[PRE REVIEW]: bmiptools: BioMaterials Image Processing TOOLS

[editorialbot]

Submitting author: !--author-handle-->@lcmpikg<!--end-author-handle-- (Luca Curcuraci) Repository: https://gitlab.mpikg.mpg.de/curcuraci/bmiptools Branch with paper.md (empty if default branch): Version: 1.0.1 Editor: !--editor-->@AoifeHughes<!--end-editor-- Reviewers: @taw10, @mooniean Managing EiC: Arfon Smith

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

@lcmpikg if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.20 s (466.7 files/s, 103924.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          52           3383           3457           5684
reStructuredText                32           2824           2310           2427
Markdown                         4            156              0            336
TeX                              1             17              0            167
JSON                             1              0              0             94
DOS Batch                        1              8              1             26
YAML                             1              4              4             13
make                             1              4              7              9
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            94           6396           5779           8759
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1503

[editorialbot]

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

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1109/83.862633 may be a valid DOI for title: Adaptive wavelet thresholding for image denoising and compression
- 10.1093/biomet/81.3.425 may be a valid DOI for title: Ideal spatial adaptation by wavelet shrinkage
- 10.1561/9781601982513 may be a valid DOI for title: Bilateral filtering: Theory and applications
- 10.1109/cvpr.2019.00223 may be a valid DOI for title: Noise2void-learning denoising from single noisy images
- 10.1364/oe.17.008567 may be a valid DOI for title: Stripe and ring artifact removal with combined wavelet—Fourier filtering
- 10.1109/tpami.2008.113 may be a valid DOI for title: Parametric image alignment using enhanced correlation coefficient maximization
- 10.1109/83.506761 may be a valid DOI for title: An FFT-based technique for translation, rotation, and scale-invariant image registration
- 10.1109/icip.2005.1529706 may be a valid DOI for title: Dense optical flow by iterative local window registration
- 10.1016/b978-0-12-336156-1.50061-6 may be a valid DOI for title: Contrast limited adaptive histogram equalization
- 10.1016/b978-012387582-2/50040-x may be a valid DOI for title: Amira: A highly interactive system for visual data analysis.
- 10.1017/s143192761800315x may be a valid DOI for title: Dragonfly as a platform for easy image-based deep learning applications
- 10.1038/nmeth.2019 may be a valid DOI for title: Fiji: an open-source platform for biological-image analysis

INVALID DOIs

- None

[arfon]

@lcmpikg - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[Kevin-Mattheus-Moerman]

@lcmpikg can you check those potentially missing DOIs :point_up:

You can call @editorialbot check references after you've made changes to check if they now pass our checks. Thanks

[Kevin-Mattheus-Moerman]

@editorialbot invite @AoifeHughes as editor

[editorialbot]

Invitation to edit this submission sent!

[AoifeHughes]

Good morning all, sure @Kevin-Mattheus-Moerman I would absolutely love to be editor for this. Looks interesting!

[Kevin-Mattheus-Moerman]

@editorialbot assign @AoifeHughes as editor

[editorialbot]

Assigned! @AoifeHughes is now the editor

[Kevin-Mattheus-Moerman]

Thats fantabulous, thanks @AoifeHughes.

[AoifeHughes]

Good morning @lcmpikg - have you had a chance to sort out these https://github.com/openjournals/joss-reviews/issues/4801#issuecomment-1259652983 missing links?

And would you have any suggestions for potential reviewers: JOSS reviewers.

[lc09c]

Hello,

I do not have any suggestion for potential reviewers at the moment. Regarding the DOI, what should I do? Change the paper.bib file and add them? Or simply confirm if the are the correct DOI for the articles cited? Or something else? If what I should do was written somewhere in JOSS documentation, simply post me the link.

Thanks and have a nice day LC

[AoifeHughes]

Check out example bib on this page. From what I understand you need a doi or a url field for the entries. I think these are currently missing from your bib file.

I'll have a look for reviewers in the mean time.

Thanks :)

[AoifeHughes]

Hi @maurov, and @taw10 - would this submission seem like something you'd be able to review?

[lc09c]

@AoifeHughes I'll add the DOI and url in the paper.bib file.

[lc09c]

@AoifeHughes DOI and URL added. I made a commit with the new version of the paper.bin file. Is it sufficient or should I do something else?

[AoifeHughes]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1109/83.862633 is OK
- 10.1093/biomet/81.3.425 is OK
- 10.1109/ICCIMA.2007.305 is OK
- 10.1023/B:JMIV.0000011325.36760.1e is OK
- 10.1561/0600000020 is OK
- 10.5201/ipol.2011.bcm_nlm is OK
- 10.48550/arXiv.1901.11365 is OK
- 10.48550/arXiv.1811.10980 is OK
- 10.1364/OE.17.008567 is OK
- 10.1109/TPAMI.2008.113 is OK
- 10.1109/83.506761 is OK
- 10.1109/ICIP.2005.1529706 is OK
- 10.1109/ICACCI.2014.6968381 is OK
- 10.7717/peerj.453 is OK
- 10.1016/B978-012387582-2/50040-X is OK
- 10.1017/S143192761800315X is OK
- 10.1038/nmeth.2019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[AoifeHughes]

Hi @lc09c - just wanted to let you know I'm still looking for reviewers, so we can begin. It will speed things up if you, yourself, know anyone who would be able to, or have suggestions. Otherwise, I'll keep asking potential reviewers in the meantime.

[AoifeHughes]

@masadcv @mh-skjelvareid, @jingpengw would you be available to review this paper/softwares?

[masadcv]

Hi @AoifeHughes

Many thanks for the invitation to review this JOSS paper. I am happy to review this, however due to some existing deadlines I may only be able to start my review at the start of next month. In case that goes in line with reviewing timeline, then please add me to reviewer list. Otherwise, I look forward to reviewing other JOSS papers in coming days.

[xiuliren]

@AoifeHughes thank you for the invitation! I am reviewing some big grant applications with close to a hundred pages in total! I do not have the time to do it in the near future.

[maurov]

Hi @maurov, and @taw10 - would this submission seem like something you'd be able to review?

@AoifeHughes thanks for considering me as possible reviewer. I am not an expert of FIB/SEM tomography and I cannot judge about this code. I had a quick read of the paper and my first impression is that it would be beneficial to have more open source tomography software around. To my opinion, the paper reports correctly the reference for standard algorithms, but for newly implemented ones, a detailed presentation is missing. In fact, the authors state : "For newly proposed functions, a systematic study of the loss behavior is presented", but I simply do not see where this is done in the paper.

Here my two cents contribution. I think it would be beneficial to find a more expert reviewer than me.

[taw10]

Hi, I can review! Sorry for the long wait for a response - the request came right at the start of a very busy week for me. I expect to have time next week to take a proper look.

[AoifeHughes]

@taw10 fab, thanks! No rush, still need to find the second (waiting for some to get back to me) - @masadcv thanks also, let me see, I'll hear back tomorrow from someone else who may be able to help out sooner, but thank you for the offer and will ping later next week if needed :) thanks all for responses!

[AoifeHughes]

@editorialbot add @taw10 as reviewer

[editorialbot]

@taw10 added to the reviewers list!

[lc09c]

Hello,

@AoifeHughes I am sorry but I do not have any reviewer to suggest. Sorry.

@maurov The "systematic study of the loss behavior" is simply in the documentation, as should be clear from the two sentences after the one you reported, which I copied below.

"For example, for the selection of the decharger and destriper parameters, novel self-supervised losses are employed, and in the “Miscellaneous” section of the documentation two corresponding case studies are discussed. There, all the implementation details about these newly proposed losses can be found, and examples of application to typical use case are discussed."

Let me know if maybe the that sentence need to be changed.

@taw10 thanks for accepting to review this work.

Have a nice day.

[maurov]

@lc09c thanks for your comment. Indeed, I had a look at the documentation only after writing my comment. Yes, your are right that everything is well documented.

[mh-skjelvareid]

@AoifeHughes : Thanks for the invitation to review! Unfortunately I won't have time for reviews in the last months of 2022.

[AoifeHughes]

Hello @mooniean, following on from our off-github conversations, I'm going to add you as a reviewer and then start the process, so we can get the review moving.

[AoifeHughes]

@editorialbot add @mooniean as reviewer

[editorialbot]

@mooniean added to the reviewers list!

[AoifeHughes]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4859.