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Image registration with EXACT

Registration works best for cytological questions and when the same slide has been stained twice.  As also described in the paper.

The registration of images is based on code from the following repository and publication.

@inproceedings{marzahl2021robust,
  title={Robust Quad-Tree based Registration on Whole Slide Images},
  author={Marzahl, Christian and Wilm, Frauke and Tharun, Lars and Perner, Sven and Bertram, Christof A and Kr{\"o}ger, Christine and Voigt, J{\"o}rn and Klopfleisch, Robert and Maier, Andreas and Aubreville, Marc and others},
  booktitle={MICCAI Workshop on Computational Pathology},
  pages={181--190},
  year={2021},
  organization={PMLR}
}

Video

A demonstration of what registration in EXACT looks like is available at the following YoutTube video

Datasets

Tutorial

  1. Please upload the images you want to register. The images do not have to be in the same ImageSet folder.
  2. Please open the Notebook: https://github.com/DeepMicroscopy/Exact/blob/master/doc/WSI-Registration.ipynb
  3. The important line is "In [7]":
registration = image_registration_api.register_image(source_image=source_image.id, target_image=target_image.id,thumbnail_size=thumbnail_size)

The source and target image id is visibile in the browser:

http://localhost:1337/annotations/{id}

The thumbnail_size is an optional parameter