Closed editorialbot closed 2 years ago
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Software report:
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Wordcount for paper.md
is 497
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot add @kasasxav as reviewer
@kasasxav added to the reviewers list!
@editorialbot remove @xaviercm94 as reviewer
@xaviercm94 removed from the reviewers list!
@jgostick I have checked the list, is the review done? I have installed the software and played with it. It runs smoothly.
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.
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?
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!
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.
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
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:
Regarding the paper:
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!
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: https://github.com/alexriss/SpmImageTycoon.jl/issues/11
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.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
All good from my side ! @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:
@editorialbot set <DOI here> as archive
@editorialbot set <version here> as version
@editorialbot generate pdf
@editorialbot check references
and ask author(s) to update as needed@editorialbot recommend-accept
@editorialbot check references
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
@jgostick Thanks a lot!
The latest version is: 0.3.8
Zenodo DOI: https://doi.org/10.5281/zenodo.7038825
And thanks a lot to @kasasxav and @jingpengw for your efforts and the help, highly appreciated!
thank you @alexriss and good luck with SpmImage Tycoon ! Thank you @jgostick for the opportunity!
@editorialbot set v0.3.8 as version
Done! version is now v0.3.8
@editorialbot set 10.5281/zenodo.7038825 as archive
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@editorialbot commands
@editorialbot recommend-accept
Paper is not ready for acceptance yet, the archive is missing
@editorialbot set 10.5281/zenodo.7038825 as archive
Done! Archive is now 10.5281/zenodo.7038825
@editorialbot set 10.5281/zenodo.7038825 as archive
Done! Archive is now 10.5281/zenodo.7038825
@editorialbot recommend-accept
Attempting dry run of processing paper acceptance...
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
:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof :point_right::page_facing_up: Download article
If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3490, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
@editorialbot accept
I'm sorry @alexriss, I'm afraid I can't do that. That's something only eics are allowed to do.
... it seems ok to me!
The editor in chief always spots a few things that I missed, so they'll do the final acceptance next tiem they're free.
@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!
Doing it live! Attempting automated processing of paper acceptance...
π¦π¦π¦ π Tweet for this paper π π¦π¦π¦
Submitting author: !--author-handle-->@alexriss<!--end-author-handle-- (Alexander Riss) Repository: https://github.com/alexriss/SpmImageTycoon.jl Branch with paper.md (empty if default branch): Version: v0.3.8 Editor: !--editor-->@jgostick<!--end-editor-- Reviewers: @jingpengw, @kasasxav Archive: 10.5281/zenodo.7038825
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