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Corrected language
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npielawski committed Oct 5, 2020
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[Image registration](https://en.wikipedia.org/wiki/Image_registration) is the
process by which multiple images are aligned in the same coordinate system.
This is useful to extract more information than by using each individual
images. We perform multimodal image registration, where we succesfully align
images from different microscopes, such that the information in each image is completely different.
images. We perform rigid multimodal image registration, where we succesfully align
images from different microscopes, even though the information in each image is completely different.

Here are three registrations of images coming from two different microscopes (Bright-Field and Second-Harmonic Generation) as an example:
<div align="center">
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We combined a state-of-the-art artificial neural network ([tiramisu](https://github.com/npielawski/pytorch_tiramisu/))
to transform the input images into a latent space representation, which we baptized
CoMIR. The CoMIRs are crafted such that they can aligned with the help of classical
CoMIR. The CoMIRs are crafted such that they can be aligned with the help of classical
registration methods.

The figure below depicts our pipeline:
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* 📉It is possible to use contrastive learning and integrate equivariance constraints during training.
* 🖼 CoMIRs can be aligned succesfully using classical registration methods.
* 🌀The CoMIRs __are__ rotation (C4) equivariant ([youtube animation](https://youtu.be/iN5GlPWFZ_Q)).
* 🌀The CoMIRs are rotation equivariant ([youtube animation](https://youtu.be/iN5GlPWFZ_Q)).
* 🤖Using GANs to generate cross-modality images, and aligning those did not work.
* 🌱If the weights of the CNN are initialized with a fixed seed, the trained CNN will generate very similar CoMIRs every time (correlation between 70-96%, depending on other factors).
* 🦾Our method performed better than Mutual Information-based registration, the previous state of the art, GANs and we often performed better than human annotators.
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## Reproduction of the results

All the results related to the Zurich sattelite images dataset can be reproduced
All the results related to the Zurich satellite images dataset can be reproduced
with the train-zurich.ipynb notebook. For reproducing the results linked to the
biomedical dataset follow the instructions below:

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