wsireg 0.3.10
python package for registering multimodal whole slide microscopy images
License: MIT license
Requires Python: >=3.8
Keywords: wsireg

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wsireg
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.. 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
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* 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`



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History
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0.3.10 (2024-07-04)
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Use headless opencv

0.3.9 (2024-03-10)
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Deprecates unused aicsimageio dependency.

0.3.8 (2023-01-10)
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Fix bug that occurs when file paths contain a period.

0.3.7 (2022-04-28)
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Add support for translation transformation. Fix writing of merge modalities in cmd line configuration.

0.3.6 (2022-04-28)
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Fixes bug in wsireg2d console script.

0.3.5 (2022-04-28)
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Add support for python 3.10 with updated itk-elastix.

0.3.4 (2022-04-27)
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Major refactor of RegImage class, various small improvements throughout to support napari-wsireg.


0.3.2.2 (2022-02-04)
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This minor update adds the ability to draw binary or label masks using RegShapes.


0.3.2.1 (2021-12-28)
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This releases fixes some small bugs around shape transforms.

* fix geojson import/export
* fix bug with geojson reading


0.3.0 (2021-09-22)
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* 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