diff --git a/README.md b/README.md index ef3c934..097e54a 100644 --- a/README.md +++ b/README.md @@ -24,35 +24,36 @@ https://napari.org/docs/plugins/index.html ## Installation -You can install `napari-ome-zarr` via [pip]: +[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 `ome-zarr` to open images that the plugin recognises as ome-zarr. +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://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/" + napari "https://uk1s3.embassy.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. - # Also works with local files - $ napari 6001240.zarr +To open a local file:: + + napari --plugin napari-ome-zarr 13457227.zarr OR in python:: import napari viewer = napari.Viewer() - viewer.open('https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/') + viewer.open("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr") napari.run() -If single zarray is passed to the plugin, it will be opened without the use of -the metadata:: - - $ napari '/tmp/6001240.zarr/0' ## Contributing @@ -68,6 +69,7 @@ Distributed under the terms of the [BSD-3] license, If you encounter any problems, please [file an issue] along with a detailed description. +[Install napari]: https://napari.org/stable/tutorials/fundamentals/installation.html [napari]: https://github.com/napari/napari [Cookiecutter]: https://github.com/audreyr/cookiecutter [@napari]: https://github.com/napari