[PRE REVIEW]: biopixR: Extracting Insights from Biological Images

[editorialbot]

Submitting author: !--author-handle-->@Brauckhoff<!--end-author-handle-- (Tim Brauckhoff) Repository: https://github.com/Brauckhoff/biopixR Branch with paper.md (empty if default branch): Version: 1.1.0 Editor: !--editor-->@fabian-s<!--end-editor-- Reviewers: @ColemanRHarris, @tijeco Managing EiC: Kevin M. Moerman

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

@Brauckhoff 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.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1216.0 files/s, 276012.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               35            472           1159           2524
TeX                              2            161              0           1867
HTML                             1            338              5           1725
Rmd                              7            624           2084           1241
Markdown                         5            171              0            579
YAML                             2             29             18            128
CSV                              6              0              0             40
-------------------------------------------------------------------------------
SUM:                            58           1795           3266           8104
-------------------------------------------------------------------------------

Commit count by author:

   235  Brauckhoff
    70  devSJR
     2  Michael Chirico

[editorialbot]

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

OK DOIs

- 10.21105/joss.06394 is OK
- 10.32614/CRAN.package.biopixR is OK
- 10.21037/jlpm.2019.04.05 is OK
- 10.1016/j.biosx.2024.100484 is OK
- 10.32614/rj-2011-002 is OK
- 10.32614/RJ-2012-018 is OK
- 10.32614/CRAN.package.countcolors is OK
- 10.21105/joss.01012 is OK
- 10.1007/978-0-387-75936-4 is OK
- 10.1109/tsmc.1973.4309314 is OK
- 10.18637/jss.v021.i05 is OK
- 10.32614/CRAN.package.cluster is OK
- 10.1007/s00604-019-3449-y is OK
- 10.1080/17425247.2016.1192122 is OK
- 10.1007/s10544-018-0314-4 is OK
- 10.1007/s00604-014-1243-4 is OK
- 10.1038/76469 is OK
- 10.1007/s11356-020-08127-2 is OK
- 10.1038/s41598-019-41136-x is OK
- 10.1021/ac103277s is OK
- 10.3390/molecules201219766 is OK
- 10.1007/s00216-019-02199-x is OK
- 10.1007/10_2011_132 is OK
- 10.21037/jlpm.2018.11.01 is OK
- 10.21037/jlpm.2018.04.10 is OK
- 10.18637/jss.v049.i09 is OK
- 10.1198/106186007X178663 is OK
- 10.32614/RJ-2015-011 is OK
- 10.5281/ZENODO.12744222 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Tcl/Tk Interface
- No DOI given, and none found for title: RStudio: Integrated Development Environment for R
- No DOI given, and none found for title: Advanced R
- No DOI given, and none found for title: ’Radiomic’ Image Processing Toolbox
- No DOI given, and none found for title: magick: Advanced Graphics and Image-Processing in ...
- No DOI given, and none found for title: R Markdown
- No DOI given, and none found for title: foodwebr: Visualise Function Dependencies

INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1986

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU Lesser General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

microViz: an R package for microbiome data visualization and statistics Submitting author: @david-barnett Handling editor: @lpantano (Active) Reviewers: @marypiper, @yoonjeongcha Similarity score: 0.7265

mxnorm: An R Package to Normalize Multiplexed Imaging Data Submitting author: @ColemanRHarris Handling editor: @osorensen (Active) Reviewers: @askerdb, @tijeco Similarity score: 0.7229

ijtiff: An R package providing TIFF I/O for ImageJ users Submitting author: @rorynolan Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.7187

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows Submitting author: @grabear Handling editor: @lpantano (Active) Reviewers: @CosteaPaul Similarity score: 0.7042

Bedtoolsr: An R package for genomic data analysis and manipulation Submitting author: @dphansti Handling editor: @mgymrek (Retired) Reviewers: @nhejazi, @mikmaksi Similarity score: 0.6977

⚠️ 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]

@Brauckhoff Dear author(s), thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

• [ ] Please study the above reference check :point_up: and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

Please note that I've just waitlisted this submission. This is because all editors in this domain are currently handling other submissions. We'll assign an editor once once becomes available.

[Brauckhoff]

Dear @Kevin-Mattheus-Moerman, thanks for the handling. We found some references to complete.

We suggest as reviewers: ZhenchenHong Yannan-Chen Alanocallaghan singhkakan MaximLippeveld

[devSJR]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.06394 is OK
- 10.32614/CRAN.package.biopixR is OK
- 10.21037/jlpm.2019.04.05 is OK
- 10.1016/j.biosx.2024.100484 is OK
- 10.32614/rj-2011-002 is OK
- 10.32614/RJ-2012-018 is OK
- 10.32614/CRAN.package.countcolors is OK
- 10.21105/joss.01012 is OK
- 10.32614/CRAN.package.magick is OK
- 10.1007/978-0-387-75936-4 is OK
- 10.1109/tsmc.1973.4309314 is OK
- 10.18637/jss.v021.i05 is OK
- 10.32614/CRAN.package.cluster is OK
- 10.1007/s00604-019-3449-y is OK
- 10.1080/17425247.2016.1192122 is OK
- 10.1007/s10544-018-0314-4 is OK
- 10.1007/s00604-014-1243-4 is OK
- 10.1038/76469 is OK
- 10.1007/s11356-020-08127-2 is OK
- 10.1038/s41598-019-41136-x is OK
- 10.1021/ac103277s is OK
- 10.3390/molecules201219766 is OK
- 10.1007/s00216-019-02199-x is OK
- 10.1007/10_2011_132 is OK
- 10.21037/jlpm.2018.11.01 is OK
- 10.21037/jlpm.2018.04.10 is OK
- 10.18637/jss.v049.i09 is OK
- 10.1198/106186007X178663 is OK
- 10.32614/RJ-2015-011 is OK
- 10.5281/ZENODO.12744222 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Tcl/Tk Interface
- No DOI given, and none found for title: RStudio: Integrated Development Environment for R
- No DOI given, and none found for title: Advanced R
- No DOI given, and none found for title: ’Radiomic’ Image Processing Toolbox
- No DOI given, and none found for title: R Markdown
- No DOI given, and none found for title: foodwebr: Visualise Function Dependencies

INVALID DOIs

- None

[devSJR]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

microViz: an R package for microbiome data visualization and statistics Submitting author: @david-barnett Handling editor: @lpantano (Active) Reviewers: @marypiper, @yoonjeongcha Similarity score: 0.7265

mxnorm: An R Package to Normalize Multiplexed Imaging Data Submitting author: @ColemanRHarris Handling editor: @osorensen (Active) Reviewers: @askerdb, @tijeco Similarity score: 0.7228

ijtiff: An R package providing TIFF I/O for ImageJ users Submitting author: @rorynolan Handling editor: @arfon (Active) Reviewers: @arfon Similarity score: 0.7187

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows Submitting author: @grabear Handling editor: @lpantano (Active) Reviewers: @CosteaPaul Similarity score: 0.7041

Bedtoolsr: An R package for genomic data analysis and manipulation Submitting author: @dphansti Handling editor: @mgymrek (Retired) Reviewers: @nhejazi, @mikmaksi Similarity score: 0.6977

⚠️ 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 @mstimberg as editor

[editorialbot]

Invitation to edit this submission sent!

[mstimberg]

@Kevin-Mattheus-Moerman I am afraid I have to decline at this time – I am about to leave for summer holiday and will only be fully back in office in September.

[fabian-s]

@Kevin-Mattheus-Moerman I can take this on as editor if you're still looking

[Kevin-Mattheus-Moerman]

@editorialbot assign @fabian-s as editor

[editorialbot]

Assigned! @fabian-s is now the editor

[fabian-s]

:wave: @ColemanRHarris & @david-barnett

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

[ColemanRHarris]

Hi @fabian-s, thanks for reaching out. I am willing to review the submission for JOSS! What do you need from me?

[david-barnett]

Hi @fabian-s - I think for me the topic isn't a good fit with my expertise, I don't work with images. So I'll have to decline. Good luck with the review!

[fabian-s]

@ColemanRHarris thanks -- nothing for now, let me find a reviewer 2 first :)

[fabian-s]

@editorialbot add @ColemanRHarris as reviewer

[editorialbot]

@ColemanRHarris added to the reviewers list!

[fabian-s]

:wave: @askerdb, @tijeco

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

[tijeco]

@fabian-s , I'd love to!

[fabian-s]

that was quick, @tijeco! thanks!

[fabian-s]

@editorialbot add @tijeco as reviewer

[editorialbot]

@tijeco added to the reviewers list!

[fabian-s]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7074.