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Colonoscopy Sample App Data

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Description

Clara Holoscan Sample App Data for AI Colonoscopy Segmentation of Polyps

Publisher

NVIDIA

Use Case

Other

Framework

Other

Latest Version

v1.1

Modified

September 12, 2022

Compressed Size

581.64 MB

Clara Holoscan Sample App Data for AI Colonoscopy Segmentation of Polyps

Overview

This resource contains a segmentation model for the identification of polyps during colonoscopies, as well as a sample colonoscopy video for inference and testing. This model was trained on the Kvasir-SEG dataset [1], using the ColonSegNet model architecture [2].

[1] Jha, Debesh, Pia H. Smedsrud, Michael A. Riegler, Pål Halvorsen, Thomas de Lange, Dag Johansen, and Håvard D. Johansen, "Kvasir-seg: A segmented polyp dataset" Proceedings of the International Conference on Multimedia Modeling, pp. 451-462, 2020.

[2] Jha D, Ali S, Tomar NK, Johansen HD, Johansen D, Rittscher J, Riegler MA, Halvorsen P. Real-Time Polyp Detection, Localization and Segmentation in Colonoscopy Using Deep Learning. IEEE Access. 2021 Mar 4;9:40496-40510. doi: 10.1109/ACCESS.2021.3063716. PMID: 33747684; PMCID: PMC7968127.

Model

The AI model for polyp identification is a segmentation model which given an RGB image of 512 x 512 provides

  • semantic segmentation of the polyps. Each pixel stores a confidence score of [0,1] for polyp presence.

For details on the model inputs and outputs see below.

Inputs

  • INPUT__0 - Input RGB image (batchsize, height, width, channels)
    • shape=[1, 512, 512, 3]
    • dtype=float32
    • range=[0, 255]

Outputs

  • output_old - Segmentation output with per-pixel confidence [0,1].
    • shape=[1, 512, 512]
    • dtype=float32
    • range=[0, 1]

Video Data

Files:

  • video/colon_exam_720x576.mp4: Colonoscopy video sample sequence provided by Simula Research Laboratory. The video sample includes a scene with a polyp identified by the model.
  • video/colonoscopy.gxf_*: Converted colon_exam_720x576.mp4 for use with GXF replayer extension.

Directory Structure

The package contains two folders:

  • the model folder with the source model in ONNX format, and .engine files for the TensorRT models optimized for the Clara AGX and Holoscan developer kits.
  • the video folder with the recorded video data, both in mp4 (source) and converted to the NVIDIA GXF tensor format.
/
├── NVIDIA-Clara-Holoscan-SDK-EULA.pdf
├── model
│   ├── colon.onnx
│   ├── graph_surgeon.py
│   └── colon_engines
│       ├── NVIDIA-RTX-A6000_c86_n84.engine
│       └── Quadro-RTX-6000_c75_n72.engine
└── video
    ├── colon_exam_720x576.mp4
    ├── colonoscopy.gxf_entities
    └── colonoscopy.gxf_index

License

Refer to the license agreement for use of the sample data.