======
wsireg
======
.. image:: https://readthedocs.org/projects/wsireg/badge/?version=latest
:target: https://wsireg.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
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 <https://github.com/InsightSoftwareConsortium/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 <https://github.com/glencoesoftware/bioformats2raw>`_ -> `raw2ometiff <https://github.com/glencoesoftware/bioformats2raw>`_ pipeline
* All registered images exported as pyramidal OME-TIFF or OME-zarr that can be viewed in software such as `Vitessce <https://vitessce.io>`_ , `vizarr <https://github.com/hms-dbmi/vizarr>`_, `QuPath <https://qupath.github.io>`_, `OMERO <https://www.openmicroscopy.org/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
=======
0.3.10 (2024-07-04)
---------------------
Use headless opencv
0.3.9 (2024-03-10)
---------------------
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
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