Skip to content

[PRE REVIEW]: Open-Source Pattern Creation Tool for Medical Extended Reality Image Quality Assessment #5798

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
editorialbot opened this issue Sep 2, 2023 · 37 comments
Closed

[PRE REVIEW]: Open-Source Pattern Creation Tool for Medical Extended Reality Image Quality Assessment #5798

editorialbot opened this issue Sep 2, 2023 · 37 comments
Assignees
@codeling @osorensen
Labels
CSS HTML JavaScript pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Sep 2, 2023 •
edited
Loading

Submitting author: @brendanc490 (Brendan Collins)
Repository: https://github.com/DIDSR/WebXR-tools.git
Branch with paper.md (empty if default branch): JOSS-Submission
Version: v1.0
Editor: @osorensen
Reviewers: @codeling, @osorensen
Managing EiC: George K. Thiruvathukal

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf"><img src="https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf/status.svg)](https://joss.theoj.org/papers/b7c917fb55a1743a539139a74229fdcf)

Author instructions

Thanks for submitting your paper to JOSS @brendanc490. Currently, there isn't a JOSS editor assigned to your paper.

@brendanc490 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
@editorialbot editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 2, 2023
@editorialbot
Copy link
Collaborator Author

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author 

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

OK DOIs

- 10.1109/VR46266.2020.00108 is OK
- 10.1002/jsid.1208 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author 

Software report:

github.com/AlDanial/cloc v 1.88  T=1.85 s (1177.9 files/s, 223210.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            12              5              0         210852
YAML                             7              1              9          97436
JavaScript                      47           8132           5941          41744
CSS                             28           5967            238          16478
SVG                           2023              0             15           8089
Sass                            19            556             72           6965
LESS                            18            552             72           6907
HTML                             5            106             51           1103
reStructuredText                 6             75             18            347
Markdown                         5             50              0            248
DOS Batch                        1              8              1             26
TeX                              1              1              0             16
Python                           1             14             31             10
TypeScript                       1              4              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                          2175          15475           6455         390240
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 871

@editorialbot
Copy link
Collaborator Author

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

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman added the query-scope Submissions of uncertain scope for JOSS label Sep 4, 2023
@Kevin-Mattheus-Moerman
Copy link
Member

@brendanc490 thanks for this submission. I am the AEiC for this track and here to help process the initial steps. For the moment I've flagged this work for a scope review by our editorial board. In particular I need some help to see if this work conforms to what we class as research software.
The paper mentions that patterns created through the website could serve to help "approve devices for medical use". This could be an important application. However this functionality does not make it research software. Could you help provide some comments here as to how you think your software would be used in scientific research? It would help if what you describe paints a clear picture as to why this work is important to scientific research, i.e. such that one would feel the need to cite it in a subsequent paper. Utility tools are typically not cited, and do not require a paper. However software that has a direct impact on scientific findings would definitely need to be cited.
As you address this query, you may also decide to amend your paper and statement of need section on the research applications of this work.
Thanks.

@brendanc490
Copy link

brendanc490 commented Sep 14, 2023 via email

@arfon
Copy link
Member

arfon commented Oct 2, 2023

@brendanc490 – could you also explain how this repository is structured? I'm seeing a lot of JavaScript which I think is the bulk of the software contribution here?

On quick inspection, it's not clear how to test the software. Could you explain how that is accomplished here?

@brendanc490
Copy link

brendanc490 commented Oct 3, 2023 via email

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman removed the query-scope Submissions of uncertain scope for JOSS label Oct 4, 2023
@Kevin-Mattheus-Moerman
Copy link
Member

@brendanc490 I am pleased to inform you that this work has passed our initial scope review. We will now proceed to find a handling editor.

@Kevin-Mattheus-Moerman
Copy link
Member

@editorialbot invite @osorensen as editor

@editorialbot
Copy link
Collaborator Author

Invitation to edit this submission sent!

@osorensen
Copy link
Member

@editorialbot assign @osorensen as editor

@editorialbot
Copy link
Collaborator Author

Assigned! @osorensen is now the editor

@osorensen
Copy link
Member

👋 @codeling, @ionlights, @jackbrookes, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@codeling
Copy link

codeling commented Oct 5, 2023

Yes I can review the submission!

@osorensen
Copy link
Member

@editorialbot add @codeling as reviewer

@editorialbot
Copy link
Collaborator Author

@codeling added to the reviewers list!

@codeling
Copy link

codeling commented Oct 6, 2023 •
edited
Loading

First quick remark: It seems that the used license (CC0-1.0) is not OSI-approved.

@osorensen
Copy link
Member

osorensen commented Oct 6, 2023 •
edited
Loading

Thanks a lot for pointing this out @codeling. I'll check this further with the editorial team and see how we proceed.

@osorensen
Copy link
Member

osorensen commented Oct 6, 2023 •
edited
Loading

@brendanc490, as pointed out by @codeling, the license CC0-1.0 is not OSI approved. Since this is a requirement for JOSS submissions, we cannot review this submission unless you change to an OSI approved license.

Please let us know in this thread whether you change the license. If so, we can proceed with the review.

@osorensen
Copy link
Member

@brendanc490, have you decided whether you will change the license or withdraw the publication?

@brendanc490
Copy link

brendanc490 commented Oct 17, 2023 via email

@osorensen
Copy link
Member

Thanks @brendanc490, then I'll continue looking for another reviewer.

@osorensen osorensen removed the paused label Oct 17, 2023
@osorensen
Copy link
Member

👋 @kyq, @sandeepchowdary7, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@osorensen
Copy link
Member

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

Five most similar historical JOSS papers:

Virtual Scanner: MRI on a Browser
Submitting author: @imr-framework
Handling editor: @arokem (Retired)
Reviewers: @nstikov, @vsoch, @mathieuboudreau
Similarity score: 0.8189

Open Source Optical Coherence Tomography Software
Submitting author: @spectralcode
Handling editor: @arfon (Active)
Reviewers: @jdavidli, @brandondube
Similarity score: 0.8142

open_iA: A tool for processing and visual analysis of industrial computed tomography datasets
Submitting author: @codeling
Handling editor: @katyhuff (Retired)
Reviewers: @trallard, @behollister
Similarity score: 0.8121

Reel1.0 - A visualization tool for evaluating powder diffraction refinements
Submitting author: @fgjorup
Handling editor: @rkurchin (Active)
Reviewers: @cmbiwer, @mikapfl
Similarity score: 0.8106

DetectorChecker: analyzing patterns of defects in detector screens
Submitting author: @tomaslaz
Handling editor: @fboehm (Active)
Reviewers: @janfreyberg, @craddm
Similarity score: 0.8072

⚠️ 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.

@osorensen
Copy link
Member

👋 @imr-framework, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@osorensen
Copy link
Member

👋 @tomaslaz, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

@osorensen
Copy link
Member

@brendanc490, I have a hard time finding a second reviewer for this submission. Do you have any suggestions for potential reviewers?

@brendanc490
Copy link

brendanc490 commented Oct 30, 2023 via email

@osorensen
Copy link
Member

@brendanc490, I'll add myself as a reviewer, so that we can proceed.

@osorensen
Copy link
Member

@editorialbot add @osorensen as reviewer

@editorialbot
Copy link
Collaborator Author

@osorensen added to the reviewers list!

@osorensen
Copy link
Member

@editorialbot start review

@editorialbot
Copy link
Collaborator Author

OK, I've started the review over in #6021.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@codeling codeling

@osorensen osorensen

Labels
CSS HTML JavaScript pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
6 participants
@arfon @codeling @Kevin-Mattheus-Moerman @osorensen @brendanc490 @editorialbot