Layer units impact rendering

This example demonstrates how units can impact rendering in napari. Two layers are added with different scales, however by specifying the units, napari is able to render them in the same physical space using the unit-aware library Pint [1]. The first layer is in nanometers and the second layer is in micrometers, but they are rendered in the same physical space because 1 μm = 1000 nm.

[1]

https://pint.readthedocs.io/en/stable/

Tags: visualization-advanced, layers

import skimage

import napari

data = skimage.data.cells3d()

membrane = data[:, 0]
nuclei = data[:, 1]

viewer = napari.Viewer()
viewer.add_image(
    membrane,
    name='membrane-nm',
    units=('nm', 'nm', 'nm'),
    scale=(210, 70, 70),
    colormap='magenta'
)
viewer.add_image(
    nuclei,
    name='nuclei-μm',
    units=('μm', 'μm', 'μm'),
    scale=(0.210, 0.07, 0.07),
    colormap='green',
    blending='additive'
)

viewer.dims.ndisplay = 3
viewer.camera.angles = (-20, 20, -20)
viewer.fit_to_view()

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