napari-ome-zarr

A reader for zarr backed OME-NGFF images.

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Installation

Install napari if not already installed.

You can install napari-ome-zarr via pip. Activate the same environment as you installed napari into, then:

pip install napari-ome-zarr

Usage

Napari will use napari-ome-zarr plugin to open images that the plugin recognises as ome-zarr. The image metadata from OMERO will be used to set channel names and rendering settings in napari::

napari "https://livingobjects.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"

If a dialog in napari pops up, encouraging you to choose a reader, choose napari-ome-zarr and click OK. You can stop it happening with addition of --plugin napari-ome-zarr as in the example below.

To open a local file::

napari --plugin napari-ome-zarr 13457227.zarr

OR in python::

import napari

viewer = napari.Viewer()
viewer.open("https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr")

napari.run()

Data support

The plugin supports all versions of OME-Zarr and will read Images, Plates, bioformats2raw layout collections and Scene graphs.

Images

Multi-channel images will be split into separate napari layers for each Channel. Any labels images found under image_path/labels will be added as label layers (initially inactive).

Plates

The first Image from each Well is displayed in a large grid, generated by concatenating the Images together.

bioformats2raw

All Images found in the series will be opened in napari.

Scenes

If the path_to_image.zarr contains a Scene, the coordinateTransformations with their input and output path/names are used to build a "graph" that includes transforms from the child images. The coordinateSystem at the "top" of the graph is used to display all the images, with all relevant transforms being applied to each image. If the graph contains multiple "top" coordinateSystems, the one with the most input images is chosen for display. Only the first coordinateSystem from each image is read in order to determine the Axes. The Scene graph is constructed purely from coordinateTransformations.

Supported coordinateTransformations currently include identity, scale, translation, rotation, affine and sequence (containing these other transforms).

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

Release process

To release, use the GitHub releases page to "Draft a new release". Create a new Tag, ensuring it starts with v, e.g. v0.10.1. This will be detected by GitHub actions and trigger a deploy of the release to Pypi. The release notes can be generated automatically and subsequently edited manually if desired.

License

Distributed under the terms of the BSD-3 license, "napari-ome-zarr" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.