Labels 2D

Display a labels layer above of an image layer using the add_labels and add_image APIs

Tags: visualization-basic

Python (.py)

Notebook (.ipynb)

/home/runner/work/docs/docs/.venv/lib/python3.12/site-packages/napari/_qt/qt_event_loop.py:50: UserWarning: System theme detection requires a Qt6 backend. Please switch to PyQt6 or PySide6 to use it.
  theme_type=get_system_theme(),
/home/runner/work/docs/docs/.venv/lib/python3.12/site-packages/napari/_qt/qt_event_loop.py:50: UserWarning: System theme detection requires a Qt6 backend. Please switch to PyQt6 or PySide6 to use it.
  theme_type=get_system_theme(),
The color of label 5 is [0.2784314  0.22745098 0.62352943 1.        ]

from skimage import data
from skimage.color import rgb2gray
from skimage.segmentation import slic

import napari

astro = data.astronaut()

# initialise viewer with astro image
viewer = napari.Viewer()
layer = viewer.add_image(rgb2gray(astro), name='astronaut', rgb=False)

# add the labels
# we add 1 because SLIC returns labels from 0, which we consider background
labels = slic(astro, channel_axis=-1, compactness=20) + 1
label_layer = viewer.add_labels(labels, name='segmentation')

# Set the labels layer mode to picker with a string
label_layer.mode = 'PICK'
print(f'The color of label 5 is {label_layer.get_color(5)}')

if __name__ == '__main__':
    napari.run()