Automated thresholding suggestions

[JeremyPike]

Three suggestions:

1. The text interpreting the histogram of data/maize-root-cluster.jpg implies that the peak at near 1.0 corresponds to the signal we are interested in (the root). This is actually the label and disk as covered later in the episode. Text altered and more detailed explanation added.
2. Variable names with underscores to be consistent.
3. In the solution to "IGNORING MORE OF THE IMAGES – IMPLEMENTATION (30 MIN - OPTIONAL, NOT INCLUDED IN TIMING)" the bright pixels (>0.95) are set to zero before calculating the Otsu threshold. I think it is best practice to just exclude them when calculating the threshold as the additional zero pixels will slightly distort the histogram. Solution altered to use this approach.

[github-actions]

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⏱️ Updated at 2024-02-01 14:16:02 +0000

[tobyhodges]

Thank you for making these suggestions @JeremyPike. They are technically correct (the best kind of correct) but I am not sure I prefer your ordering of things in terms of managing cognitive load/designing a learning experience.

I would like a second opinion and have requested input from my fellow Maintainers. Given her recent engagement with the curriculum, I will also tag @mkcor.

[tobyhodges]

I'd like to get this PR resolved soon, and we would benefit from input on the discussion above from other @datacarpentry/image-processing-curriculum-maintainers and/or @datacarpentry/curriculum-advisors-image

[uschille]

Thanks for this PR @JeremyPike , these are great observations. I taught the curriculum last week and indeed framed the binary thresholding as a way to separate foreground and background, as @tobyhodges mentioned. I agree though that it would be good to be a bit more precise about the peaks in the histogram (I was actually expecting questions from learners). I've taken a stab at editing the suggestion.

As a side note, Otsu's method does not work well for the first image (the colored shapes) in the lesson. This could be a good example for instructors to discuss provided there is time. I've added an instructors note on this.

[tobyhodges]

Thanks for engaging @uschille. @JeremyPike if you have time to respond and let us know how you feel about Ulf's (and my) proposed changes, we may be able to get this merged soon.

[JeremyPike]

Thanks for engaging @uschille. @JeremyPike if you have time to respond and let us know how you feel about Ulf's (and my) proposed changes, we may be able to get this merged soon.

Thank you @uschille @mkcor and @tobyhodges for all the great suggestions and comments. In order to bring this together I've made some commits which try to implement what I perceive the consensus to be. Its potentially ready to merge now after a quick sanity check but happy to put in more changes too :)

[tobyhodges]

I have made one suggestion to fix my own typo from yesterday, but otherwise this is looking very good. Thanks so much for coming back to it, @JeremyPike.

[tobyhodges]

If I recall correctly, @JeremyPike will be teaching the lesson in a workshop soon. I hope it goes well, and please return with more constructive feedback and suggested improvements based on your experience!

[JeremyPike]

If I recall correctly, @JeremyPike will be teaching the lesson in a workshop soon. I hope it goes well, and please return with more constructive feedback and suggested improvements based on your experience!

Thanks @tobyhodges, will do!