[REVIEW]: PiSCAT: A Python Package for Interferometric Scattering Microscopy

[whedon]

Submitting author: @po60nani (Houman Mirzaalian Dastjerdi)
Repository: https://github.com/SandoghdarLab/PiSCAT
Branch with paper.md (empty if default branch): JOSS-paper
Version: 0.1.23
Editor: @emdupre
Reviewers: @ziatdinovmax, @aquilesC
Archive: 10.5281/zenodo.6389882

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Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/81fb6452cdd3d3f792d50a4e8763940c"><img src="https://joss.theoj.org/papers/81fb6452cdd3d3f792d50a4e8763940c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/81fb6452cdd3d3f792d50a4e8763940c/status.svg)](https://joss.theoj.org/papers/81fb6452cdd3d3f792d50a4e8763940c)

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

@ziatdinovmax & @aquilesC, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 ✨

Review checklist for @ziatdinovmax

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@po60nani) 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

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 and who the target audience is?
• 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?

Review checklist for @aquilesC

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@po60nani) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ziatdinovmax, @aquilesC it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #4024 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.29 s (418.5 files/s, 89978.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         101           4152           2738          12292
Markdown                         7            330              0            964
Jupyter Notebook                 5              0           5035            432
reStructuredText                 6            159            130            123
DOS Batch                        1              9              1             27
CSS                              1              2              0             11
make                             1              4              7             10
YAML                             1              4              6              7
-------------------------------------------------------------------------------
SUM:                           123           4660           7917          13866
-------------------------------------------------------------------------------


Statistical information for the repository 'ebfb0353e28a7dbe1bf5f3a9' was
gathered on 2021/12/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Houman Mirzaalian Da            78         19770           1046           96.56
Matthias Baer                    1           215            137            1.63
Reza Gholami M                   2             5              5            0.05
rgholam                          1           380              0            1.76

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Houman Mirzaalian Da      18583           94.0          1.0                3.17
Matthias Baer               215          100.0          7.0                5.58
rgholam                     384          101.1          2.3                4.17

[emdupre]

@whedon generate pdf from branch JOSS-paper

[whedon]

Attempting PDF compilation from custom branch JOSS-paper. Reticulating splines etc...

[whedon]

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

[emdupre]

@whedon check references from branch JOSS-paper

[whedon]

Attempting to check references... from custom branch JOSS-paper

[whedon]

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

OK DOIs

- 10.1364/OE.401374 is OK

MISSING DOIs

- 10.1103/physrevlett.93.037401 may be a valid DOI for title: Detection and Spectroscopy of Gold Nanoparticles Using Supercontinuum White Light Confocal Microscopy
- 10.1021/acs.nanolett.9b01822 may be a valid DOI for title: Interferometric scattering microscopy: seeing single nanoparticles and molecules via Rayleigh scattering
- 10.1101/2021.08.16.456463 may be a valid DOI for title: Optimized analysis for sensitive detection and analysis of single proteins via interferometric scattering microscopy
- 10.1038/ncomms5495 may be a valid DOI for title: Direct optical sensing of single unlabelled proteins and super-resolution imaging of their binding sites
- 10.1021/acs.nanolett.8b02240.s001 may be a valid DOI for title: High-speed microscopy of diffusion in pore-spanning lipid membranes

INVALID DOIs

- None

[emdupre]

Hi everyone 👋 Thanks again @ziatdinovmax and @aquilesC for agreeing to review this submission ! The review will take place in this issue.

Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software. If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to reach out with any questions !

I'll flag in advance that I know this is a generally difficult time of year, and that @aquilesC has already confirmed that he will not be able to provide a review until the first or second week of January. This should keep us well within the six week window suggested by JOSS's reduced service mode, but just to make sure everyone is aware of the approximate timeline.

[emdupre]

@po60nani a few initial points on the JOSS paper itself, rather than the software :

• The manuscript does not yet have a 'Statement of Need' section. You can find more information in the submission guidelines on what the statement of need section should contain
• Several references cited in the paper are missing DOIs, with whedon suggesting possible additions in this comment. Could you please confirm whether the automatically suggested DOIs are appropriate for your references, and either add or correct them ?

[po60nani]

@whedon generate pdf from branch JOSS-paper

[whedon]

Attempting PDF compilation from custom branch JOSS-paper. Reticulating splines etc...

[whedon]

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

[po60nani]

@whedon check references from branch JOSS-paper

[whedon]

Attempting to check references... from custom branch JOSS-paper

[whedon]

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

OK DOIs

- 10.1103/PhysRevLett.93.037401 is OK
- 10.1021/acs.nanolett.9b01822 is OK
- 10.1007/978-3-030-21722-8 is OK
- 10.1088/1361-6463/ac2f68 is OK
- 10.1038/ncomms5495 is OK
- 10.1021/acs.nanolett.8b02240 is OK
- 10.1364/OE.401374 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[po60nani]

@whedon generate pdf from branch JOSS-paper

[whedon]

Attempting PDF compilation from custom branch JOSS-paper. Reticulating splines etc...

[whedon]

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

[po60nani]

@emdupre Thank you for taking the time to provide comments. We made changes to the manuscript in response to your comments.

• The manuscript does not yet have a 'Statement of Need' section. You can find more information in the submission guidelines on what the statement of need section should contain

• The new section called 'Statement of Need' was added to the manuscript.

• Several references cited in the paper are missing DOIs, with whedon suggesting possible additions in this comment. Could you please confirm whether the automatically suggested DOIs are appropriate for your references, and either add or correct them ?

• All DOIs were added to the bibliography.

[whedon]

👋 @aquilesC, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @ziatdinovmax, please update us on how your review is going (this is an automated reminder).

[po60nani]

@kyleniemeyer, Thank you, I fixed it.

[po60nani]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04024 joss-papers#3107
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04024
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @po60nani on your article's publication in JOSS!

Many thanks to @ziatdinovmax and @aquilesC for reviewing this, and @emdupre for editing.

[editorialbot]

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

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

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  <img src="https://joss.theoj.org/papers/10.21105/joss.04024/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04024/status.svg
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