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readme.md

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[Image registration](https://en.wikipedia.org/wiki/Image_registration) is the
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process by which multiple images are aligned in the same coordinate system.
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This is useful to extract more information than by using each individual
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images. We perform multimodal image registration, where we succesfully align
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images from different microscopes, such that the information in each image is completely different.
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images. We perform rigid multimodal image registration, where we succesfully align
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images from different microscopes, even though the information in each image is completely different.
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Here are three registrations of images coming from two different microscopes (Bright-Field and Second-Harmonic Generation) as an example:
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<div align="center">
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We combined a state-of-the-art artificial neural network ([tiramisu](https://github.com/npielawski/pytorch_tiramisu/))
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to transform the input images into a latent space representation, which we baptized
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CoMIR. The CoMIRs are crafted such that they can aligned with the help of classical
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CoMIR. The CoMIRs are crafted such that they can be aligned with the help of classical
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registration methods.
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The figure below depicts our pipeline:
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* 📉It is possible to use contrastive learning and integrate equivariance constraints during training.
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* 🖼 CoMIRs can be aligned succesfully using classical registration methods.
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* 🌀The CoMIRs __are__ rotation (C4) equivariant ([youtube animation](https://youtu.be/iN5GlPWFZ_Q)).
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* 🌀The CoMIRs are rotation equivariant ([youtube animation](https://youtu.be/iN5GlPWFZ_Q)).
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* 🤖Using GANs to generate cross-modality images, and aligning those did not work.
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* 🌱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).
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* 🦾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
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All the results related to the Zurich sattelite images dataset can be reproduced
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All the results related to the Zurich satellite images dataset can be reproduced
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with the train-zurich.ipynb notebook. For reproducing the results linked to the
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biomedical dataset follow the instructions below:
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