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 typesTiffFileRegImage
(.scn, .ndpi,.tiff,.tif) : usesdask
+zarr
to do memory-efficient computation of necessary data for registration / transformationCziRegImage
(.czi) : Carl Zeiss image format, can perform read-time pre-processing like RGB -> greyscale or selection of individual channels to limit memory footprintOmeTiffRegImage
(.ome.tiff,ome.tif): uses TiffFile to read images and parses OME metadata to get interleaved RGB informationMergeRegImage
(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 anumpy
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)
- Masks can be used in
Add class to manage transformations
- use
RegTransform
class to manage transformations