Open Image with Napari¶

Open image data (e.g. RGB, gray, hyperspectral) with an interactive Napari viewer. Labeled masks may be colorized for better visualization.

plantcv.annotate.napari_open(img, mode='native', show=True)

returns napari viewer object

• Parameters:

  • img - image data (compatible with gray, RGB, and hyperspectral data. If data is hyperspecral it should be the array e.g. hyperspectral.array_data)
  • mode - 'native' or 'colorize'. If 'colorized' is selected gray images will be colorized.
  • show - if show = True, viewer is launched. False setting is useful for test purposes.

• Context:

  • Used to open image data with Napari.

• Example use:

  • Open image data to annotate it with other Napari functions (e.g. napari_label_classes)

import plantcv.plantcv as pcv 
import plantcv.annotate as pcvan

# Create an instance of the Points class
img, path, name = pcv.readimage("./grayimg.png")

viewer = pcvan.napari_open(img=img, mode='colorize')

# Should open interactive napari viewer

Source Code: Here