[PRE REVIEW]: Thresholdmann: A Web tool for interactively creating adaptive thresholds to segment MRI data.

[editorialbot]

Submitting author: !--author-handle-->@katjaq<!--end-author-handle-- (Katja Heuer) Repository: https://github.com/neuroanatomy/thresholdmann Branch with paper.md (empty if default branch): joss-paper-branch Version: v1.1.0 Editor: !--editor-->@adamltyson<!--end-editor-- Reviewers: @sneakers-the-rat, @62442katieb, @anibalsolon Managing EiC: Kevin M. Moerman

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

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[editorialbot]

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

OK DOIs

- 10.1016/j.cortex.2019.04.011 is OK
- 10.1038/s42003-023-05553-z is OK
- 10.3897/rio.2.e9113 is OK
- 10.21105/joss.02670 is OK
- 10.1016/j.neuroimage.2006.01.015 is OK
- 10.1016/j.neuron.2019.12.023 is OK
- 10.1016/j.neuron.2021.10.015 is OK
- 10.1016/j.neuroimage.2020.117519 is OK
- 10.5281/ZENODO.3402456 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (482.7 files/s, 192636.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             2              0              0           7232
JavaScript                       8            415            160           2476
HTML                             3             43             13            426
CSS                              1              8              3            285
SVG                              7              3              3            207
TeX                              1              9              0            109
Markdown                         5             42              0            102
YAML                             2              1              4             33
-------------------------------------------------------------------------------
SUM:                            29            521            183          10870
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1109

[editorialbot]

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

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@katjaq thanks for this submission. I am the AEiC on this track and here to help with initial steps.

For the moment I am trying to determine if this work is in scope for JOSS. Could you help clarify if the above software report is accurate :point_up:. Would it be correct to say that your creative contribution is captures by the 2476 lines of JavaScript? If so would you say all of that is your work or is some of it content from other libraries or auto-generated?

[katjaq]

Hi @Kevin-Mattheus-Moerman . Thank you very much for your message.

Yes, the code inspection looks about correct. Our creative contribution includes 2816 lines of Javascript. This combines the code directly included within the Thresholdmann repo, as well as code that we wrote, but include here as a module we call from jsdelivr.

Within our Thresholdmann repo, all code except for one file is exclusively our contribution:

• thresholdmann.js : 829 lines
• worker.js : 88 lines
• test.mjs : 144 lines
• render3D/index.js : 113 lines
• surfacenets.worker.js : about 20 lines from 151 are from us, and some adaptations

The code we wrote and include here in form of modules includes

• mui.js : 250 lines
• mriviewer.js : 831 lines, which are both called from Thresholdmann/index.html, and
• mri.js : 541 lines, called from mriviewer.js.

So, 829+88+144+113+20+250+541+831 = 2816 lines our contribution. plus 284 lines in our eslint config file which we wrote to enforce our coding style (across all our code). But we didn't count that here as we are not sure how you consider eslint :)

Thresholdmann css and html are also important for the functioning of our GUI. Together with the documentation html, they add up to additional 778 lines of original contribution.

Thank you for your consideration.

[katjaq]

For potential reviewers, we checked the JOSS list, and thought that Katie Bottenhorn (62442katieb), Anibal Sólon (anibalsolon) and Jonny Saunders (sneakers-the-rat) could be potential great reviewers. :)

[r03ert0]

hi @Kevin-Mattheus-Moerman, did you reach a conclusion on whether our work fulfils the criteria for JOSS?

[Kevin-Mattheus-Moerman]

@editorialbot invite @emdupre as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@r03ert0 @katjaq apologies for the delay. I have started looking for a handling editor.

[emdupre]

Hi @Kevin-Mattheus-Moerman, thanks for the invitation !

Just to be transparent : I've coauthored with both the first and senior author for this submission on this 2021 paper , which would qualify under the COI policy. Although I had worked closely with these authors in a volunteer committee through 2020, we have had no formal or informal affiliation since.

[Kevin-Mattheus-Moerman]

@emdupre those would quality as potential/perceived COIs so I'll have to recruit an alternative editor. Thanks for reporting that.

[katjaq]

Hello @Kevin-Mattheus-Moerman ,

Would it help if we suggest possible editors? Maybe Olivia Guest would be available for having a look? Thank you for your help in moving this forward.

Best, Katja & Roberto

[Kevin-Mattheus-Moerman]

@katjaq thanks for your message. Unfortunately you can't help here. I'm aware of the potentially suitable editors but unfortunately they are all busy handling other submissions. We will assign an editor once one becomes available. We are also recruiting new editors at the moment who may be able to help. I hope we'll be able to assign an editor within 2 weeks.

[katjaq]

I see 😰
Thank you :)

[Kevin-Mattheus-Moerman]

@editorialbot invite @adamltyson as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@katjaq I have just invited @adamltyson, a newly recruited editor, however, I believe they may be out of the office for 2 weeks.

[adamltyson]

Hi @Kevin-Mattheus-Moerman,

Happy to take this on, but yes I'm away until the 5th.

[Kevin-Mattheus-Moerman]

@editorialbot assign @adamltyson as editor

[editorialbot]

Assigned! @adamltyson is now the editor

[adamltyson]

Hi @katjaq, thanks for the reviewer suggestions!

@62442katieb, @anibalsolon, @sneakers-the-rat would you be able to review this submission to JOSS? I think you've all reviewed for JOSS before, but if you have any questions about the process, please let me know. Thanks!

[sneakers-the-rat]

hello! i always love a reason to take a look at what @katjaq has been up to.

I have also been recruited as an editor but have not yet been able to finish my onboarding because i got pulled between several things since then, so i'm not sure if that's a problem or not. if it's not, then yes! would love to! i'll be free to start next week.

edit: one more thing, i have reviewed a previous JOSS submission from this group ( https://github.com/openjournals/joss-reviews/issues/2670 ) I don't know if that's a COI (it doesn't feel like one) but i figured i'd ask

[62442katieb]

Hello! Yes, I'm happy to review :))

[danielskatz]

hello! i always love a reason to take a look at what @katjaq has been up to.

I have also been recruited as an editor but have not yet been able to finish my onboarding because i got pulled between several things since then, so i'm not sure if that's a problem or not. if it's not, then yes! would love to! i'll be free to start next week.

edit: one more thing, i have reviewed a previous JOSS submission from this group ( #2670 ) I don't know if that's a COI (it doesn't feel like one) but i figured i'd ask

In my opinion as an associate-editor-in-chief, an editor should dedicate most of their JOSS time to editing, not reviewing, but if you haven't started editing yet, it seems reasonable for you to be a reviewer.

[sneakers-the-rat]

can i pretty please do one more review before putting on editor hat? this looks like a bit of fun :)

[anibalsolon]

Happy to review as well!

[adamltyson]

In my opinion as an associate-editor-in-chief, an editor should dedicate most of their JOSS time to editing, not reviewing, but if you haven't started editing yet, it seems reasonable for you to be a reviewer.

Sounds good to me. @sneakers-the-rat you get to sneak one last review in!

Thank you @62442katieb and @anibalsolon for agreeing too!

[adamltyson]

@editorialbot add @sneakers-the-rat as reviewer

[editorialbot]

@sneakers-the-rat added to the reviewers list!

[adamltyson]

@editorialbot add @62442katieb as reviewer

[editorialbot]

@62442katieb added to the reviewers list!

[adamltyson]

@editorialbot add @anibalsolon as reviewer

[editorialbot]

@anibalsolon added to the reviewers list!

[adamltyson]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6336.