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OMERO CLI plugin to view images in napari

Project description

omero-napari

OMERO CLI client to open images in the napari viewer.

Requires Python 3.6 or higher and install https://github.com/ome/omero-py to connect to OMERO.

Install conda from https://docs.conda.io/en/latest/miniconda.html, 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

Features

  • 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.

Project details


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