[REVIEW]: TACtool: A targeting and co-ordination tool for spatial sampling and data traceability applied to scanning electron microscopy and laser ablation ICP-MS

[editorialbot]

Submitting author: @leorudczenko (Leo Rudczenko)
Repository: https://github.com/britishgeologicalsurvey/tactool
Branch with paper.md (empty if default branch): paper
Version: v1.3.0
Editor: @philipcardiff
Reviewers: @uellue, @kstenio
Archive: Pending

Status

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Reviewer instructions & questions

@uellue & @kstenio, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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

✨ Please start on your review when you are able; the expectation is that it will take 2-4 weeks to complete. ✨

Checklists

📝 Checklist for @uellue

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[editorialbot]

Repository Analysis Report

Code breakdown

github.com/AlDanial/cloc v 1.98  T=0.04 s (761.5 files/s, 117496.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            554            853           2238
Markdown                         3            136              0            480
YAML                             5             14              5            211
TeX                              1             10              0             91
CSV                              5              0              0             37
-------------------------------------------------------------------------------
SUM:                            30            714            858           3057
-------------------------------------------------------------------------------

Commit Count by Author

99	leorud
    56	Leo Rudczenko
     3	John A Stevenson
     1	leorudczenko

Repository History

Repository age: First commit on April 03, 2023

Code distribution (top 3 48-hour windows):

Period	Insertions	% of Total	Signal	View Changes
Jan 24, 2024 - Jan 26, 2024	3483	33.9%	🟡	View diff
Apr 01, 2023 - Apr 03, 2023	3242	31.5%	🟡	View diff
Apr 01, 2024 - Apr 03, 2024	2451	23.8%	🟢	View commit

GitHub Activity Metrics

Metric	Count
GitHub stars	6
Forks	1
GitHub contributors	3
Releases	4
Total issues	7
Total pull requests	9
Unique commenters/reviewers (excluding authors)	4

[editorialbot]

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

✅ OK DOIs

- 10.1016/j.chemgeo.2020.119917 is OK
- 10.1007/s00410-018-1503-0 is OK
- 10.1111/1755-6724.13406 is OK
- 10.1016/j.lithos.2018.08.033 is OK
- 10.1016/j.gca.2020.05.019 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: GeoStar μGIS TM Software
- No DOI given, and none found for title: ImageJ Docs Fiji
- No DOI given, and none found for title: QUARTZ PCI: Microscope Software
- No DOI given, and none found for title: Microscopes International
- No DOI given, and none found for title: MIPAR
- No DOI given, and none found for title: PIBC

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1329

✅ The paper includes a Statement of need section

✅ The paper includes a State of the field section

✅ The paper includes a Software design section

✅ The paper includes a Research impact statement section

✅ The paper includes an AI usage disclosure section

[editorialbot]

License info:

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

[editorialbot]

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

[uellue]

Review checklist for @uellue

AI usage

• I confirm that I have read the JOSS AI policy and understand that:
  • AI may only be used for non-substantive assistance (e.g., grammar checking my review text, contextualizing public materials)
  • All evaluative decisions—including scoring, accept/reject recommendations, and assessments of originality, correctness, significance, and ethics compliance—must be made exclusively by me, not AI
  • I bear full responsibility for all judgments, recommendations, and technical claims in my review
  • I will disclose any AI assistance at the conclusion of my review

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/britishgeologicalsurvey/tactool?
• 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 (@leorudczenko) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Scope and significance: Does this submission demonstrate clear research impact or credible scholarly significance as 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.

Development history and open-source practice

• Development timeline: Does the project show evidence of sustained development over time (preferably months or years) rather than rapid, recent code generation?
• Open development: Was the software developed openly from early stages? For projects with recent public repositories, is there at least six months of public development history with evidence of releases, public issues/pull requests, and ideally external engagement?
• Collaborative effort: Does the project show evidence of community engagement such as contributions from multiple developers, issues/discussions from external users, or community influence on the development described in the paper?
• Good practices: Does the project look like a reusable, non-throwaway research software project that follows good open-source practices (license, documentation, tests and/or verification processes, releases, and clear contribution/support pathways).

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 (required section): 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 (required section): 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 (required section): Do the authors describe how this software compares to other commonly-used packages? If related tools exist, do they provide a clear "build vs. contribute" justification explaining their unique scholarly contribution and why alternatives are insufficient?
• Software Design (required section): Does the paper include a "Software Design" section that explains the trade-offs weighed, the design/architecture chosen, and why it matters? Is the content compelling and does it demonstrate meaningful design thinking?
• Research Impact Statement (required section): Does the paper include a "Research Impact Statement" section providing evidence of realized impact (publications, external use, integrations) or credible near-term significance (benchmarks, reproducible materials, community-readiness signals)? Is the evidence presented compelling?
• AI usage disclosure (required section): Does the paper include an "AI usage disclosure" section that transparently discloses any use of generative AI in the software creation, documentation, or paper authoring?
• 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?

[uellue]

All in all it looks like a simple, but very handy tool with a clearly defined use case: Ergonomic coordinate labeling for further downstream processing. However, a few points from the review checklist are still open for me. Most importantly, I'd need more and better high-level documentation to understand what TACtool does, exactly, how to apply it in practice and also use it beyond a very specific laser ablation tool. Such wider application is advertised in the "Research Impact Statement", meaning the documentation should match this claim.

Installation

• Developer installation can be made much simpler by turning it into a proper Python package. The provided installation method with very specific environment files didn't work for me because Anaconda repositories are blocked for my organization and we have to use conda-forge only. I've opened a PR with changes that made developer installation very easy for me and follows the pattern of many Python-based projects: Installable Python package with pyproject.toml BritishGeologicalSurvey/tactool#17

State of the field

• Which tools are supported / reported to work / still TODO / ...? Right now it seems only one specific tool by ESI is supported? It looks like the role and functionality of labeling software is closely intertwined with the workflows and user interfaces of laser ablation tools, so the two should be put in relation here.

Documentation, functionality

• The referencing process between SEM and laser ablation coordinate systems should be described more clearly. In the GUI I found an option to set "reference points", but I couldn't easily work out what I'd have to do with a real-world SEM image. Also, I have a number of additional questions:
  • Does TACtool read any kind of metadata, e.g. scale and offset, from the SEM images or are they just plain images with pixel coordinates?
  • Specifically, do the reference points have to be included in the same image as the intended measurements, or can the software relate them through embedded metadata in the SEM images?
  • What SEM image formats are supported? Anything specific from ISO/DIS 20171, which seems relevant for SEM?
  • The role of "scale" is completely unclear to me. TACtool asks for me to set it, but how and why was not easy to figure out.
  • How exactly does the laser ablation tool deal with the referencing? In the very detailed "ESI import" instructions it seems that the user finds and marks their reference points using the GUI of the tool? Do all tools work the same or are there differences? That should be described in a generic high-level workflow description.
  • Is it possible to output coordinates in the CSV file in a calibrated coordinate system, e.g. by assigning coordinates to the reference points, or are the coordinates always calibrated and transformed by a downstream tool, like it seems in the ESI example? The paper hints at generating lists of calibrated coordinates, so this should be clarified.
  • How should one approach reference points in practice? Are alignment marks included on the mounts, or does one pick specific features on the specimen itself? Or does one add markers somehow during specimen preparation or imaging? Any practical guidance will probably be valuable for novice users!
  • What SEM magnifications are a good choice? It seems that the SEM can achieve a much higher spatial resolution than optical images from the laser ablation tool?
  • How can a user check if the alignment is correct? E.g. look for the "impact craters" in SEM images after ablation? I'm not an expert for this method at all, but since you mention reproducibility and reliability, would it make sense to collect another set of SEM images post ablation routinely to verify the correct locations were hit, or verify the locations through some other means?
• The schema for CSV files generated by TACtool resp. accepted by various ablation tools should be described or referenced. Right now one has to guess. In particular, units are important and not always obvious! Is it the same for all tools, or is the input vendor-specific? Is a standard or quasi-standard established and documented somewhere?
• Is it possible to specify/load schemas for different tools? It would be great if the output was configurable, that would make it much more useful for wider application! We have very similar issues in TEM -- relating coordinates from different analysis methods.
• The instructions.md should include more high-level workflow descriptions. Right now it contains a lot of info that is kind of obvious ("material: The material assigned to the analysis point", detailed instructions on how to use a common file selection dialogue, ...), but not what role that info plays in the larger picture. E.g., is "material" interpreted by the ablation tool, and how does it influence results? What role does the colour play? ...

Since I don't have access to laser ablation tools, I can't test the functionality completely. I'd check off the functionality and documentation items once I can understand from the documentation how the referencing process works for the targeted laser ablation tools, what role TACtool and the generated CSV files play, and the functionality is described in such a way that I can gauge if and how I can apply TACtool for techniques that I am more familiar with, such as TEM-related workflows.