1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
|
"""
Add labels
==========
Display a labels layer above of an image layer using the ``add_labels`` and
``add_image`` APIs
.. tags:: layers, visualization-basic
"""
from skimage import data
from skimage.filters import threshold_otsu
from skimage.measure import label
from skimage.morphology import closing, remove_small_objects, square
from skimage.segmentation import clear_border
import napari
image = data.coins()[50:-50, 50:-50]
# apply threshold
thresh = threshold_otsu(image)
bw = closing(image > thresh, square(4))
# remove artifacts connected to image border
cleared = remove_small_objects(clear_border(bw), 20)
# label image regions
label_image = label(cleared).astype('uint8')
# initialise viewer with coins image
viewer = napari.Viewer()
layer = viewer.add_image(image, name='coins', rgb=False)
# add the labels
label_layer = viewer.add_labels(label_image, name='segmentation')
if __name__ == '__main__':
napari.run()
|
