Image points 3D

Display points overlaid on a 3D image

Tags: visualization-nD

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(),

from skimage import data, feature, filters

import napari

cells = data.cells3d()
nuclei = cells[:, 1]
smooth = filters.gaussian(nuclei, sigma=10)
pts = feature.peak_local_max(smooth)
viewer = napari.Viewer(ndisplay=3)
membranes, nuclei = viewer.add_image(
    cells, channel_axis=1, name=['membranes', 'nuclei']
)
viewer.add_points(pts)
viewer.camera.angles = (10, -20, 130)
viewer.fit_to_view()

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