OMERO CLI plugin to view images in 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
- 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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