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.
- GUI interface to browse remote OMERO data, with thumbnail previews.
- Loads remote nD images from an OMERO server into napari
- Planes 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 napari
as a napari dock widget¶
To launch napari with the OMERO browser added, install this package and run:
The OMERO browser widget can also be manually added to the napari viewer:
import napari viewer = napari.Viewer() viewer.window.add_plugin_dock_widget('napari-omero') napari.run()
as a napari plugin¶
This package provides a napari reader plugin that accepts OMERO resources as
"proxy strings" (e.g.
omero://Image:<ID>) or as OMERO webclient
viewer = napari.Viewer() # omero object identifier string viewer.open("omero://Image:1") # or URLS: https://help.openmicroscopy.org/urls-to-data.html viewer.open("http://yourdomain.example.org/omero/webclient/?show=image-314")
these will also work on the napari command line interface, e.g.:
napari omero://Image:1 # or napari http://yourdomain.example.org/omero/webclient/?show=image-314
as an OMERO CLI plugin¶
This package also serves as a plugin to the OMERO CLI
omero napari view Image:1
- 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.
Requires python 3.7 - 3.10.
It's easiest to install
omero-py from conda, so the recommended procedure
is to install everything from conda, using the
conda install -c conda-forge napari-omero
napari-omero itself can be installed from pip, but you will still need
conda create -n omero -c conda-forge python=3.9 omero-py conda activate omero pip install napari-omero[all] # the [all] here is the same as `napari[all]`
|❗||This is alpha software & some things will be broken or sub-optimal!|
- experimental & definitely still buggy! Bug reports are 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 for asynchronous
tiled loading from OMERO
may eventually improve the subjective performance... but remote data loading
will likely always be a limitation here.
To try asyncronous loading, start the program with
Contributions are welcome! To get setup with a development environment:
# clone this repo: git clone https://github.com/tlambert03/napari-omero.git # change into the new directory cd napari-omero # create conda environment conda env create -f environment.yml # activate the new env conda activate napari-omero # install in editable mode pip install -e .
# install pre-commit which will run code checks prior to commits pre-commit install
The original OMERO data loader and CLI extension was created by Will Moore.
The napari reader plugin and GUI browser was created by Talley Lambert
- 10 April 2023
- 24 June 2020
- Stars: 30
- Forks: 10
- Issues + PRs: 13