An experimental OMERO.web plugin to open OMERO.table data in Vitessce.
NB: work in progress...
This aims to display a scatter plot in Vitessce, with points corresponding to Polygons displayed on an Image.
You need to have an OMERO.table or CSV file with 2 number columns for the scatter
plot data and a shape_id column for the Polygons in OMERO.
If the table also has an Image or an image_id column, then that Image ID
will be used, or you can choose a different ID or an OME-Zarr URL to load the image.
In this workflow, we start by opening an OMERO.table or CSV using it's File ID:
your-omero-server/vitessce/table/{FILE_ID}
This shows the column names and first few rows of the table.
Two select inputs allow you to choose 2 Number columns.
The Image ID is shown and the corresponding image thumbnail.
Clicking Open Vitessce launches Vitessce in the iframe below, with a URL like this
for the screenshot below:
That omero-server URL will load a Vitessce config containing URLs for loading the cells.json and
the OME-Zarr image:
-
Currently this only works with
publicdata in the OMERO server, since Vitescce doesn't include the OMERO session credentials when loading data from OMERO. -
When loading Images from OMERO, tiled images are not supported, so the size is limited by the maximum plane size that can be loaded from OMERO (e.g. 10k * 12k).
-
The channel controllers are not displayed in Vitessce when loading images from OMERO or from a locally-hosted URL, but work OK when loading from s3 (reason unknown)
This app is a plugin of OMERO.web and needs to be installed in the same environment.
$ cd omero-vitessce
$ pip install -e .
$ omero config append omero.web.apps '"omero_vitessce"'
# Then restart your omero-web server
To open a OMERO table using File ID, go to:
your-omero-server/vitessce/table/{FILE_ID}