Visualization of a SpatialData object

Import dependencies

[ ]:

import os
from os.path import join, isfile, isdir
from urllib.request import urlretrieve
import zipfile

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

[ ]:

data_dir = "data"
zip_filepath = join(data_dir, "visium.spatialdata.zarr.zip")
spatialdata_filepath = join(data_dir, "visium.spatialdata.zarr")

[ ]:

if not isdir(spatialdata_filepath):
    if not isfile(zip_filepath):
        os.makedirs(data_dir, exist_ok=True)
        urlretrieve('https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zip', zip_filepath)
    with zipfile.ZipFile(zip_filepath,"r") as zip_ref:
        zip_ref.extractall(data_dir)
        os.rename(join(data_dir, "data.zarr"), spatialdata_filepath)

Configure Vitessce

Vitessce needs to know which pieces of data we are interested in visualizing, the visualization types we would like to use, and how we want to coordinate (or link) the views.

[ ]:

vc = VitessceConfig(
    schema_version="1.0.16",
    name='Visium SpatialData Demo (visium_associated_xenium_io)',
)
# 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/CytAssist_FFPE_Human_Breast_Cancer_full_image",
    table_path="tables/table",
    obs_feature_matrix_path="tables/table/X",
    obs_spots_path="shapes/CytAssist_FFPE_Human_Breast_Cancer",
    region="CytAssist_FFPE_Human_Breast_Cancer",
    coordinate_system="global",
    coordination_values={
        # The following tells Vitessce to consider each observation as a "spot"
        "obsType": "spot",
    }
)
dataset = vc.add_dataset(name='Breast Cancer Visium').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)
vc.link_views_by_dict([spatial, layer_controller], {
    'imageLayer': CL([{
        'photometricInterpretation': 'RGB',
    }]),
}, scope_prefix=get_initial_coordination_scope_prefix("A", "image"))
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 / obs_sets));