Change shapes image #99

stellaprins · 2025-11-10T11:50:41Z

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.

only suitable -> best suitable

github-actions · 2025-11-10T11:50:55Z

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}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

🎯 correct output
🖼️ correct figures
❓ new warnings
‼️ new errors

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:

episodes/filters-and-thresholding.md

Co-authored-by: Kimberly Meechan <[email protected]>

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 · 2025-11-19T22:28:44Z

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.

episodes/filters-and-thresholding.md

K-Meech

Thanks @stellaprins - I'll merge this now 🎉

Auto-generated via `{sandpaper}` Source : ec1da21 Branch : main Author : Kimberly Meechan <[email protected]> Time : 2025-11-21 09:10:04 +0000 Message : Merge pull request #99 from stellaprins/sp/otsu Change shapes image

Auto-generated via `{sandpaper}` Source : 1439450 Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2025-11-21 09:10:54 +0000 Message : markdown source builds Auto-generated via `{sandpaper}` Source : ec1da21 Branch : main Author : Kimberly Meechan <[email protected]> Time : 2025-11-21 09:10:04 +0000 Message : Merge pull request #99 from stellaprins/sp/otsu Change shapes image

stellaprins added 4 commits November 7, 2025 15:48

swap brightness rectangle and triangle

0b66d97

slightly change wording to increase nuance

916d35f

only suitable -> best suitable

Merge branch 'HealthBioscienceIDEAS:main' into sp/otsu

2415e9c

update shape images

0f3b5e3

github-actions bot pushed a commit that referenced this pull request Nov 10, 2025

differences for PR #99

e937955

remove unused images

049ae14

github-actions bot pushed a commit that referenced this pull request Nov 10, 2025

differences for PR #99

5cd8e7a

K-Meech self-requested a review November 13, 2025 11:07

K-Meech reviewed Nov 13, 2025

View reviewed changes

episodes/filters-and-thresholding.md Outdated Show resolved Hide resolved

episodes/filters-and-thresholding.md Outdated Show resolved Hide resolved

best -> most

24a6f20

Co-authored-by: Kimberly Meechan <[email protected]>

github-actions bot pushed a commit that referenced this pull request Nov 18, 2025

differences for PR #99

b34ff29

add mean and update descriptions

f55917e

github-actions bot pushed a commit that referenced this pull request Nov 19, 2025

differences for PR #99

819d99b

stellaprins requested a review from K-Meech November 19, 2025 11:10

K-Meech reviewed Nov 19, 2025

View reviewed changes

update shapes-thresholds png

4e7df6d

github-actions bot pushed a commit that referenced this pull request Nov 19, 2025

differences for PR #99

ca35871

K-Meech reviewed Nov 20, 2025

View reviewed changes

episodes/filters-and-thresholding.md Show resolved Hide resolved

swarp triangle and square in list of peaks histogram

3e9a7cc

stellaprins requested a review from K-Meech November 21, 2025 07:29

github-actions bot pushed a commit that referenced this pull request Nov 21, 2025

differences for PR #99

4d4c9b6

K-Meech approved these changes Nov 21, 2025

View reviewed changes

K-Meech merged commit ec1da21 into HealthBioscienceIDEAS:main Nov 21, 2025
4 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Change shapes image #99

Change shapes image #99

Uh oh!

stellaprins commented Nov 10, 2025 •

edited

Loading

Uh oh!

github-actions bot commented Nov 10, 2025 •

edited

Loading

Uh oh!

K-Meech left a comment

Uh oh!

Uh oh!

Uh oh!

K-Meech left a comment

Uh oh!

stellaprins commented Nov 19, 2025

Uh oh!

K-Meech left a comment

Uh oh!

Uh oh!

K-Meech left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Change shapes image #99

Change shapes image #99

Uh oh!

Conversation

stellaprins commented Nov 10, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Previous mask created by Otsu thresholding

New mask created by Otsu thresholding

New figure mask panels with thresholding labels

Uh oh!

github-actions bot commented Nov 10, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Thank you!

Rendered Changes

Uh oh!

K-Meech left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

K-Meech left a comment

Choose a reason for hiding this comment

Uh oh!

stellaprins commented Nov 19, 2025

Uh oh!

K-Meech left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

K-Meech left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

stellaprins commented Nov 10, 2025 •

edited

Loading

github-actions bot commented Nov 10, 2025 •

edited

Loading