[REVIEW]: biopixR: Extracting Insights from Biological Images #7074

editorialbot · 2024-08-06T11:35:08Z

Submitting author: @Brauckhoff (Tim Brauckhoff)
Repository: https://github.com/Brauckhoff/biopixR
Branch with paper.md (empty if default branch):
Version: v1.2.0
Editor: @fabian-s
Reviewers: @ColemanRHarris, @tijeco
Archive: 10.5281/zenodo.13899162

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68/status.svg)](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ColemanRHarris & @tijeco, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fabian-s know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @tijeco

📝 Checklist for @ColemanRHarris

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-08-06T11:35:12Z

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editorialbot · 2024-08-06T11:35:38Z

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

editorialbot · 2024-08-06T11:35:45Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1134.5 files/s, 257540.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               35            472           1159           2524
TeX                              2            161              0           1868
HTML                             1            338              5           1725
Rmd                              7            624           2084           1241
Markdown                         5            171              0            580
YAML                             2             29             18            128
CSV                              6              0              0             40
-------------------------------------------------------------------------------
SUM:                            58           1795           3266           8106
-------------------------------------------------------------------------------

Commit count by author:

   236	Brauckhoff
    70	devSJR
     2	Michael Chirico

editorialbot · 2024-08-06T11:35:49Z

Paper file info:

📄 Wordcount for paper.md is 1986

✅ The paper includes a Statement of need section

editorialbot · 2024-08-06T11:35:51Z

License info:

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

editorialbot · 2024-08-06T11:36:33Z

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

fabian-s · 2024-08-06T11:37:07Z

hi @tijeco & @ColemanRHarris,

this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#7074 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@fabian-s) if you have any questions/concerns.

tijeco · 2024-08-06T11:42:56Z

Review checklist for @tijeco

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/Brauckhoff/biopixR?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@Brauckhoff) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

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

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

fabian-s · 2024-08-06T11:44:01Z

@Brauckhoff
while we wait for reviewers to start working on this, please start fixing the missing DOIs the bot pointed out above.

devSJR · 2024-08-06T13:13:58Z

@editorialbot generate pdf

devSJR · 2024-08-06T13:14:07Z

Dear @fabian-s, thanks for pointing out the issue with the DOIs. We are eager to cite everything we use or refer to with state-of-the-art technologies. Therefore, we fixed most missing DOIs shortly after submission during the PRE REVIEW. It appears, that we missed a DOI for RMarkown, which I just added.

However, we fear, there is little we can do for the others, since these items have no DOI. For example:

foodwebr is on GitHub only and
radiomics is archived on CRAN. We cite radiomics because it is an R package, which allows extracting Haralick features and clusters information using Partitioning Around Medoids (PAM). However, we will remove the reference to the package since the reader is still guided to appropriate literature.

Is this acceptable, or do you see another solution to this?

editorialbot · 2024-08-06T13:15:21Z

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

devSJR · 2024-08-06T13:16:59Z

@editorialbot generate pdf

editorialbot · 2024-08-06T13:18:23Z

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

ColemanRHarris · 2024-08-06T15:00:57Z

Review checklist for @ColemanRHarris

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/Brauckhoff/biopixR?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@Brauckhoff) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

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

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

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

fabian-s · 2024-08-07T08:27:17Z

However, we fear, there is little we can do for the others, since these items have no DOI. For example:

* [foodwebr](https://github.com/lewinfox/foodwebr) is on GitHub only and

* [radiomics is archived on CRAN](https://cran.r-project.org/web/packages/radiomics/index.html). We cite radiomics because it is an R package, which allows extracting Haralick features and clusters information using Partitioning Around Medoids (PAM). However, we will remove the reference to the package since the reader is still guided to appropriate literature.

Is this acceptable, or do you see another solution to this?

@devSJR
thanks, perfect!

devSJR · 2024-08-07T12:43:38Z

Just a short note. We have added a new function to the package, which didn't end up in a branch but in main. Sorry for that, we will fix that. The package submitted for review is the stable version 1.x after bug fixes (→ 1.1.0).

devSJR · 2024-08-15T11:47:24Z

Dear @fabian-s, @tijeco and @ColemanRHarris,

we forgot to mention that we already moved our latest commit, which caused a problem:

Just a short note. We have added a new function to the package, which didn't end up in a branch but in main. Sorry for that, we will fix that. The package submitted for review is the stable version 1.x after bug fixes (→ 1.1.0).

For the moment being, we decided to halt all pending commits of experimental new functions and new data sets, since we haven't tested them intensively in our current research. We decided it is also better not to submit anything until the review process is finished. Better than saying, “Let's commit. What could possibly go wrong?”, in my humble opinion. I hope you consent with this approach.

tijeco · 2024-08-16T17:37:33Z

@fabian-s , for clarity, we should be reviewing https://github.com/Brauckhoff/biopixR/tree/1880095c8bca6701b5363857f1cf4bba9738379b, corresponding to their release 1.1.0?

tijeco · 2024-08-16T17:52:25Z

@devSJR Could you provide clarification about contribution and authorship? The authors in the manuscript are Tim Brauckhoff, Coline Kieffer, and Stefan Rödiger. The first and last authors appear to have made contributions in the commit history. I don't see the middle author's contribution. Also, it looks like Michael Chirico contributed to the software via pull request, but I don't see them in the manuscript.

devSJR · 2024-08-16T19:49:21Z

Dear @tijeco, sure, I can do that.

Tim does the main programming and documentation of biopixR.

I lead this project (active project direction) and usually review the code (sometimes we even did paired programming), make contributions, fixes, and help with the documentation.

Coline Kieffer contributes the various datasets that are central to the package. For this, she prepared wet lab samples, did the imaging and subsequent insight into the data jointly with us. So to speak, she provided the oil. She also, raised issues (albeit personally in the lab or by decentralized digital messaging) and reflects part of the target audience (biologists in the wet lab). We also specifically mention her in the supplement to this paper https://zenodo.org/doi/10.5281/zenodo.12744222 on page 78 (this supplement is referenced as Brauckhoff, T., & Rödiger, S. (2024). biopixR: Extracting insights from biological images. https://doi.org/10.5281/ZENODO.12744222). You will certainly notice that there are more people mentioned. However, considering invested time and dedication, Coline certainly contributed significantly.

Michael Chirico contributed, indeed a software pull request. But truth to be told, I don't know if we should/must include him. @fabian-s, would you be so kind and tell me how to deal with this?

I hope this answers your question.

fabian-s · 2024-08-19T08:24:31Z

@tijeco

for clarity, we should be reviewing https://github.com/Brauckhoff/biopixR/tree/1880095c8bca6701b5363857f1cf4bba9738379b, corresponding to their release 1.1.0?

that's how i understood @devSJR 's remark, too.

ColemanRHarris · 2024-10-01T16:37:23Z

@Brauckhoff I ran into the same issues as @tijeco since I am on an M2 Mac. I will add my thoughts here as I go through my review, but one note on the documentation you added to the README.

The command you listed, brew cask install xquartz, is outdated. When I ran this, I received the following error:

Error: `brew cask` is no longer a `brew` command. Use `brew <command> --cask` instead.

Hence, the proper command should be:

brew install xquartz --cask

tijeco · 2024-10-01T16:43:44Z

@ColemanRHarris , that's actually what they have in their github actions! https://github.com/Brauckhoff/biopixR/blob/1880095c8bca6701b5363857f1cf4bba9738379b/.github/workflows/R-CMD-check.yml#L58

Brauckhoff · 2024-10-01T16:56:30Z

@ColemanRHarris, thank you for the correction. I rechecked the documentation in the CI, as mentioned by @tijeco, and I found a minor mistake in the order of commands that could be responsible for the error. The correct command should be brew install --cask xquartz, I will update this in the README.

devSJR · 2024-10-01T17:11:15Z

@Brauckhoff I ran into the same issues as @tijeco since I am on an M2 Mac. I will add my thoughts here as I go through my review, but one note on the documentation you added to the README.

The command you listed, brew cask install xquartz, is outdated. When I ran this, I received the following error:
Error: `brew cask` is no longer a `brew` command. Use `brew <command> --cask` instead.
Hence, the proper command should be:
brew install xquartz --cask

We certainly need some input here. Linux is our major platform. We try our best regarding Mac.

ColemanRHarris · 2024-10-01T17:17:32Z

@devSJR Updating the README is sufficient, as that will be useful for any future users with a Mac.

ColemanRHarris · 2024-10-01T17:20:16Z

Only two notes on the documentation (not sure if this is for @Brauckhoff or @devSJR), otherwise everything looks and works as expected 👍

When loading the biopixR library from R at the command line, I get the following warning. This did not prevent me from running any of the documentation examples, but might be worth investigating this or suppressing the warning.

Loading required package: tcltk
Warning message:
In fun(libname, pkgname) :
  no display name and no $DISPLAY environment variable

Change links to vignettes in the README and elsewhere from https://github.com/Brauckhoff/biopixR/blob/main/vignettes/biopixR.Rmd to https://cran.r-project.org/web/packages/biopixR/vignettes/biopixR.html so that the vignette examples are readable.

Brauckhoff · 2024-10-02T12:44:01Z

@ColemanRHarris, I updated the URL in the README file as you noted.

Regarding the warning you mentioned, I tried to reproduce it on my console, but I couldn’t replicate the issue. It seems I am still able to access a display environment, even when running R through the console.

To address the warning message, I removed tcltk from the dependencies and moved it to the suggests section. Additionally, I added code to check for a display environment (X11) to ensure that tcltk is only loaded if the requirements are met. This way, we should be able to maintain the same functionality as before.

ColemanRHarris · 2024-10-02T14:54:58Z

Hi @Brauckhoff, I uninstalled the package and re-installed the current version from GitHub. I do see some of the changes you made, but still get this output when loading the package, e.g. library(biopixR):

Loading required package: magick
Linking to ImageMagick 6.9.12.93
Enabled features: cairo, fontconfig, freetype, heic, lcms, pango, raw, rsvg, webp
Disabled features: fftw, ghostscript, x11
X11 not available, skipping tcltk.
Warning message:
In fun(libname, pkgname) :
  no display name and no $DISPLAY environment variable

I looked through your repository, it seems like you still import tcltk in the NAMESPACE file, have you re-run the build with your current code changes?

Brauckhoff · 2024-10-02T16:28:14Z

Hi @ColemanRHarris, yes I realized that I forgot to remove the import statement in the corresponding function, which caused it to stay in the roxygen documentation. It should work now, as I have removed the import from both the function and the NAMESPACE.

ColemanRHarris · 2024-10-02T18:03:24Z

@Brauckhoff Fantastic, thank you! Can confirm that I installed the updated version and produced no warnings! 👍 See output below:

Loading required package: magick
Linking to ImageMagick 6.9.12.93
Enabled features: cairo, fontconfig, freetype, heic, lcms, pango, raw, rsvg, webp
Disabled features: fftw, ghostscript, x11
X11 not available, skipping tcltk.

fabian-s · 2024-10-07T07:19:11Z

@ColemanRHarris @Brauckhoff @tijeco Thank you all for the collaborative and constructive review process.

fabian-s · 2024-10-07T07:19:19Z

@editorialbot check references

fabian-s · 2024-10-07T07:19:43Z

@editorialbot generate pdf

editorialbot · 2024-10-07T07:19:58Z

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
- 10.1201/9781138359444 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

🟡 SKIP 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: foodwebr: Visualise Function Dependencies

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-07T07:21:15Z

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

fabian-s · 2024-10-07T07:23:31Z

@Brauckhoff

At this point could you:

Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

Brauckhoff · 2024-10-07T18:03:16Z

@fabian-s
We have made a tagged release of biopixR with version 1.2.0. The package has been successfully archived in Zenodo with the title and author list matching the information in the paper.

The DOI for the archived version is: 10.5281/zenodo.13899162 (https://doi.org/10.5281/zenodo.13899162)

fabian-s · 2024-10-08T07:32:55Z

@editorialbot set 10.5281/zenodo.13899162 as archive

editorialbot · 2024-10-08T07:32:58Z

Done! archive is now 10.5281/zenodo.13899162

fabian-s · 2024-10-08T07:33:19Z

@editorialbot set v1.2.0 as version

editorialbot · 2024-10-08T07:33:21Z

Done! version is now v1.2.0

fabian-s · 2024-10-08T07:33:37Z

@editorialbot recommend-accept

editorialbot · 2024-10-08T07:33:39Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-10-08T07:35:23Z

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5975, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2024-10-08T07:36:06Z

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
- 10.1201/9781138359444 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

🟡 SKIP 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: foodwebr: Visualise Function Dependencies

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

devSJR · 2024-10-08T08:05:39Z

I have checked the proof and think it is correct.

devSJR · 2024-10-09T11:11:09Z

@fabian-s is it our task to move forward with the command @editorialbot accept?

fabian-s · 2024-10-09T11:35:07Z

nah, @bcm-eics need to look this over and give their thumbs up

devSJR · 2024-10-09T11:40:08Z

Thanks for the rapid feedback.

editorialbot added HTML R review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Aug 6, 2024

editorialbot assigned fabian-s Aug 6, 2024

editorialbot mentioned this issue Aug 6, 2024

[PRE REVIEW]: biopixR: Extracting Insights from Biological Images #7002

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 8, 2024

[REVIEW]: biopixR: Extracting Insights from Biological Images #7074

[REVIEW]: biopixR: Extracting Insights from Biological Images #7074

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Review checklist for @tijeco

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Review checklist for @ColemanRHarris

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