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Signed-off-by: YunLiu <[email protected]>
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modules/omniverse/omniverse_integration.ipynb

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"# From 3D Segmentation to USD: A Complete Workflow for Hierarchical Mesh Conversion, USD Export, and NVIDIA Omniverse Integration\n",
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"In this tutorial, we’ll cover:\n",
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"\n",
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"- **Download the Model Bundle**: First, we download a pre-trained model bundle from the MONAI Model Zoo. This model bundle contains the necessary models and configurations for medical image analysis, which can accelerate our development process.\n",
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"- **Download the MONAI Bundle**: First, we download a pre-trained model bundle from the MONAI Model Zoo. This model bundle contains the necessary models and configurations for medical image analysis, which can accelerate our development process.\n",
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"\n",
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"- **Run the Inference Workflow of the Bundle**: Using the downloaded model bundle, we run its built-in inference workflow to automatically segment or analyze the input medical imaging data and obtain the desired results.\n",
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"\n",
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"!python -c \"import pxr\" || pip install -q usd-core\n",
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"!python -c \"import trimesh\" || pip install -q trimesh\n",
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"!apt update\n",
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"!apt install -y libgl1-mesa-glx"
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"!apt install -y libgl1-mesa-glx\n",
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"!apt install libxrender1"
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]
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{
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"source": [
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"## Generate segmentation from MAISI\n",
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"\n",
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"### Download the Model Bundle\n",
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"### Download the MONAI Bundle\n",
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"In this section, we download the MAISI bundle from monai model-zoo."
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]
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"We define a function `nii_to_mesh` to handle the conversion of NIfTI files to OBJ files. The workflow is as follows:\n",
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"\n",
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"- **Preprocessing**:\n",
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"The function uses a series of transformations (`Compose`, `LoadImaged`, `BorderPadd`, and `SqueezeDimd`) to load and preprocess the input NIfTI file, ensuring it is ready for segmentation.\n",
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"The function uses a series of transformations (`LoadImaged`, `BorderPadd`, and `SqueezeDimd`) to load and preprocess the input NIfTI file, ensuring it is ready for convertion.\n",
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"\n",
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"- **Organ Label Mapping**:\n",
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"It iterates over a dictionary mapping organ names to their respective label values. For each organ:\n",
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Convert 3D model contain all organs to OpenUSD format\n",
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"## Convert 3D model contain all organs to USD format\n",
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"\n",
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"[Universal Scene Description (OpenUSD)](https://openusd.org/release/index.html) is an extensible ecosystem of file formats, compositors, renderers, and other plugins for comprehensive 3D scene description."
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