[PRE REVIEW]: SAMBA: A Trainable Segmentation Web-App with Smart Labelling

[editorialbot]

Submitting author: @rmdocherty (Ronan Docherty)
Repository: https://github.com/tldr-group/samba-web
Branch with paper.md (empty if default branch): paper
Version: v1.0.0
Editor: @AJQuinn
Reviewers: @pchlap, @jingpengw
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/fddb3a679cbe8c6eb91d08509120f23f"><img src="https://joss.theoj.org/papers/fddb3a679cbe8c6eb91d08509120f23f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/fddb3a679cbe8c6eb91d08509120f23f/status.svg)](https://joss.theoj.org/papers/fddb3a679cbe8c6eb91d08509120f23f)

Author instructions

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

@rmdocherty 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]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (828.9 files/s, 163305.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TypeScript                      14            360            222           2662
Python                           9            384            712           1546
JavaScript                       6            177            112           1492
Markdown                         4             65              0            228
TeX                              1             13              0            103
JSON                             2              0              0            102
YAML                             2              7              8             46
HTML                             2              8              1             21
CSS                              1              0              0              3
Sass                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            42           1014           1055           6206
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1233

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0582-9 is OK
- 10.1093/bioinformatics/btx180 is OK
- 10.1038/nmeth.2019 is OK
- 10.1101/2023.08.21.554208 is OK
- 10.7717/peerj.453 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

SIAL: A simple image analysis library for wet-lab scientists
Submitting author: @d-tear
Handling editor: @jni (Retired)
Reviewers: @bogovicj, @haesleinhuepf
Similarity score: 0.8266

Ipyannotator: the infinitely hackable annotation framework
Submitting author: @itepifanio
Handling editor: @danielskatz (Active)
Reviewers: @csadorf, @matthewfeickert
Similarity score: 0.8188

BIDSonym: a BIDS App for the pseudo-anonymization of neuroimaging datasets
Submitting author: @peerherholz
Handling editor: @oliviaguest (Active)
Reviewers: @deep-introspection, @chrisgorgo, @neuromusic
Similarity score: 0.8185

Sapsan: Framework for Supernovae Turbulence Modeling with Machine Learning
Submitting author: @pikarpov-lanl
Handling editor: @dfm (Active)
Reviewers: @kburns, @milescranmer
Similarity score: 0.8172

GAMA: Genetic Automated Machine learning Assistant
Submitting author: @PGijsbers
Handling editor: @arokem (Retired)
Reviewers: @jsgalan
Similarity score: 0.8138

⚠️ 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]

@editorialbot invite @AJQuinn as editor

[editorialbot]

Invitation to edit this submission sent!

[Kevin-Mattheus-Moerman]

@AJQuinn 👋

[AJQuinn]

Hi @Kevin-Mattheus-Moerman - apologies for the delay, I can take this one. Thanks

[Kevin-Mattheus-Moerman]

@editorialbot assign @AJQuinn as editor

[editorialbot]

Assigned! @AJQuinn is now the editor

[rmdocherty]

Hi,
In terms of reviewer suggestions, user haesleinhuepf who reviewed the SIAL paper above does good work on segmentation and has used SAM before, though doesn’t appear on the list of people who’ve agreed to review.

For users who do appear on the list above, user pchalp has done deep learning and segmentation in Python and user pr4deepr has done work with tools like ImageJ, napari and cellpose which are similar to this tool.

[Kevin-Mattheus-Moerman]

@AJQuinn are you able to pick up the search for reviewers here? Thanks!

[AJQuinn]

Hi @Kevin-Mattheus-Moerman @rmdocherty - my sincere apologies for letting this drift - I'm back on this now.

[AJQuinn]

👋 Hello - @haesleinhuepf @pr4deepr @pchlap would you be willing to review this submission for JOSS? The code repository and paper details are further up in this thread.

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html - please check them out for more information and please feel free to ask questions in this thread.

Cheers!

[pchlap]

Sounds good @AJQuinn. This looks like an interesting piece of work. I'm happy to review.

[pr4deepr]

Hi
Thanks @rmdocherty for the considering me. Unfortunately, at this time I cannot commit to reviewing this manuscript due to other obligations. It does look like a nice piece of work and I will be checking this out.

Cheers
Pradeep

[AJQuinn]

No problem @pr4deepr - thanks for letting me know.

Thanks @pchlap - I'll add you now, look out for the review thread starting up.

[AJQuinn]

@editorialbot add @pchlap as reviewer

[editorialbot]

@pchlap added to the reviewers list!

[AJQuinn]

Hello 👋 @jonbmartin @jingpengw - would you be willing to review this submission for JOSS? The code repository and paper details are further up in this thread.

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html - please check them out for more information and please feel free to ask questions in this thread.

Cheers!

[jingpengw]

thank you for the invitation! looks interesting!
I am happy to review it.

[AJQuinn]

Fantastic - thanks @jingpengw!

[AJQuinn]

@editorialbot add @jingpengw as reviewer

[editorialbot]

@jingpengw added to the reviewers list!

[AJQuinn]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6159.