OMERO Vitessce

An experimental OMERO.web plugin to open OMERO.table data in Vitessce.

NB: work in progress...

Initial proof of concept

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:

http://vitessce.io/index.html?url=http://omero-server/vitessce/vitessce_config/64805/max/mean/?image=3676

That omero-server URL will load a Vitessce config containing URLs for loading the cells.json and the OME-Zarr image:

Known issues

• Currently this only works with public data 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)

Dev install

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}