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OMERO CLI plugin to view images in napari

Project description


OMERO CLI client to open images in the napari viewer.

Requires Python 3.6 or higher and install to connect to OMERO.

Install conda from, then:

# Create a conda environment named 'napari' and install omero-py

conda create -n napari -c ome python=3.6 zeroc-ice36-python omero-py
conda activate napari

# Install omero-napari (includes napari)

pip install omero-napari

# View an image in OMERO (will prompt for server and login)

omero napari view Image:1

# By default we lazy-load planes as needed. To load all planes:

omero napari view Image:1 --eager


  • Loads planes from OMERO as 2D numpy arrays and opens the image in napari.
  • Z and T dimensions from OMERO are supported with Z and T sliders in napari.
  • Only the required planes are loaded (“lazy loading”). Additional planes are loaded when the Z/T sliders are changed.
  • All channels from OMERO are shown in napari.
  • Rendering settings from OMERO are applied to napari so it looks the same:
    • The range and settings of the contrast sliders.
    • The color of each channel.
    • Only active layers are loaded and visible in napari.
    • The Z/T sliders are set to the default Z/T index from OMERO.
  • ROIs created in napari can be saved back to OMERO via a “Save ROIs” button.
  • napari viewer console has BlitzGateway ‘conn’ and ‘omero_image’ in context.

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