OpenHI Documentation

OpenHI is an open source platform for development of digital pathology. OpenHI can:

1. Annotate with different level of gradings. For example (G1, G2, G3) or (0, 1)

2. Provide different sizes of pre-defined segmentation segments with superpixel segmentation algorithm .

3. Fluidly view the whole-slide image from different vendors. Thanks to OpenSlide

4. Provide option to create a list of focused region.

5. Provide accompanying slide information parsed from GDC XML format.

Contents:

• OpenHI Installation and Usage
  • Installation
  • Usage (running the framework)
• OpenHI Modules
  • Suggestive annotation module
  • WSI Downloading from NIH-GDC repository
• OpenHI Image Processing APIs
  • Whole-slide image (WSI)
  • Image processing
  • Nucleus histomorphometry analysis
• Legacy APIs
  • Image Compatibility
  • SQL Module
  • Image processing module
  • Web module
  • Other documentations
• Tutorials
  • Read whole-slide images using OpenHI
  • OpenHI coordinate system
  • Abbreviations in the project’s code

How to cite OpenHI

Puttapirat Pargorn, Haichuan Zhang, Yuchen Lian, Chunbao Wang, Xiangrong Zhang, Lixia Yao, Chen Li, “OpenHI - An open source framework for annotating histopathological image,” 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1076-1082.

DOI: 10.1109/BIBM.2018.8621393

IEEE URL or IEEE PDF.

Option: Proof version (PDF 9.2 MB)

Source code

OpenHI is available at GitLab under GNU LGPL v3.0.

Indices and tables

• Index

• Module Index

• Search Page