About

The repository contains the software used by the AGH team during the ANHIR challenge organized jointly with the IEEE ISBI 2019 conference. The purpose of the repository is to make the results fully reproducible.

Example

The example how to use the code is presented in files:

• Example Single Pair
• Example All Pairs

Dataset

For the dataset access and full description please visit ANHIR Webiste.

Dependencies

• NumPy
• SciPy
• Matplotlib
• OpenCV (contrib)
• SimpleITK
• Pandas

Limitations

The software was tested on Ubuntu 16.04 LTS and Ubuntu 18.04 LTS and Python version >=3.5.x. The current version will not work correctly on Windows operating system.

Acknowledgmnets

If you found the software useful please cite:

• J. Borovec et.al., ANHIR: Automatic Non-rigid Histological Image Registration Challenge, IEEE Transactions on Medical Imaging, 2020, DOI: 10.1109/TMI.2020.2986331 Link
• M. Wodzinski and A. Skalski, Multistep, automatic and nonrigid image registration method for histology samples acquired using multiple stains, Physics in Medicine and Biology, 2020, DOI: 10.1088/1361-6560/abcad7 Link Open Access