wsireg 0.3.2.1

python package for registering multimodal whole slide microscopy images

wsireg

Multi-modal or mono-modal whole slide image registration in a graph structure for complex registration tasks using elastix.

• Documentation: https://wsireg.readthedocs.io.

Features

• 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

History

0.3.0 (2021-09-22)

• add “ome.tiff-bytile” writer to write transformed images tile-by-tile

• unify data reading from tiffs to use dask

• numerous improvements, bug fixes, and additional tests

0.3.2.1 (2021-12-28)

This releases fixes some small bugs around shape transforms.

• fix geojson import/export

• fix bug with geojson reading