Legacy example · Python · Version 1.0

Medical Imaging Segmentation with Vista-3D

Authors	Holoscan Team (NVIDIA)
Supported platforms	x86_64, aarch64
Language	Python
Version	1.0
Compatibility	HSDK 2.0.2
Contribution level	Level 1 · Very high-quality code
Source	HoloHub

Legacy HoloHub application

This application comes from HoloHub and was last tested with Holoscan SDK (HSDK) 2.0.2. It runs with the HoloHub CLI, ./holohub.

Vista-3D is a specialized interactive foundation model for segmenting and annotating human anatomies. This sample application demonstrates using the Vista-3D NVIDIA Inference Microservice (NIM) in a Holoscan pipeline.

The application instructs the Vista-3D NIM API to process the given dataset and downloads and extracts the results of a segmentation NRRD file onto a local directory.

Visit build.nvidia.com to learn more about Vista-3D and generate an API key to use with this application.

Quick Start

Add API key in nvidia_nim.yaml
./holohub run nvidia_nim_imaging

Configuring the sample application

Use the nvidia_nim.yaml configuration file to configure the sample application:

Connection Information

nim:
 base_url: https://integrate.api.nvidia.com/v1
 api_key:

base_url: The URL of your NIM instance. Defaults to NVIDIA-hosted NIMs.
api_key: Your API key to access NVIDIA-hosted NIMs.

Build and Run the sample application

# This first builds and runs the Docker images, then builds and runs the application.
./holohub run nvidia_nim_imaging

Display the Results

In this section, we will show how to view the sample data and segmentation results returned from Vista-3D.

Download 3D Slicer: https://download.slicer.org/
Decompress and launch 3D Slicer

tar -xvzf Slicer-5.6.2-linux-amd64.tar.gz

Locate the sample data volume and the segmentation results in build/nvidia_nim_imaging/applications/nvidia_nim/nvidia_nim_imaging

drwxr-xr-x 3 user domain-users     4096 Jul  3 11:41 ./
drwxr-xr-x 4 user domain-users     4096 Jul  3 11:40 ../
-rw-r--r-- 1 user user         27263336 Jul 23 14:22 example-1_seg.nrrd
-rw-r--r-- 1 user user         33037057 Jul 23 14:21 sample.nii.gz

In 3D Slicer, click File, Add Data and click Choose File(s) to Add. From the Add Data into the scene dialog, find and add the sample.nii.gz file and the example-1_seg.nrrd file. For the sample.nrrd file, select Segmentation and click Ok.
3D Slicer shall display the volume and the segmentation results as shown below:

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