wsireg v0.3.5

Release supporting napari-wsireg, new features and code improvements to support GUI.

wsireg v0.3.0

This version includes numerous bug fixes and improvements. Experimentally, images can now be transformed by tile rather than by plane, which can greatly reduce memory consumption.

wsireg v0.2.1

This is a minor release with some improvements.

Update RegImage to support more image formats as well as make it easy to add new formats

• add RegImage sub-classes for different file types
  • TiffFileRegImage (.scn, .ndpi,.tiff,.tif) : uses dask + zarr to do memory-efficient computation of necessary data for registration / transformation
  • CziRegImage (.czi) : Carl Zeiss image format, can perform read-time pre-processing like RGB -> greyscale or selection of individual channels to limit memory footprint
  • OmeTiffRegImage (.ome.tiff,ome.tif): uses TiffFile to read images and parses OME metadata to get interleaved RGB information
  • MergeRegImage (meta): used to transform multiple images' channels to a single OME-TIFF after registration if they output to the same size and data type (i.e. for cyclic IF)
  • 'NpRegImage' (np.ndarray): Supports adding a registration image from a numpy array
  • `SitkRegImage' (everything else): uses SimpleITK to read images as a last resort. Will read entire image into memory!

Add mask support and crop-to-mask support for registration

• support masks for registration
  • Masks can be used in elastix to define pixels used in metric calculation
  • add ability to automatically crop images based on associated masks's bounding box (can be useful if image dimensions differ greatly)

Add class to manage transformations

• use RegTransform class to manage transformations

wsireg v0.2.0

First release integrating ITKElastix