[JOSS Review] Statement of need and the paper

[mbarzegary]

Dear authors,

The paper is written well, but these issues should be addressed:

• More elaboration is needed on "The updated version is better designed, more efficient, and significantly more user-friendly" and "significant enhancements over its predecessor, such as new algorithms for improved sarcomere detection and tracking, faster computation times, and a more user-friendly library design". These sentences seem to be qualitative. Can you provide more details leading to such a conclusion?
• Why is the new algorithm more efficient than the previous one (Zhao et al. 2021)? A quantitative comparison is needed here. Comparing and elaborating on the differences between Fig 4 in this paper and Fig 6 of the previous publication can be helpful here.
• "SarcGraph is readily customizable and adaptable by the user", how is this going to come into practice? How is this customizability foreseen considering that the software comprises only 2 big source files?
• The scale bar is missing in the paper figures.
• It can be nice to mention how the reader should proceed to reproduce the figures of the paper?
• The JOSS guidelines require the paper to contain a section titled "statement of need", which is missing in this case. Part of the summary is already discussing it, but a separate section with more elaboration on the target group of users is desired. The software should also be compared to other available tools in this section.
• I think it is beneficial if you mention the limitations of the library briefly (can be in the documentation instead).

P.S. This issue is related to https://github.com/openjournals/joss-reviews/issues/5322

[saeedmhz]

We appreciate your thorough feedback on the manuscript and the opportunity to address the concerns raised. In response to your comments, we have directly implemented the following changes:

1. We introduced a new section in the manuscript titled “SarcGraph vs. Legacy Sarc-Graph,” which discusses the key differences and improvements between the two versions.
2. In the same section, we offer a quantitative comparison of the run time and sarcomere tracking performance for both versions of SarcGraph using an experimental sample video (displayed in Figure 2, left panel) and a synthetically generated sample (depicted in Figure 4).
3. We believe that the addition of specific guides for developer in response to Sarc-Graph/sarcgraph#2 and Sarc-Graph/sarcgraph#3 will better facilitate users interested in extending the software. By customizability, we mostly meant that our code is structured to enable the use of individual steps in isolation or to be replaced with further development. This distinction should be clearer in the revised manuscript.
4. We have incorporated a scale bar in Figure 2, as it was the only plot requiring one.
5. In the appendix, we included code snippets for reproducing the figures 2-4 and added ground truth data for the synthetic sample in Figure 4 to the repository under the ‘validation-data’ folder.
6. We have added a “Statement of Need” section that comprehensively addresses the challenges of the field and the target user group.
7. Lastly, we included a section in the manuscript titled “Current Limitations and Plans for Future Development,” which outlines the software’s limitations and potential future directions. We hope that these revisions adequately address your concerns, and we welcome any further comments or suggestions. Again, the time taken to provide this comprehensive feedback is much appreciated.

We hope that these revisions adequately address your concerns, and we welcome any further comments or suggestions. Again, the time taken to provide this comprehensive feedback is much appreciated.