vitessce spatialdata

[ArneDefauw]

Thanks for the great package!

I want to visualize a spatialdata object using vitessce using the widget. I used the code from https://github.com/vitessce/vitessce-python/blob/main/docs/notebooks/spatial_data_blobs.ipynb. This notebook works, but now I also want to visualize the 'gene expression' spatially, similar as in https://github.com/vitessce/vitessce-python/blob/main/docs/notebooks/spatial_data.ipynb, but this does not seem to work.

This is my code:

import spatialdata

import os

from vitessce import CoordinationLevel as CL
from vitessce import CoordinationType as ct
from vitessce import (
    SpatialDataWrapper,
    VitessceConfig,
    get_initial_coordination_scope_prefix,
)
from vitessce import ViewType as vt

sdata = spatialdata.datasets.blobs()

spatialdata_filepath = os.path.join("data", "blobs.spatialdata.zarr")

sdata.write(spatialdata_filepath)

sdata.table.uns

vc = VitessceConfig(
    schema_version="1.0.16",
    name='Visium SpatialData Demo',
)
# Add data to the configuration:
wrapper = SpatialDataWrapper(
    sdata_path=spatialdata_filepath,
    # The following paths are relative to the root of the SpatialData zarr store on-disk.
    image_path="images/blobs_image",
    table_path="tables/table_transcriptomics",
    obs_feature_matrix_path="tables/table/X",
    labels_path="labels/blobs_labels",
    region="blobs_labels",
    coordinate_system="global",
    coordination_values={
        # The following tells Vitessce to consider each observation as a "blobs"
        "obsType": "blobs",
    }
)
dataset = vc.add_dataset(name='blobs').add_object(wrapper)

# Add views (visualizations) to the configuration:
spatial = vc.add_view("spatialBeta", dataset=dataset)
feature_list = vc.add_view(vt.FEATURE_LIST, dataset=dataset)
layer_controller = vc.add_view("layerControllerBeta", dataset=dataset)

obs_sets = vc.add_view(vt.OBS_SETS, dataset=dataset)
vc.link_views([spatial, layer_controller, feature_list, obs_sets], ['obsType'], [wrapper.obs_type_label])

# Layout the views
vc.layout(spatial | (feature_list / layer_controller ));

vw = vc.widget()
vw

This gives me

If I select 'channel_0_sum', I would expect this would color the blobs given the "expression" found.