Multi-modal or mono-modal whole slide image registration in a graph structure for complex registration tasks using elastix.
- Documentation: https://wsireg.readthedocs.io.
- Graph based approach to defining modalities and arbitrary transformation paths between associated images
- Use of elastix (through ITKElastix) to perform registration
- Support for linear and non-linear transformation models
- Transform associated data (masks, shape data) along the same path as the images.
- Supports images converted to OME-TIFF using bioformats2raw -> raw2ometiff pipeline
- All registered images exported as pyramidal OME-TIFF or OME-zarr that can be viewed in software such as Vitessce , vizarr, QuPath, OMERO or any platform that supports these formats.
- All transforms for complex registration paths are internally composited and only 1 interpolation step is performed, avoiding accumulation of interpolation error from many registrations
- Shape data (polygons, point sets, etc.) in GeoJSON format (future portable format for QuPath detection/annotation data) can be imported and transformations applied producing a modified GeoJSON
- Some support for reading native WSI formats: currently reads .czi and .scn but could be expanded to other formats supported by python package tifffile