New Tutorial: Detection of Mitoflashes

[dianichj]

New Imaging Tutorial Alert! 🚨🔬🚀

Summary:
This PR introduces a new tutorial for the Detection of Mitoflashes workflow. It guides users through tracking mitochondrial movement and identifying mitoflashes using Galaxy tools, covering data preparation, mitochondrial region detection, movement tracking, and mitoflash analysis.

TODO:

• Polish the tutorial content for clarity and quality.
• Verify that all tool links in the tutorial are correct and functional. Update links if necessary.
• Review all new files to ensure they are in the correct format and contain accurate content:
  • Confirm that tutorial.md follows the required structure and format for Galaxy tutorials.
  • Check any included datasets, images, and supplementary files for accuracy and relevance.
  • Ensure that all files meet Galaxy Training Network (GTN) standards.
• Confirm that any images used are approved for re-hosting by the GTN and are appropriately licensed.
• Test each step in the tutorial workflow to ensure completeness and accuracy, making modifications as needed to improve clarity and usability.

cc: @kostrykin 🤝

[dianichj]

Hi @kostrykin! When you have time, could you please check the tutorial again? I submitted it for review. I wanted to add an image that shows/explains the biological mechanism of mitoflashes but couldn't find one with a flexible license. If you have ideas on an image or can add an image to the tutorial, I think it will super helpful.
Thank you!

[dianichj]

Fantastic job, @dianichj!

A few comments inside.

Please also consider using the Oxford comma. I'm not aware of any guideline by the GTN, but personally I think it greatly improves readability in technical documents.

Thanks a lot @kostrykin. I checked the file where I missed the Oxford comma. I hope that I didn't miss any comma spots. I also added two images to the tutorial. One of the them is of the Curve fitting file output.

[kostrykin]

Much thanks for all your work @dianichj

I have a few more comments :)

[kostrykin]

Not quite clear what the parameters Amplitude, T50, and Tpk refer to. The tool doesn't have those parameters?

[dianichj]

Thank you for asking! These parameters—Amplitude, Tpk, and T50—are not input parameters of the tool but are derived metrics used to measure mitoflash events. In biology, they are commonly reported to quantify and analyze mitochondrial dynamics.

For example:

• Amplitude measures the peak intensity of the flash.
• Tpk reflects the time it takes to reach this peak.
• T50 indicates the duration of the flash.

These values are useful for plotting and interpreting mitoflash dynamics in biological studies. Perhaps it would be more accurate to call these "metrics that can be extracted from the output for plotting"?

Several papers mention these metrics; for example, this one.

Rather than being annotations, these metrics are quantitative descriptors that help summarize and interpret key features of mitoflash events. Please let me know what you think and if this helps the clarification. I wanted to add this info to guide the user to the analysis and interpretation part.

[kostrykin]

Very cool! Now this might be somewhat picky of me, but if you have the time, I think it would be better to show the table for a different spot (I suspect that there is a spot for which the INTENSITY value somewhere exceeds the CURVE_A value, is there?)

[dianichj]

I will find it and add it =D! Maybe we can add a question here for it then? - Hahah more work

[kostrykin]

I think this needs to be adapted to be more consistent with the description of the curves above (see this and this comment). Where do those terms Amplitude, Tpk, T50 come from? I couldn't find them in the curve fitting tool.