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Merge branch 'main' of https://github.com/haesleinhuepf/napari-segmen…
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…t-blobs-and-things-with-membranes
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@haesleinhuepf
haesleinhuepf committed Mar 26, 2024
2 parents 1ed7b9a + c547b79 commit ac81a86
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157 changes: 153 additions & 4 deletions napari_segment_blobs_and_things_with_membranes/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,12 @@
from skimage.filters import threshold_otsu as sk_threshold_otsu, gaussian, sobel
from skimage.segmentation import watershed
from skimage.feature import peak_local_max
from skimage.morphology import binary_opening
from skimage.measure import label
from skimage.morphology import local_maxima, local_minima
from skimage.morphology import local_maxima, local_minima, opening, closing, erosion, dilation, disk, ball
from skimage.morphology import binary_opening as sk_binary_opening
from skimage.morphology import binary_closing as sk_binary_closing
from skimage.morphology import binary_erosion as sk_binary_erosion
from skimage.morphology import binary_dilation as sk_binary_dilation
from skimage.restoration import rolling_ball
from napari_tools_menu import register_function
from skimage.measure import regionprops
Expand Down Expand Up @@ -61,7 +64,15 @@ def napari_experimental_provide_function():
Manually_split_labels,
rescale,
resize,
extract_slice
extract_slice,
grayscale_erosion,
binary_erosion,
grayscale_dilation,
binary_dilation,
grayscale_closing,
binary_closing,
grayscale_opening,
binary_opening
]


Expand All @@ -88,6 +99,16 @@ def _sobel_3d(image):
return ndi.convolve(image, kernel)


def _generate_disk_footprint(radius, ndim):
"""Generate a disk/sphere footprint (for 2D or 3D) with the given radius."""
if ndim == 2:
return disk(radius)
elif ndim == 3:
return ball(radius)
else:
raise ValueError("Disk footprints are only implemented for 2D or 3D images")


@register_function(menu="Segmentation post-processing > Split touching objects (nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
Expand Down Expand Up @@ -125,7 +146,7 @@ def split_touching_objects(binary:"napari.types.LabelsData", sigma: float = 3.5)
edges2 = _sobel_3d(binary)

almost = np.logical_not(np.logical_xor(edges != 0, edges2 != 0)) * binary
return binary_opening(almost)
return sk_binary_opening(almost)


@register_function(menu="Segmentation / binarization > Threshold (Otsu et al 1979, scikit-image, nsbatwm)")
Expand Down Expand Up @@ -944,3 +965,131 @@ def sub_sample(image:"napari.types.ImageData", sample_x: int = 1, sample_y: int
@time_slicer
def squeeze(image:"napari.types.ImageData") -> "napari.types.ImageData":
return np.squeeze(image)


@register_function(menu="Filtering / background removal > Grayscale erosion (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def grayscale_erosion(labels: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies grayscale erosion to an image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.erosion
"""

footprint = _generate_disk_footprint(radius, labels.ndim)
return erosion(labels, footprint=footprint)


@register_function(menu="Segmentation post-processing > Binary erosion (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def binary_erosion(binary_image: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies binary erosion to a binary image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.binary_erosion
"""

footprint = _generate_disk_footprint(radius, binary_image.ndim)
return sk_binary_erosion(binary_image, footprint=footprint)


@register_function(menu="Filtering / background removal > Grayscale dilation (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def grayscale_dilation(labels: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies grayscale dilation to an image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.dilation
"""

footprint = _generate_disk_footprint(radius, labels.ndim)
return dilation(labels, footprint=footprint)


@register_function(menu="Segmentation post-processing > Binary dilation (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def binary_dilation(binary_image: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies binary dilation to a binary image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.binary_dilation
"""

footprint = _generate_disk_footprint(radius, binary_image.ndim)
return sk_binary_dilation(binary_image, footprint=footprint)


@register_function(menu="Filtering / background removal > Grayscale opening (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def grayscale_opening(labels: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies grayscale opening to an image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.opening
"""

footprint = _generate_disk_footprint(radius, labels.ndim)
return opening(labels, footprint=footprint)


@register_function(menu="Segmentation post-processing > Binary opening (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def binary_opening(binary_image: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies binary opening to a binary image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.binary_opening
"""

footprint = _generate_disk_footprint(radius, binary_image.ndim)
return sk_binary_opening(binary_image, footprint=footprint)


@register_function(menu="Filtering / background removal > Grayscale closing (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def grayscale_closing(labels: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies grayscale closing to an image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.closing
"""

footprint = _generate_disk_footprint(radius, labels.ndim)
return closing(labels, footprint=footprint)


@register_function(menu="Segmentation post-processing > Binary closing (scikit-image, nsbatwm)")
@jupyter_displayable_output(library_name='nsbatwm', help_url='https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes')
@time_slicer
def binary_closing(binary_image: "napari.types.LabelsData", radius: int = 1) -> "napari.types.LabelsData":
"""
Applies binary opening to a binary image, using a disk/sphere footprint with the given radius.
See also
--------
..[0] https://scikit-image.org/docs/stable/api/skimage.morphology.html#skimage.morphology.binary_closing
"""

footprint = _generate_disk_footprint(radius, binary_image.ndim)
return sk_binary_closing(binary_image, footprint=footprint)
49 changes: 37 additions & 12 deletions napari_segment_blobs_and_things_with_membranes/_tests/test_function.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,14 +42,24 @@ def test_something():
butterworth, \
extract_slice, \
sub_sample, \
squeeze
squeeze, \
grayscale_erosion, \
binary_erosion, \
grayscale_dilation, \
binary_dilation, \
grayscale_opening, \
binary_opening, \
grayscale_closing, \
binary_closing

import numpy as np

image = np.asarray([[0, 1, 2, 3],
[2, 0, 1, 3],
[2, 253, 1, 3],
[255, 253, 1, 3]])
image_2d = np.asarray([[0, 1, 2, 3],
[2, 0, 1, 3],
[2, 253, 1, 3],
[255, 253, 1, 3]])

image_3d = np.ones((4, 4, 4))

for operation in [gaussian_blur,
subtract_background,
Expand Down Expand Up @@ -84,7 +94,7 @@ def test_something():

print(operation)

operation(image)
operation(image_2d)

for operation in [
seeded_watershed,
Expand All @@ -94,13 +104,28 @@ def test_something():

print(operation)

operation(image, image)

skeletonize(image > 0)
operation(image_2d, image_2d)

seeded_watershed_with_mask(image, image, image)

mode_filter(image.astype(int))
for operation in [
grayscale_erosion,
binary_erosion,
grayscale_dilation,
binary_dilation,
grayscale_opening,
binary_opening,
grayscale_closing,
binary_closing
]:
for image in (image_2d, image_3d):
labels = image > 0
print(f"{operation} with {labels.ndim}d image")
operation(labels)

skeletonize(image_2d > 0)

seeded_watershed_with_mask(image_2d, image_2d, image_2d)

mode_filter(image_2d.astype(int))

def test_remove_labels_on_edges_sequential_labeling():
image = np.asarray([
Expand Down

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