze scanning probe microscopy data

[editorialbot]

Submitting author: @alexriss (Alexander Riss)
Repository: https://github.com/alexriss/SpmImageTycoon.jl
Branch with paper.md (empty if default branch):
Version: v0.3.8
Editor: @jgostick
Reviewers: @jingpengw, @kasasxav
Archive: 10.5281/zenodo.7038825

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Reviewer instructions & questions

@xaviercm94 & @jingpengw, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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Checklists

📝 Checklist for @jingpengw

📝 Checklist for @kasasxav

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Software report:

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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 497

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.2478/s11534-011-0096-2 is OK
- 10.1063/1.2432410 is OK
- 10.1016/j.softx.2016.04.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jgostick]

@editorialbot add @kasasxav as reviewer

[editorialbot]

@kasasxav added to the reviewers list!

[jgostick]

@editorialbot remove @xaviercm94 as reviewer

[editorialbot]

@xaviercm94 removed from the reviewers list!

[xiuliren]

Review checklist for @jingpengw

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/alexriss/SpmImageTycoon.jl?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@alexriss) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[xiuliren]

@jgostick I have checked the list, is the review done?
I have installed the software and played with it. It runs smoothly.

[xcasas]

Review checklist for @kasasxav

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/alexriss/SpmImageTycoon.jl?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@alexriss) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[xcasas]

Hi @alexriss,

I am still going through the review process, looks good so far! But there are a few requirements that you are missing:

In the documentation,

• Statement of need: you do write that SpmImage Tycoon is a "Cross-platform app to manage and edit scanning probe microscopy (SPM) images and spectra", but it would be nice if you provide more information about what problems it can solve or features it has. I know you have included that in the paper, but I think it would help if you have something similar in Github too.

• Community guidelines: there is no information about what are the guidelines for people that want to contribute to your software.

• I also miss documentation regarding the tests, how to run them and what do they cover?

• I see the scripts are commented, but I can't find a general documentation of the API. I am not sure if this is necessary so I leave it as a suggestion.

Regarding the paper,

• Statement of the field is missing, what are the available software packages in the field of scanning probe microscopy image analysis, and how does your solution compare to them?

• Just two small typos:
  line 11 -> into a OpenDocument -> into an OpenDocument
  line 34 -> stored in a HDF5 -> stored in an HDF5

• Would be nice to develop more in some areas:
  line 18-19: "However, much less emphasis has been placed on improving the managing and organization of the measured datasets". Here you can develop in which work has been done.
  line 37: "Due to its modular design, new features can be simply added". How can one add new features?

• And one suggestion. You mention the included features in the summary, but you could also explain more them more in detail so the reader can fully capture the potential of your software. Maybe you could even include a figure.

[xcasas]

Hi again,

I am going through the videos and I installed the software, I was wondering if there is a dataset I could use for trying out the functionality?
Maybe it would be nice to provide it in general for the users, but otherwise do you know of any publicly available data?

[alexriss]

HI - thank you very much for your efforts. I will go through your comments soon. I just wanted to mention that the app is geared towards "end users", i.e. people interacting via the GUI. Thus, I prefer to keep the docs simple. This is the reason that there is no documentation on the API. However, the libraries used by this app are released separately (SpmImages.jl, SpmSpectroscopy.jl) and more information can be found on the respective github repositories.

Regarding the tests, you can run them via julia> ] (to change into the pkg manager and then pkg> test SpmImageTycoon. They cover most function of the software and are run automatically via github actions. Again, I would prefer to not specifically mention this procedure in the docs because it should not be necessary for the end users to run these tests (they might even be overwhelmed by the instructions). And the more "julia-savy" probably already know how to run them if needed (this is pretty much standard practice for julia packages).

But if required, I can of course add this information.

There is a test dataset here:
https://github.com/alexriss/SpmImageTycoon.jl/tree/main/test/data
It is used for the automated tests., too.

Thanks again!

[xcasas]

Hi @alexriss,

Thank you! Thank you for the explanations and test data, looks good then!

I also tried the software and followed the videos in youtube to check that the functionality was working, and everything was fine. The software presented, as I understand, is for users of SPM and similar techniques that wish to browse and analyze their images. There is a list of shortcuts easily accessible that I count as documentation, and one can easily browse and adjust the image contrast, trace line profiles to the data, etc. The software is very intuitive and easy to use, I think it would make an impact and help users navigate and organize their data. Furthermore, the images contain metadata that one can access, filter and copy.

My only concern is, if a developer wants to implement let's say an image processing algorithm into your software, how would they do it? or add new fields into the metadata? I think that would be useful to implement/document and facilitate the project to grow. For example, performing some kind of transformation to the data or filtering (smoothing or others). I understand though that's not the focus of your project since it's targetted to end users, but not having certain functionality could prevent users from using the software. Maybe some users have expertise to contribute or other people in their groups that can help out with programming. I am not so familiar with SPM though so I don't know if that would be a common situation, but I could imagine this happening in other microscopy modalities. I am also not that familiar with Julia so I don't actually know if implementing new functionality would be hard. Could you maybe list the steps that would be required for that?

Thank you!

/Xavier.

[xcasas]

P.S. I would suggest to have the link to the metadata in the main repo or a possibility to browse through it from the main software. Then users can see the potential of the software even if they don't have available images

[alexriss]

To address your comments, I have now updated the paper and the project README.md, on github. Furthermore, I added a CODE_OF_CONDUCT.md and CONTRIBUTING.md.

A point-by-point response to your comments follows.

Regarding the project documentation:

• I expanded the feature list in the project documentation, see https://github.com/alexriss/SpmImageTycoon.jl#features (it is more detailed than in the paper)
• Added more detailed description of the files and how to contribute to the project.
• As outlined above, no particular changes on how to run the tests - but I added a link to the test dataset.
• As outlined above, there is no explicit documentation of the API in this project - but I have added a description of where to find the files for the HTML/CSS/JavaScript frontend, as well as for the Julia backend.

Regarding the paper:

• I have expanded the "statement of need" and now list other processing/analysis tools and typical data organization workflows - which I hope this app improves.
• corrected the typos - thank you!
• more details on the improvement of the workflows are given (see above); reformulated the sentence on addition of new features (more explanation is given below).
• I would prefer to not add a screenshot to the paper. The app is still being developed and I plan to add a menu and improve the navigation more, and I would like to avoid having outdated screenshots in a paper that will be available for many years to come. Of course there are screenshots and videos in the project documentation - potential users will hopefully always look at the project website - and I can keep these up-to-date.

Regarding contributions from other people, I have added a few sections to the project documentation. However, it is not completely easy: there is a Julia backend and a HTML/CSS/JavaScript (via Electron) frontend. And of course these need to communicate. So for most new features, coders will need to adapt both, the backend and the frontend. And for this, contributors will have to "dive" into the code to some extent. The best starting point is probably to get in touch with me.

However, for image or spectrum filters, I am planning to add an interface, in which users can stack mathematical operations (e.g. Laplace, Gauss filters). This would be very flexible and hopefully accessible to end users. And there could even be a plugin interface. But this is more of a long-term project...

Thanks again for all your efforts. I am very happy to hear that you found the software easy to use - this was one of my main design goals!

[xcasas]

Hi!

Great! It looks good for me. I have checked the review points that were missing.

Just check that the new sentence you added in the paper is not gramatically complete: "but filesystem folders and manually created lists of best measurements for organization of the data" needs a verb.

I also think you can expand it a bit more. From the cited works I have only worked with ImageJ. I think there is a clear difference between SpmImage Tycoon and ImageJ. While ImageJ focuses on the processing and analysis of the images, tycoon is more about the organization of them, the accessibility of the metadata and the fact that you can explore easily within a folder and correct multiple images together, for example. So I would say expanding on that would definitely be interesting. For example, if you have a folder with 100 images and you need to browse through them and apply some basic operations easily, intuitively and quickly, I think that would become challenging with ImageJ. And most likely you find similar reasons for the other software packages, I think describing that in your paper would be helpful.

I think the image filtering idea would be really nice! You could even have a generic function that people can reimplement with the desired operation, with an input and output image. I don't know if it could be some kind of "superclass" that then you can create "subclasses" of it, so that all the links with the backend are already implemented in the "superclass" (sorry for my lack of Julia knowledge). I don't see this as a requirement for the revision, though.

I also added an issue that @alexriss solved: alexriss/SpmImageTycoon.jl#11

[alexriss]

Hi - thanks again. Yes, exactly, these apps are focused on processing and analysis, but they aren't really geared as much towards browsing and organization - and with that batch editing of course gets harder. I have seen plenty of scanning probe users' workflows and many of them really just create lists of their best data, or copy the best files into some directory, or they keep browsing through all images every time to find the best images/spectra. I wanted to improve the efficiency of these workflows, this is why I started this project in the first place. And I think this is now more clearly outlined in the paper: the other apps are great for editing/analysis, but tycoon's focus is more on organization and management - with some editing (also batch editing) and analysis features baked in, and more to come - hopefully with a new type of filter or plugin system at some point.

[alexriss]

@editorialbot generate pdf

[editorialbot]

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

[xcasas]

All good from my side ! @jgostick

[jgostick]

Alright, great job @kasasxav and @jingpengw! Thanks so much for your time and energy, which I know is a valuable and limited resource.

@alexriss, congrats, I will recommend this paper to be published! But first there are a few more items to check off:

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

Editor Tasks Prior to Acceptance

• Set article DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Do a 'dry run' of acceptance with @editorialbot recommend-accept

[jgostick]

@editorialbot set 10.5281/zenodo.7038825 as archive

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[jgostick]

@editorialbot recommend-accept

[editorialbot]

Paper is not ready for acceptance yet, the archive is missing

[jgostick]

@editorialbot set 10.5281/zenodo.7038825 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7038825

[jgostick]

@editorialbot set 10.5281/zenodo.7038825 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7038825

[jgostick]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.2478/s11534-011-0096-2 is OK
- 10.1063/1.2432410 is OK
- 10.1016/j.softx.2016.04.001 is OK
- 10.1038/nmeth.2089 is OK
- 10.1186/s12859-017-1934-z is OK
- 10.1038/nmeth.2019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3490, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[alexriss]

@editorialbot accept

[editorialbot]

I'm sorry @alexriss, I'm afraid I can't do that. That's something only eics are allowed to do.

[alexriss]

... it seems ok to me!

[jgostick]

The editor in chief always spots a few things that I missed, so they'll do the final acceptance next tiem they're free.

[arfon]

@editorialbot accept

The editor in chief always spots a few things that I missed, so they'll do the final acceptance next tiem they're free.

Not this time @jgostick. Looks good to me!

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04644 joss-papers#3501
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04644
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@jingpengw, @kasasxav – many thanks for your reviews here and to @jgostick for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@alexriss – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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