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omniverse_integration.ipynb missing required libs #1954

@yiheng-wang-nv

Description

@yiheng-wang-nv

Describe the bug
Current setup environment:

!python -c "import monai" || pip install -q "monai-weekly[nibabel]"
!python -c "import vtk" || pip install -q vtk
!python -c "import pxr" || pip install -q usd-core
!python -c "import trimesh" || pip install -q trimesh
!python -c "import ipyvtklink" || pip install -q ipyvtklink
!apt update
!apt install -y libgl1-mesa-glx
!apt install libxrender1

is not enough, when uncomment workflow.run(), will see missing skimage error like:

bundle_root = os.path.join(root_dir, "maisi_ct_generative")
override = {
    "output_size_xy": 256,
    "output_size_z": 256,
    "spacing_xy": 1.5,
    "spacing_z": 1.5,
    "autoencoder_def#num_splits": 16,
    "mask_generation_autoencoder_def#num_splits": 16,
}
workflow = create_workflow(
    config_file=os.path.join(bundle_root, "configs/inference.json"),
    workflow_type="inference",
    bundle_root=bundle_root,
    **override,
)

# uncomment this line to run the inference workflow
# then you will get the generated CT images and paired masks which can be used for the following steps.
# In this tutorial, we just use the tested data (IntegrationTest-AbdomenCT.nii.gz) from bundle for demonstration.
workflow.run()

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