Image preprocessing

To ensure consistent performance of our tools on a variety of images, we apply a standard preprocessing strategy that consists of the following steps:

• Invert so that background is black
• Remove background gradient, by fitting a linear model through points sampled just outside the tissue
• Remove background with OneCut (optional)
• Enhance contrast with CLAHE (optional)
• Resize images to common size
• Center images

The steps are implemented as part of the registration pipeline collab:

https://drive.ebrains.eu/d/67ca7ef8c35b45ec99b9/