Skip to content

Colonoscopy Polyp Segmentation

Authors: Holoscan Team (NVIDIA)
Supported platforms: x86_64, aarch64
Last modified: March 18, 2025
Language: Python
Latest version: 1.0
Minimum Holoscan SDK version: 0.5.0
Tested Holoscan SDK versions: 0.5.0
Contribution metric: Level 1 - Highly Reliable

Full workflow including a generic visualization of segmentation results from a polyp segmentation models.

Requirements

  • Python 3.8+
  • The provided applications are configured to either use the AJA capture card for input stream, or a pre-recorded video of the colonoscopy data (replayer). Follow the setup instructions from the user guide to use the AJA capture card.

Data

📦️ (NGC) Sample App Data for AI Colonoscopy Segmentation of Polyps

The data is automatically downloaded and converted to the correct format when building the application. If you want to manually convert the video data, please refer to the instructions for using the convert_video_to_gxf_entities script.

Run Instructions

To run this application, you'll need to configure your PYTHONPATH environment variable to locate the necessary python libraries based on your Holoscan SDK installation type.

You should refer to the glossary for the terms defining specific locations within HoloHub.

If your Holoscan SDK installation type is:

  • python wheels:
export PYTHONPATH=$PYTHONPATH:<HOLOHUB_BUILD_DIR>/python/lib
  • otherwise:
export PYTHONPATH=$PYTHONPATH:<HOLOSCAN_INSTALL_DIR>/python/lib:<HOLOHUB_BUILD_DIR>/python/lib

Next, run the commands of your choice:

  • Using a pre-recorded video 

    cd <HOLOHUB_SOURCE_DIR>/applications/colonoscopy_segmentation
python3 colonoscopy_segmentation.py --source=replayer --data=<DATA_DIR>/colonoscopy_segmentation --no-contours

  • Using an AJA card 

    cd <HOLOHUB_SOURCE_DIR>/applications/colonoscopy_segmentation
python3 colonoscopy_segmentation.py --source=aja --no-contours
    Note that segmentation contours can be shown (instead of segmentation masks) by changing --no-contours to --contours.

Holoscan SDK version

Colonoscopy segmentation application in HoloHub requires version 0.6+ of the Holoscan SDK. If the Holoscan SDK version is 0.5 or lower, following code changes must be made in the application:

  • In python/CMakeLists.txt: update the holoscan SDK version from 0.6 to 0.5
  • In python/multiai_ultrasound.py: InferenceOp is replaced with MultiAIInferenceOp

Dev Container

To start the the Dev Container, run the following command from the root directory of Holohub:

./dev_container vscode

VS Code Launch Profiles

There are two launch profiles configured for this application:

  1. (debugpy) colonoscopy_segmentation/python: Launch colonoscopy_segmentation using a launch profile that enables debugging of Python code.
  2. (pythoncpp) colonoscopy_segmentation/python: Launch colonoscopy_segmentation using a launch profile that enables debugging of Python and C++ code.

Note: the launch profile starts the application with Video Replayer. To adjust the arguments of the application, open launch.json, find the launch profile named (debugpy) colonoscopy_segmentation/python, and adjust the args field as needed.