[PRE REVIEW]: TrackSegNet: a tool for trajectory segmentation into diffusive states using supervised deep learning

[editorialbot]

Submitting author: !--author-handle-->@hkabbech<!--end-author-handle-- (Hélène Kabbech) Repository: https://github.com/hkabbech/TrackSegNet Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @imagejan, @ajasja Managing EiC: Kevin M. Moerman

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[ajasja]

@Kevin-Mattheus-Moerman Yes, I could do it. Does it matter that the method was already described in this article: https://academic.oup.com/nar/article/51/20/10992/7288829

[Kevin-Mattheus-Moerman]

@editorialbot add @ajasja as reviewer

[editorialbot]

@ajasja added to the reviewers list!

[Kevin-Mattheus-Moerman]

@ajasja thanks for volunteering to review. At first sight it looks like the core purpose of that newer paper is to describe the application of this work to a particular scientific research topic. I will review this in more detail. For the moment I'll ask the authors to point out the key difference/purpose for these papers.

@hkabbech could you please provide a brief but clear description of the major advances you've made to the software since this paper: doi.org/10.1038/s41598-019-53663-8 (I have this in the notes to the editor but would be good to reiterate this clearly here for the reviewers too), and could you clarify the key differences with the current paper and this new one: https://academic.oup.com/nar/article/51/20/10992/7288829 thanks.

[hkabbech]

At the moment of submitting our work, the idea was to submit the software to JOSS for a better review of the tool/method, and a particular application (together with other experiments) to a biology journal where reviewers focus more on the discovery and biological methods employed. Both papers were submitted around the same time this year, while the biology paper got reviewed and published in only a few months (https://doi.org/10.1093/nar/gkad803), the pre-review process of the software paper was severely delayed.. Thus, in the meantime, we had to publish the code on Zenodo (https://zenodo.org/records/7767750).

The method was initially developed in our research group and published in 2019 (https://doi.org/10.1038/s41598-019-53663-8). The current software presents major improvements of our method and permits the replicability on other trajectory datasets. It contains also additional plotting measurements for interpretability of trajectory segmentation results.

We are still interested in getting our software reviewed by JOSS and hope this will still be possible.

[Kevin-Mattheus-Moerman]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6157.