Package: napari-omero
napari-omeroThis package provides interoperability between theOMEROimage management platform, andnapari: a fast, multi-dimensional image
viewer for python.It provides a GUI interface for browsing an OMERO instance from within napari,
as well as command line interface extensions for both OMERO and napari CLIs.FeaturesGUI interface to browse remote OMERO data, with thumbnail previews.Loads remote nD images from an OMERO server into napariPlanes are loading on demand as sliders are moved ("lazy loading").session management (login memory)OMERO rendering settings (contrast limits, colormaps, active channels, current
Z/T position) are applied in naparias a napari dock widgetTo launch napari with the OMERO browser added,installthis
package and run:napari-omeroThe OMERO browser widget can also be manually added to the napari viewer:importnapariviewer=napari.Viewer()viewer.window.add_plugin_dock_widget('napari-omero')napari.run()as a napari pluginThis package provides a napari reader plugin that accepts OMERO resources as
"proxy strings" (e.g.omero://Image:<ID>) or asOMERO webclient
URLS.viewer=napari.Viewer()# omero object identifier stringviewer.open("omero://Image:1")# or URLS: https://help.openmicroscopy.org/urls-to-data.htmlviewer.open("http://yourdomain.example.org/omero/webclient/?show=image-314")these will also work on the napari command line interface, e.g.:napariomero://Image:1# ornaparihttp://yourdomain.example.org/omero/webclient/?show=image-314as an OMERO CLI pluginThis package also serves as a plugin to the OMERO CLIomeronapariviewImage:1ROIs 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.installationRequires python 3.7 - 3.10.from condaIt's easiest to installomero-pyfrom conda, so the recommended procedure
is to install everything from conda, using theconda-forgechannelcondainstall-cconda-forgenapari-omerofrom pipnapari-omeroitself can be installed from pip, but you will still needomero-pycondacreate-nomero-cconda-forgepython=3.9omero-py
condaactivateomero
pipinstallnapari-omero[all]# the [all] here is the same as `napari[all]`issues❗This is alpha software & some things will be broken or sub-optimal!experimental & definitely still buggy!Bug
reportsare welcome!remote loading can be very slow still... though this is not strictly an issue
of this plugin.  Datasets are wrapped as delayed dask stacks, and remote data
fetching time can be significant.  Plans forasynchronous
renderingin
napari andtiled loading from OMEROmay eventually improve the subjective performance... but remote data loading
will likely always be a limitation here.
To try asyncronous loading, start the program withNAPARI_ASYNC=1 napari-omero.contributingContributions are welcome!  To get setup with a development environment:# clone this repo:gitclonehttps://github.com/tlambert03/napari-omero.git# change into the new directorycdnapari-omero# create conda environmentcondaenvcreate-fenvironment.yml# activate the new envcondaactivatenapari-omero# install in editable modepipinstall-e.To maintain good code quality, this repo usesflake8,mypy, andblack.  To enforce code quality when you commit
code, you can install pre-commit# install pre-commit which will run code checks prior to commitspre-commitinstallThe original OMERO data loader and CLI extension was created byWill
Moore.The napari reader plugin and GUI browser was created byTalley
Lambert