[REVIEW]: Reorient: A Web tool for reorienting and cropping MRI data.

[whedon]

Submitting author: @katjaq (Katja Heuer) Repository: https://github.com/neuroanatomy/reorient Version: v1.0.0 Editor: @oliviaguest Reviewer: @sneakers-the-rat, @pauldmccarthy Archive: 10.5281/zenodo.4165153

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Review checklist for @sneakers-the-rat

Conflict of interest

• [x] 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

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

General checks

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

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

Review checklist for @pauldmccarthy

Conflict of interest

• [x] 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

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

General checks

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

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sneakers-the-rat, @pauldmccarthy it looks like you're currently assigned to review this paper :tada:.

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[whedon]

PDF failed to compile for issue #2670 with the following error:

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[oliviaguest]

Hi all! 👋 Thank you so much, @sneakers-the-rat, @pauldmccarthy for accepting to review this. Please read the instructions above. Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread so we can all keep track of them. 🌸

For an example of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

[oliviaguest]

@whedon generate pdf from branch joss-paper-branch

[whedon]

Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...

[whedon]

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

[oliviaguest]

@whedon generate pdf from branch joss-paper-branch

[whedon]

Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...

[whedon]

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

[oliviaguest]

Hey @sneakers-the-rat, @pauldmccarthy — could you please let us know when your reviews might be ready by?

[pauldmccarthy]

Hi @oliviaguest, I'm aiming to complete my review in the next 7 days.

[oliviaguest]

@whedon remind @pauldmccarthy in 2 weeks

[whedon]

Reminder set for @pauldmccarthy in 2 weeks

[sneakers-the-rat]

yes give me the same - setting reminder for 10/7

[oliviaguest]

@whedon remind @sneakers-the-rat in 2 weeks

[whedon]

Reminder set for @sneakers-the-rat in 2 weeks

[oliviaguest]

@sneakers-the-rat you got it! ✨

[sneakers-the-rat]

may need an extra day or two but i am with ya

[sneakers-the-rat]

nvm just finished <3

loved it! very straightforward to review, tool worked as expected and was quite intuitive. I made a few suggestions (wasn't sure where to put them) and raised a few issues but nothing that would prevent me from accepting the paper according to the checklist & claims in the paper.

Olivia let me know if i've messed anything up/need to do anything further. Katja & Roberto, thanks for this tool!

[oliviaguest]

@sneakers-the-rat Amazing! Can you do me a favour and move what you wrote into a comment in the issue as opposed to into the OP? I'd prefer it if everything to-be-addressed was a comment here to make it easier to keep track of. ☺️

[oliviaguest]

PS: @sneakers-the-rat if you need examples/inspiration, check: #2285 and #2348. 🌼

[sneakers-the-rat]

gotcha, will clean up op in 1 sec. only copying things here where i've made a comment

tbc none of these are comments that i think are worthy of holding up the manuscript, very little touches that don't get in the way of the central function of the program

General checks

• [x] Contribution and authorship: Has the submitting author (@katjaq) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Can't get the contribution metrics to load, though I have no reason to doubt the author's contribution & wouldn't want to punish them for github being glitchy.

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
  • the software is a static page hosted on github and thus doesn't require installation.
  • I was also able to open the page locally with the npm http-server without issue.
• [x] Functionality: Have the functional claims of the software been confirmed?

Functional claims from manuscript:

• [x] data dragged onto web interface
• [x] translate and rotate by dragging in interface
• [x] selection box to crop image
• [x] save affine matrix
• [x] save selection box
• [x] save reoriented and cropped volume
• [x] existing rotation matrices loaded
• [x] append to existing rotation matrices
  • i'm not entirely sure what it means to append an affine matrix, so i'm not sure what i should be expecting when i click it, but something happens that hopefully makes sense to the authors.

Potential bugs question mark?

• Fails without notification for image in MNI space -- since there is no description in manuscript of supported/unsupported formats/filetypes/etc. I don't consider it a bug for the purposes of the review, but that would be a good thing to document & failures like this should give some indication to the user even if the format isn't supported. raised issue at https://github.com/neuroanatomy/reorient/issues/6

ux feedback/"would be nice" recommendations:

• strongly recommend adding progress bars when loading/saving images - the page becomes unresponsive while loading/saving and it wasn't clear to me if the page had crashed or if i just needed to keep waiting.

• an additional set of handles for translation/rotation in addition to dragging. the current handles seem to move the image in the direction normal to the plane, but it would be nice to be able to do the 'dragging' controls with handles for when eg. the rotation doesn't behave exactly as expected.

• 'reset selection box' button

• 'load new nifti' button rather than having to refresh

• would be nice to export matrix in different formats like csv, npy, etc. (unless this .mat format is universal across libraries, which i don't know)

• display metadata of file, mostly in order to give some sense of scale to the matrix/crop box but also to keep track of what file you're working on if you're working on a bunch of similar-looking images

• keep filename when saving, perhaps appending _reoriented rather than always defaulting to just reoriented.nii.gz for the same reason as ^^

• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

  • [x] reorientation matrix and selection box can be obtained in 1m for a typical brain -- didn't time, but i think this is a reasonable statement. tested with dolphin brain: https://braincatalogue.org/Bottlenose_dolphin , 1GB human scan: https://datadryad.org/stash/downloads/file_stream/223922 , both worked, 1GB was a bit sluggish but still useable. I was unable to get an 8GB scan (https://datadryad.org/stash/downloads/file_stream/223921) to load, and without progress bar or error message I couldn't tell why - raised issue https://github.com/neuroanatomy/reorient/issues/7. Since I'm not sure if that high-res scan is a 'typical brain' I'll still count this as passing.

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?

  • yes and love it!!

• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

  • web tool, no installation.

• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

  • the docs essentially function like an example as they document a typical workflow.

• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

  • source/methods/functions don't seem to be intended for direct access by the user, so considering 'API' to be the user interface.
  • the program is relatively simple and i was able to figure out how to use it without too much guidance, i actually didn't find the documentation until i was almost finished with the review, so i think the docs should be put in the README of the repository (or another .md file if you'd rather) or else be linked to from there. I consider the core functionality reasonably documented, but there are some minor things that could do with additional documentation:
    • this may be a personal ignorance thing, but i can't really figure out what it means to append affine matrices, may be good to document
    • what the displayed matrices are, eg. i'm not sure what 'world to voxel' vs. 'voxel to world' means
    • what the format of the generated files are: are the reorient.mat and selection.txt standard file formats? what are each of the numbers in them? I get that they're an affine transformation matrix & crop box but would be good to document the format. additional details on the output image file (or even just saying that the image is unmodified except for transformation/cropping) would also be useful.
    • what the anatomical axes are: i was able to figure out the orientations of the panels, but it would be good to explicitly document what the axes are as well as what the displayed values in the top right of each panel (eg. LR: -10 in the screenshot in the README) are.
    • what file/image formats are supported

• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

  • the mocha tests pass:

    Test Reorient
    Unit tests
    eye()
    ✓ should return identity matrix
    alpha(π/2)
    ✓ should return a 90 deg X rotation matrix
    beta(π/2)
    ✓ should return a 90 deg Y rotation matrix
    gamma(π/2)
    ✓ should return a 90 deg Z rotation matrix
    matrix2str
    ✓ should return a string representation of a matrix
    End to end tests
    Load a file
    ✓ should display title
    ✓ should display "Choose..." message
    ✓ init with test nifti file (672ms)
    ✓ has the expected dimensions (107ms)
    ✓ has the expected datatype
    ✓ can rotate the image (135ms)
    ✓ can translate the image (96ms)   
    12 passing (2s)

  • I can't get istanbul/nyc to give me code coverage, i can't access the circleci report, and locally running circleci fails because sandboxing is not configured explicitly in the config.yml and chromium fails to launch. not sure if there are code coverage requirements for JOSS or just the existance of CI, but can't verify coverage. tests are a little barebones (eg. tests with single hardcoded values from example image file rather than programmatically generated tests/stress tests) but they are there and seem to test what they purport to.
  • the npm package is slightly malformed, but it's not a huge problem. is there a reason why mocha is specified separately in the .circleci/config.yml file rather than in the package.json dependencies? The http-server should be started by the npm test command rather than separately if it's required for the tests to work, would recommend something like

    "scripts": {
    "test": "http-server . & sleep 2 && mocha --exit"
    },

• [x] 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

  • uses the mozilla community participation guidelines <3
  • refers users to submit issues & message on twitter which seems appropriate.
  • lack of API-level documentation makes it sorta unclear to me how i would go about contributing, but I think that's fine for this project -- the source is reasonably clear and names are clear enough that I think I could find what was looking for.

Software paper

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • yes and i still love it!
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • comparison made to automated atlas registration -> need for tool. can't tell if there are other tools like this but doesn't matter for this project.

[oliviaguest]

@sneakers-the-rat perfect! @katjaq let us know when you have checked these out and addressed them. ☺️

[oliviaguest]

@pauldmccarthy was this just one you missed out on accidentally?

State of the field: Do the authors describe how this software compares to other commonly-used packages?

[pauldmccarthy]

@oliviaguest, No, I wanted to re-read the article/docs before signing off on everything - planning to finish it off tonight!

[oliviaguest]

@whedon generate pdf from branch joss-paper-branch

[whedon]

Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...

[whedon]

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

[pauldmccarthy]

Apart from a few minor issues and suggestions (listed below), I think this is a really neat piece of work!

There is just one point made in the manuscript which I would like clarification on:

The affine matrix and selection box can be used later within a scripted workflow

I couldn't find any further mention of this point in the manuscript, nor in the source repository or app help. I presume the intent is that other tools (e.g. fslroi, flirt, etc - highlighting my bias towards FSL there) would be used for using the outputs in a scripted workflow?

I'm not necessarily requesting any changes to the manuscript or tool documentation, but it was just something which stood out to me, and which I wasn't sure what to make of, so was hoping for this point to be clarified.

Thanks!

• neuroanatomy/reorient#3
• neuroanatomy/reorient#4
• neuroanatomy/reorient#8
• neuroanatomy/reorient#9

[pauldmccarthy]

[addendum, after looking at the extremely comprehensive review by @sneakers-the-rat] indeed, it may be worth adding an overview somewhere in the help documentation (I don't think this belongs in the manuscript) about how to use the selection box/affine files "off-line", i.e. outside of the reorient web interface, in an automated pipeline.

Unfortunately there are substantial differences across the different neuroimaging packages in the ways that files/information such as these are applied. I suppose the assumption is that if a user wished to use these outputs in their own workflow, they would know how to apply them using their tools of choice, which is fair enough. But I feel that, given that it is mentioned in the manuscript, it probably should be mentioned, if only briefly, somewhere in the documentation :)

[oliviaguest]

@sneakers-the-rat, @pauldmccarthy thank you both so much! Your reviews look very detailed and useful. Please, @katjaq tag me when you have had a chance to discuss and address these. ☺️

[r03ert0]

hello! quick update. We've pushed several commits to address the issues left by @sneakers-the-rat and @pauldmccarthy. There's in particular a python script (reorient.py) which can take the original MRI file, plus the affine matrix and the selection box produced by the Web app, and reproduce the result of "Save Nifti" from the interface (so that there's no need for the Web app for just re-running the process automatically). We still want to update the doc to take into account some of your comments, and then will draft a detailed answer :)

[oliviaguest]

@r03ert0 excellent — sounds like you have your work all planned out. ✨

[oliviaguest]

👋 @katjaq @r03ert0 👋

Just a little bump for this review thread: is everything going OK?

[katjaq]

Hello :)

A huge thank you to the reviewers for their amazing detailed reviews. We addressed all of the points mentioned, implemented the suggested add ons, and included more info in the doc as well as a pointer to the doc in the Readme. Please find the detailed answers to each issue below.

Q: "append to existing rotation matrices i'm not entirely sure what it means to append an affine matrix, so i'm not sure what i should be expecting when i click it, but something happens that hopefully makes sense to the authors." A: Each MRI volume has its own affine matrix. The options are to change original_matrix into loaded_matrix, or original_matrix into original_matrix*loaded_matrix. This information was added to the doc.

Q: "Fails without notification for image in MNI space -- since there is no description in manuscript of supported/unsupported formats/filetypes/etc. I don't consider it a bug for the purposes of the review, but that would be a good thing to document & failures like this should give some indication to the user even if the format isn't supported. raised issue at neuroanatomy/reorient#6" A: Accepted file formats are now checked, and an alert displayed in case of incorrect format. Additionally, why added the possibility of reading uncompressed nii files in addition to nii.gz (Commit e2e6eb9)

Q: "strongly recommend adding progress bars when loading/saving images - the page becomes unresponsive while loading/saving and it wasn't clear to me if the page had crashed or if i just needed to keep waiting." A: We added a message to show uploading, and better error message in case of failure (commit 7ad208f)

Q: "an additional set of handles for translation/rotation in addition to dragging. the current handles seem to move the image in the direction normal to the plane, but it would be nice to be able to do the 'dragging' controls with handles for when eg. the rotation doesn't behave exactly as expected." A: Translation handles would be a good idea, but we haven't found a way of making a good controller for that. The traditional way of doing translation is by clicking on the center of the selection box and dragging. However, in our experience it happened that we could translate instead of move a single side by mistake, which then requires to re-adjust the whole selection. Our current approach may take a bit longer, but it's always safer... Concerning Rotation handles, our focus is currently to align the MRI to the orthogonal anterior-posterior/left-right/superior-inferior axes. A general tool for reorienting with arbitrary directions could be useful in some other contexts, however.

Q: "'reset selection box' button" A: added in commit d9e5fd7

Q: 'load new nifti' button rather than having to refresh" A: We discussed this at length. It would be very simple to add, but we actually prefer the reload, and having one button less in the interface. However, we do explicitly state in the documentation now that a "reload" is requited for working with a new MRI. (commit c6f8ec9)

Q: "would be nice to export matrix in different formats like csv, npy, etc. (unless this .mat format is universal across libraries, which i don't know)" A: The .mat format is widely used in neuroimaging. It is actually just a text file with four rows of 4 numbers separated by spaces, and can be easily read using python or other languages. We included a python script for reproducing a reorientation offline (reorient.py, commit 6083a41). This info is added now to the doc as well.

Q: "display metadata of file, mostly in order to give some sense of scale to the matrix/crop box but also to keep track of what file you're working on if you're working on a bunch of similar-looking images" A: We now display the file name on top of the MRI viewers.

Q: "keep filename when saving, perhaps appending _reoriented rather than always defaulting to just reoriented.nii.gz for the same reason as ^^" A: This could be a feature, or a bug... In our case, we keep subject ID only in the directory name, and all files inside that directory have standard names (t2.nii.gz, dwi.nii.gz, etc). We like it because scripts look cleaner. Adding the filename to the reorient.mat or selection.txt files would force us to manually remove the file name every time... It's true that some people may have the opposite approach, and will have to manually add the names... we took a selfish decision...

Q: "reorientation matrix and selection box can be obtained in 1m for a typical brain" A: Typical MRI file sizes go from ~10 MB to about 100 MB. In animal MRI sometimes file sizes are larger, and we do have some files which are 300 MB. We haven't tried with larger files, and it is a nice surprise to know that the browser didn't break for 1GB . In case of a loading failure, we now check if the file is too large, and provide that information as feedback to the user (commit 7ad208f).

Q: " i think the docs should be put in the README" A: We added a link to the documentation to the Readme file. Users do not need to go to the github repo to use the tool, so they may never see the README file there. The "?" tab in the tool links to the documentation from the tool :)

Q: "what the displayed matrices are, eg. i'm not sure what 'world to voxel' vs. 'voxel to world' means" A: This is the standard way of naming in neuroimaging a matrix that would convert voxel indices (integer numbers starting from 0) into millimeters : that's the voxel_to_world. The world_to_voxel matrix does the inverse: it takes a coordinate in millimeters from real (world) space into voxel indices. Because world coordinates can be anything, they may not map inside the voxel volume, in which case the voxel index coordinates would be either negative, or larger than the volume dimensions (in voxels). This information is now also included in the doc.

Q: "what the format of the generated files are: are the reorient.mat and selection.txt standard file formats?" A: The .mat format is standard (although it is just a text file). The selection.txt format is not. The first row in the selection format represents the coordinates of the "minimum" corner, the second row the coordinates of the "maximum" corner. We now provide a python script that can take the source MRI, the reorient.mat file, and the selection.txt file to produce the reoriented volume (commit 6083a41). This info has also been added to the doc.

Q: "what the anatomical axes are:" A: LR is left/right, AP is anterior/posterior, SI is superior/inferior.

Q: "is there a reason why mocha is specified separately" A: Not really... but we added now the "test" call to the npm package as suggested.

Q: "lack of API-level documentation" A: We used jsdoc-style comments which could allow us to generate an API documentation.

Q: "The affine matrix and selection box can be used later within a scripted workflow" A: reorient.py script added (commit 6083a41). We also added an offline workflow description to the doc.

Q: it may be worth adding an overview somewhere in the help documentation (I don't think this belongs in the manuscript) about how to use the selection box/affine files "off-line", i.e. outside of the reorient web interface, in an automated pipeline. A: We added a "Reproduce the workflow offline" entry in the doc.

Finally, we addressed some other issues that had been directly added in reorient's repo. In particular, @pauldmccarthy had found a bug in our data display that was evident when the volumes were very small (-> voxels very big). We fixed the issue, and tested the interface extensively: https://github.com/neuroanatomy/reorient/issues/4

Thank you very much again for reviewing our tool! Katja & Roberto

[oliviaguest]

@whedon generate pdf from branch joss-paper-branch

[whedon]

Attempting PDF compilation from custom branch joss-paper-branch. Reticulating splines etc...

[whedon]

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

[oliviaguest]

@katjaq @r03ert0 can you deposit the code on zenodo or similar and post the DOI here, please?

[oliviaguest]

@katjaq @r03ert0 Has neuroanatomy/reorient/issues/9 been addressed? Can you close if so.

[katjaq]

Hello, issue #9 has bee addressed and is now closed. Thanks.

The code is deposited on Zenodo under DOI 010.5281/zenodo.4165153

Thank you!

[oliviaguest]

@whedon set 010.5281/zenodo.4165153 as archive

[whedon]

010.5281/zenodo.4165153 doesn't look like an archive DOI.

[oliviaguest]

@whedon set 10.5281/zenodo.4165153 as archive

[whedon]

OK. 10.5281/zenodo.4165153 is the archive.

[oliviaguest]

@katjaq @r03ert0 great! can you also change the title of the zenodo repo to the same as the JOSS paper, please? ☺️

Oh, and is the version number at the top correct? If not, what's the current version?

[r03ert0]

Done! I updated the title to match that of the paper. The DOI which appears in the Zenodo badge in reorient's repo is automatically set to the one of the latest version (10.5281/zenodo.4165154). The DOI Katja sent is the umbrella DOI for all versions (10.5281/zenodo.4165153). It's better to use that one, no?

[oliviaguest]

@katjaq @r03ert0 I mean this version here in the OP, get me?

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...