python package for registering multimodal whole slide microscopy images
Project description
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
0.3.9 (2023-01-10)
Deprecates unused aicsimageio dependency.
0.3.8 (2023-01-10)
Fix bug that occurs when file paths contain a period.
0.3.7 (2022-04-28)
Add support for translation transformation. Fix writing of merge modalities in cmd line configuration.
0.3.6 (2022-04-28)
Fixes bug in wsireg2d console script.
0.3.5 (2022-04-28)
Add support for python 3.10 with updated itk-elastix.
0.3.4 (2022-04-27)
Major refactor of RegImage class, various small improvements throughout to support napari-wsireg.
0.3.2.2 (2022-02-04)
This minor update adds the ability to draw binary or label masks using RegShapes.
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
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for wsireg-0.3.9-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fc58d58e3b6c9c3cabdfc5c22b187f3dceef0a78aa90ceed3fd8acfa15674ddf |
|
MD5 | fcf8cf82d54d8166042ac45501f8b285 |
|
BLAKE2b-256 | d17dafb39692613f61bc65137c4f0b41e59c75c707ae0e086a0adf7929dcf860 |