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remove use of deprecated binary_erosion #123

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Merged
K-Meech merged 1 commit into from
Jun 5, 2026
Merged

remove use of deprecated binary_erosion #123

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18 changes: 9 additions & 9 deletions episodes/instance-segmentation-and-measurements.md
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Original file line number Diff line number Diff line change
Expand Up @@ -281,15 +281,15 @@ apparent size of the nuclei by eroding the image.
Image erosion is an image filter, similar to those we covered in the
[filters and thresholding](filters-and-thresholding.md) lesson.
We will use scikit-image's
[binary_erosion](
https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.binary_erosion)
function. In this lesson we will run the binary erosion function using
[erosion](
https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.erosion)
function. In this lesson we will run the erosion function using
the Napari console to help develop our scripting skills. It is also
possible to run the binary erosion function through a plugin:
`Layers > Filter > Morphology > Binary Morphology (napari skimage)`
possible to run the erosion function through a plugin:
`Layers > Filter > Morphology > Morphology (napari skimage)`
if you prefer.

The binary erosion function sets a pixel to the
The erosion function sets a pixel to the
minimum value in the neighbourhood defined by a `footprint` parameter.
We'll use scikit-image's [ball](
https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.ball)
Expand All @@ -303,11 +303,11 @@ the `semantic_seg` layer with different integer values for the radius.
What radius do you need to ensure all nuclei are separate?

```python
from skimage.morphology import binary_erosion, ball
from skimage.morphology import erosion, ball

# With radius = 1
radius = 1
eroded_mask = binary_erosion(semantic_seg, footprint = ball(radius))
eroded_mask = erosion(semantic_seg, footprint = ball(radius))
viewer.add_labels(eroded_mask, name = f'eroded ball {radius}')
```

Expand All @@ -324,7 +324,7 @@ which enables us to test multiple values of radius quickly.
# The for loop will repeat the indented lines of codes for each value
# of radius in the list (1, 5, 10).
for radius in 1, 5, 10:
eroded_mask = binary_erosion(semantic_seg, footprint = ball(radius))
eroded_mask = erosion(semantic_seg, footprint = ball(radius))
viewer.add_labels(eroded_mask, name = f'eroded ball {radius}')

```
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4 changes: 2 additions & 2 deletions episodes/quality-control-and-manual-segmentation.md
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Expand Up @@ -192,11 +192,11 @@ the details of what's happening here - we'll look at some of these concepts in
later episodes.

```python
from skimage.morphology import binary_erosion, ball
from skimage.morphology import erosion, ball
from skimage.segmentation import expand_labels
from skimage.measure import label

eroded = binary_erosion(semantic_seg, footprint=ball(10))
eroded = erosion(semantic_seg, footprint=ball(10))
instance_seg = label(eroded)
instance_seg = expand_labels(instance_seg, distance=10)

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