Browse your OMERO database from within napari.
GPL-2.0 License
This package provides interoperability between the OMERO image management platform, and napari: 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.
To launch napari with the OMERO browser added, install this package and run:
napari-omero
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()
This package provides a napari reader plugin that accepts OMERO resources as
"proxy strings" (e.g. omero://Image:<ID>
) or as OMERO webclient
URLS.
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
This package also serves as a plugin to the OMERO CLI
omero napari view Image:1
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-forge
channel
conda install -c conda-forge napari-omero
napari-omero
itself can be installed from pip, but you will still need
omero-py
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! |
---|
NAPARI_ASYNC=1 napari-omero
.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 .
To maintain good code quality, this repo uses flake8, mypy, and black. To enforce code quality when you commit code, you can install pre-commit
# 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