1. 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: