Visualization of Multi-Modal Imaging Data

We visualize IMS, PAS, and AF imaging data overlaid from the Spraggins Lab of the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University, uploaded to the HuBMAP data portal.

[ ]:
from vitessce import (
    VitessceConfig,
    Component as cm,
    CoordinationType as ct,
    OmeTiffWrapper,
    MultiImageWrapper,
)
from os.path import join

1. Configure Vitessce

Set up the images from the three different assays, with the use_physical_size_scaling set to True so that the IMS image scales to the other images based on their physical sizes.

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vc = VitessceConfig(name='Spraggins Multi-Modal', description='PAS + IMS + AF From https://portal.hubmapconsortium.org/browse/collection/6a6efd0c1a2681dc7d2faab8e4ab0bca')
dataset = vc.add_dataset(name='Spraggins').add_object(
    MultiImageWrapper(
        image_wrappers=[
            OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/f4188a148e4c759092d19369d310883b/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-PAS_images/VAN0006-LK-2-85-PAS_registered.ome.tif?token=', name='PAS'),
            OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/2130d5f91ce61d7157a42c0497b06de8/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-AF_preIMS_images/VAN0006-LK-2-85-AF_preIMS_registered.ome.tif?token=', name='AF'),
            OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/be503a021ed910c0918842e318e6efa2/ometiff-pyramids/ometiffs/VAN0006-LK-2-85-IMS_PosMode_multilayer.ome.tif?token=', name='IMS Pos Mode'),
            OmeTiffWrapper(img_url='https://assets.hubmapconsortium.org/ca886a630b2038997a4cfbbf4abfd283/ometiff-pyramids/ometiffs/VAN0006-LK-2-85-IMS_NegMode_multilayer.ome.tif?token=', name='IMS Neg Mode')
        ],
        use_physical_size_scaling=True,
 )
)
spatial = vc.add_view(dataset, cm.SPATIAL)
status = vc.add_view(dataset, cm.STATUS)
lc = vc.add_view(dataset, cm.LAYER_CONTROLLER).set_props(disableChannelsIfRgbDetected=True)
vc.layout(spatial | (lc / status));

2. Create the Vitessce widget

[ ]:
vw = vc.widget()
vw