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remove use of deprecated binary_erosion#123

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K-Meech merged 1 commit into
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km/remove-binary-erosion
Jun 5, 2026
Merged

remove use of deprecated binary_erosion#123
K-Meech merged 1 commit into
mainfrom
km/remove-binary-erosion

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@K-Meech

@K-Meech K-Meech commented Jun 4, 2026

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Closes #121

binary_erosion has been deprecated in the last skimage release. To avoid deprecation warnings (see issue), this PR removes binary_erosion in favour of erosion. I checked and all segmentation results look the same.

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K-Meech requested a review from thompson318 June 4, 2026 14:24
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github-actions Bot commented Jun 4, 2026

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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
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Rendered Changes

🔍 Inspect the changes: https://github.com/HealthBioscienceIDEAS/microscopy-novice/compare/md-outputs..md-outputs-PR-123

The following changes were observed in the rendered markdown documents:

 instance-segmentation-and-measurements.md  | 18 +++++++++---------
 md5sum.txt                                 |  4 ++--
 quality-control-and-manual-segmentation.md |  4 ++--
 3 files changed, 13 insertions(+), 13 deletions(-)
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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.

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⏱️ Updated at 2026-06-04 14:26:21 +0000

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K-Meech requested a review from stellaprins June 4, 2026 14:24

@thompson318 thompson318 left a comment

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Works for me.

@K-Meech

K-Meech commented Jun 5, 2026

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Thanks @thompson318 - I'll go ahead and merge this.

@stellaprins - just tagging you here so you are aware of this change (as it affects the segmentation episodes you'll be teaching next week) - this is a simple replacement of binary_erosion with erosion, as binary_erosion has been deprecated.

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K-Meech merged commit 87f4e36 into main Jun 5, 2026
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@K-Meech
K-Meech deleted the km/remove-binary-erosion branch June 5, 2026 12:53
github-actions Bot pushed a commit that referenced this pull request Jun 5, 2026
Auto-generated via `{sandpaper}`
Source  : 87f4e36
Branch  : main
Author  : Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Time    : 2026-06-05 12:52:57 +0000
Message : Merge pull request #123 from HealthBioscienceIDEAS/km/remove-binary-erosion

remove use of deprecated binary_erosion
github-actions Bot pushed a commit that referenced this pull request Jun 5, 2026
Auto-generated via `{sandpaper}`
Source  : 621e5ef
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2026-06-05 12:55:05 +0000
Message : markdown source builds

Auto-generated via `{sandpaper}`
Source  : 87f4e36
Branch  : main
Author  : Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Time    : 2026-06-05 12:52:57 +0000
Message : Merge pull request #123 from HealthBioscienceIDEAS/km/remove-binary-erosion

remove use of deprecated binary_erosion
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Update instance segmentation code to avoid deprecation warnings

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