Change shapes image

[stellaprins]

Why is this PR needed?
A demonstration of the Otsu thresholding method not performing robustely on images that do not have bimodal distributions of pixel values would make more sense given the context of the lesson material.

What does this PR do?

• Swaps around the average pixel intensity of the rectangle with that of the triangle.
• Updates Figures with the new masks and image with shapes and figure of image histogram
• Instead of having Figures of all the masks seperately they are presented as one figure with different panels with Thresholding method labels
• Adds nuance about the Otsu method: "This means it’s only most suitable for images that show two clear peaks in their histogram (also known as a ‘bimodal’ histogram"

Previous mask created by Otsu thresholding

New mask created by Otsu thresholding

New figure mask panels with thresholding labels

Linked issues
Resolves #98

How was this PR tested?
I built and checked the documentation locally and checked whether it looked like I expected.

[github-actions]

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

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Rendered Changes

🔍 Inspect the changes: https://github.com/HealthBioscienceIDEAS/microscopy-novice/compare/md-outputs..md-outputs-PR-99

The following changes were observed in the rendered markdown documents:

 fig/shapes-histogram.png (new)  | Bin 0 -> 6045 bytes
 fig/shapes-thresholds.png (new) | Bin 0 -> 289934 bytes
 fig/shapes.png (new)            | Bin 0 -> 33012 bytes
 filters-and-thresholding.md     |  48 +++++++++++++++-------------------------
 md5sum.txt                      |   2 +-
 5 files changed, 19 insertions(+), 31 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2025-11-21 07:30:27 +0000

[K-Meech]

Thanks @stellaprins - this looks great! I agree this change makes the differences between the thresholding methods clearer + the otsu explanation less confusing.

I've put a couple of very minor comments below:

[K-Meech]

Thanks @stellaprins - looking great!
Could you possibly put the mask images into a grid (e.g. around 2 per line), rather than all in one line? Now there are 5, they end up quite small in the final rendered site, so it's a bit hard to see the differences. No worries if this is hard to change!

[stellaprins]

Yes, good call! What do you think of 3 per line (and including the original) as I've done now?

Happy to change it to 2 per line :)

[K-Meech]

Thanks @stellaprins - really like the new grid layout! Much easier to see the images 😄

I noticed one final part that needs to be updated in the text (the order of the peaks in the first exercise), but otherwise this is ready to merge.

[K-Meech]

Thanks @stellaprins - I'll merge this now 🎉