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[REVIEW]: LenslessPiCam: A Hardware and Software Platform for Lensless Computational Imaging with a Raspberry Pi #4747

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editorialbot opened this issue Sep 9, 2022 · 69 comments
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accepted C++ published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review Shell Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Sep 9, 2022

Submitting author: @ebezzam (Eric Bezzam)
Repository: https://github.com/LCAV/LenslessPiCam
Branch with paper.md (empty if default branch):
Version: v1.0.4
Editor: @danasolav
Reviewers: @raolivei13, @siddiquesalman
Archive: 10.5281/zenodo.8036869

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/251f14f2ffe4ccf239796ad4a71e2bb7"><img src="https://joss.theoj.org/papers/251f14f2ffe4ccf239796ad4a71e2bb7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/251f14f2ffe4ccf239796ad4a71e2bb7/status.svg)](https://joss.theoj.org/papers/251f14f2ffe4ccf239796ad4a71e2bb7)

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

@antipa & @vboomi & @raolivei13, 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 @danasolav 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 @raolivei13

📝 Checklist for @siddiquesalman

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Hello humans, 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

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (578.0 files/s, 79113.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          35            727           1008           3548
Markdown                         7            159              0            569
TeX                              1             11              0            114
Arduino Sketch                   1              2              1             12
Bourne Shell                     1              1              0              7
-------------------------------------------------------------------------------
SUM:                            45            900           1009           4250
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 2069

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

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

OK DOIs

- 10.1364/OPTICA.431361 is OK
- 10.1109/ICASSP.2017.8005297 is OK
- 10.1109/ICASSP.2019.8682923 is OK
- 10.1561/2200000016 is OK
- 10.1109/CVPR.2018.00068 is OK
- 10.1137/080716542 is OK
- 10.1364/OE.27.028075 is OK

MISSING DOIs

- Errored finding suggestions for "Build your own DiffuserCam: Tutorial", please try later
- Errored finding suggestions for "Pycsou", please try later
- Errored finding suggestions for "A method for solving the convex programming proble...", please try later

INVALID DOIs

- None

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danasolav commented Sep 9, 2022

@editorialbot remove @antipa from reviewers

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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@editorialbot remove @antipa from reviewers

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@antipa removed from the reviewers list!

@editorialbot editorialbot added the Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials label Sep 10, 2022
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@vboomi, @raolivei13 the review process takes place here.
Please see the instructions in the thread above (generate your checklists etc.) and in this link.
Thanks!

@raolivei13
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raolivei13 commented Sep 12, 2022

Review checklist for @raolivei13

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/LCAV/LenslessPiCam?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@ebezzam) 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?

@ebezzam
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ebezzam commented Oct 17, 2022

Hi @raolivei13 thank you for your review. I was wondering if you could elaborate on some of the points you haven't checked? I've left a comment on each point below.

Perhaps some of these things were not made clear in the paper, which would be great to receive your feedback on how we can better present / what we should include to fill in the gaps. Thanks!

Substantial scholarly effort

Why do you think the work the doesn't meet the scope eligibility described in the JOSS guidelines?

Data sharing

We describe in the README where to get the data for our examples.

Reproducibility

It's true that when it comes to hardware, it takes more of an effort to reproduce. To this end, we tried to be as detailed as possible to reproduce our camera though Medium posts. Otherwise in terms of reconstruction, we provided scripts that we hope are straightforward to reproduce the results we present in the paper.

Functionality

Again, as hardware is involved the functionality for measurement may be difficult to reproduce. But in terms of reconstruction, we hope the following scripts make it straightforward to confirm that side of things:

Performance

The "Efficient reconstruction" section describes some of our performance claims, which can be reproduced with these scripts:

Automated tests

We provide unit tests in this folder which can be run with pytest

@vboomi
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vboomi commented Oct 24, 2022

Review checklist for @vboomi

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/LCAV/LenslessPiCam?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@ebezzam) 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?

@raolivei13
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raolivei13 commented Oct 24, 2022 via email

@danasolav
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@raolivei13, @vboomi , how is the review process going?

@danasolav
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@raolivei13 @vboomi could you please provide an update on your review process?

@raolivei13
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Hello,
I have reviewed some of the missing points. When it comes to "Reproducibility" I was a little hesitant on checking this off, because it can be interpreted in different ways. Reproducibility in terms of the Software? Or Reproducibility in terms of the Hardware? Since this is a paper which is probably getting published in a Software Journal, we are probably looking at how the Software cab be easily re - used for a similar experiment, which involves some sort of image reconstruction with a Lensless Camera. The Hardware on the other hand, seems to go hand in hand with the Software, i.e "there would be no problem here if we didn't consider the use of a lensless camera". The paper illustrates the problem quite well, but If I were to reproduce this experiment, I would be a little lost on how to set up the experiment on the hardware side of things. For example: "How do I carefully remove the lens from the PiCamera?", "How to capture the Impulse Response of the system (i.e PSF) ?". Not sure if this Hardware Reproducibility is important considering the nature of the paper, which is leaning on the software approach. This is all I have to say, I hope this comment was somewhat insightful, but at the end of the day, as I mentioned before this is a Software paper, and maybe the Hardware aspects of the paper might not be too important.

Best,
Richard

@danasolav
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@raolivei13, thank you for the important comment.
@ebezzam, since this software is inherently linked to certain hardware. I recommend adding to your repository sufficient details on the hardware and experimental setup, such that replication of your setup by new users is straightforward and unambiguous.

@ebezzam
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ebezzam commented Dec 13, 2022

Hi @raolivei13, thank you for that comment on reproducing the hardware. I agree that it is a bit ambiguous whether the hardware is also meant to be reproduced. Nonetheless, this is something we did strive to achieve (reproducibility of hardware and accessibility of components), and you can find the instructions on building the camera in the blog post that is referenced in the README and the "About" section of the repository. Moreover, I just added another comment in the Setup section. It is also mentioned in Line 80 of the paper. Please let me know if you think there is another way this information could be made clearer.

We opted for a Medium article as we found it to be a much more friendlier/interactive way to present the hardware side of things:

  • The first section links to articles that discuss how to set up the Raspberry Pi.
  • The second section links to articles on how to remove the lens, and place the diffuser.
  • The third section talks about measuring the PSF and raw data.

But if you feel like more of this info should be place in the README, let us know!

@ebezzam
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ebezzam commented Jan 26, 2023

@editorialbot generate pdf

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

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ebezzam commented Jan 26, 2023

I've updated the PDF as there have been developments in the project, most notably:

  • Added new simulation framework so users can test the whole pipeline without having to build the camera. More on that in this blog post.
  • A ReadTheDocs site: https://lensless.readthedocs.io
  • Added the implementations for 2D autocorrelation and the real-valued FFT, such that they are no longer left to be completed in the code base. So we have removed the educational resource section from the paper.

@danasolav
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@siddiquesalman, are you able to join this review in place of @vivek?
Thanks,
Dana

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ebezzam commented Jun 7, 2023

@editorialbot generate pdf

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

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ebezzam commented Jun 7, 2023

@danasolav, thank you for the detailed and very helpful comments! I've addressed everything in the above generated PDF. Please let me know if I missed anything.

Below are some comments on a few of your points:

Line 40: please add more information on the comparison shown in Figure 1. They don't seem to compare a reconstruction of the same image, so what is the significance of this comparison?

The purpose is to compare:

  • the DiffuserCam tutorial (Biscarrat et al., 2018) which we reimplemented, and
  • the camera of our toolkit

to show that reconstructions aren’t as good and limited to grayscale. I’ve done a new measurement with DiffuserCam so that the image is the same for both cameras in Figure 1.

Line 95: the function name does not compile properly and extends beyond the line. Could you force a manual new line?

In the Docker compiled version (without line numbers) it renders correctly, example. Could it be an artifact from the peer-reviewed version with line numbers?

Line 143: it would be helpful to explain the meaning of these numbers and their limits, where applicable.

I’ve added more description about each metric, their limits, and links/references. In 154-160, I’ve added an interpretation of Figure 6 and Table 2, which motivates the next section on using measured / simulated data.

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ebezzam commented Jun 13, 2023

Hi @danasolav, just wondering if you had time to look at the changes I made and if they satisfy your points? We'll be presenting LenslessPiCam as demo at a conference next week, and would be great (if possible) to have it published by then. Thanks!

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@editorialbot check references

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

OK DOIs

- 10.1364/OPTICA.431361 is OK
- 10.1109/ICASSP.2017.8005297 is OK
- 10.1109/ICASSP.2019.8682923 is OK
- 10.1561/2200000016 is OK
- 10.1109/CVPR.2018.00068 is OK
- 10.1137/080716542 is OK
- 10.1364/OE.27.028075 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@danasolav
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@ebezzam @raolivei13 @siddiquesalman, Thank you all for your good work and for recommending acceptance of this submission!
@ebezzam, please issue a new tagged release and archive it (on Zenodo, figshare, or other). Then, please post the version number and archive DOI here.

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ebezzam commented Jun 14, 2023

@danasolav, @raolivei13, @siddiquesalman thank you for your input and taking the time to review the work!

@danasolav here is the DOI: 10.5281/zenodo.8036869
The version is 1.0.4, which can be found on GitHub and installed from PyPI.

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Done! archive is now 10.5281/zenodo.8036869

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@editorialbot set v1.0.4 as version

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Done! version is now v1.0.4

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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.1364/OPTICA.431361 is OK
- 10.1109/ICASSP.2017.8005297 is OK
- 10.1109/ICASSP.2019.8682923 is OK
- 10.1561/2200000016 is OK
- 10.1109/CVPR.2018.00068 is OK
- 10.1137/080716542 is OK
- 10.1364/OE.27.028075 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @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#4321, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 17, 2023
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Kevin-Mattheus-Moerman commented Jun 26, 2023

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a PR)
  • Check the references in the paper for corrections (e.g. capitalization)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

@openjournals openjournals deleted a comment from editorialbot Jun 26, 2023
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@ebezzam I've checked the repository, the paper, the archive link, and this review issue. All seems in order and I will now proceed to process this work for acceptance in JOSS.

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@editorialbot accept

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Bezzam
  given-names: Eric
  orcid: "https://orcid.org/0000-0003-4837-5031"
- family-names: Kashani
  given-names: Sepand
  orcid: "https://orcid.org/0000-0002-0735-371X"
- family-names: Vetterli
  given-names: Martin
  orcid: "https://orcid.org/0000-0002-6122-1216"
- family-names: Simeoni
  given-names: Matthieu
  orcid: "https://orcid.org/0000-0002-4927-3697"
doi: 10.5281/zenodo.8036869
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bezzam
    given-names: Eric
    orcid: "https://orcid.org/0000-0003-4837-5031"
  - family-names: Kashani
    given-names: Sepand
    orcid: "https://orcid.org/0000-0002-0735-371X"
  - family-names: Vetterli
    given-names: Martin
    orcid: "https://orcid.org/0000-0002-6122-1216"
  - family-names: Simeoni
    given-names: Matthieu
    orcid: "https://orcid.org/0000-0002-4927-3697"
  date-published: 2023-06-26
  doi: 10.21105/joss.04747
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4747
  title: "LenslessPiCam: A Hardware and Software Platform for Lensless
    Computational Imaging with a Raspberry Pi"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04747"
  volume: 8
title: "LenslessPiCam: A Hardware and Software Platform for Lensless
  Computational Imaging with a Raspberry Pi"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04747 joss-papers#4346
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04747
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 26, 2023
@Kevin-Mattheus-Moerman
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@ebezzam congratulations on this publication in JOSS!

@danasolav thanks for editing this submission!

And a special thanks to the reviewers: @raolivei13, @siddiquesalman !!!!!

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04747/status.svg)](https://doi.org/10.21105/joss.04747)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04747">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04747/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04747/status.svg
   :target: https://doi.org/10.21105/joss.04747

This is how it will look in your documentation:

DOI

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