Features
Below is a list of features which are either already implemented or are on the roadmap.
Registration
Pairwise registration
- [x] phase correlation
- [x] ANTsPy
- [ ] elastix (
itk-elastix
) will be used for up to affine transformations - [ ] bead alignment
- [ ] phase correlation for rotation + translation
Group registration
- [x] registration graph construction
- [x] automatic determination of suitable reference view
- [x] parameter concatenation along graph connectivity paths
- [ ] global optimization of registration parameters from (potentially overdetermined) pairwise transforms
- [ ] drift correction / temporal alignment
Transformations
- [x] chunked
dask_image.ndinterp.affine_transform
- [ ] cupy-based transform
- [ ] chaining transformations instead of working with static coordinate systems
Fusion
- [x] chunkwise
- [ ] modular API to plug in different fusion functions including:
- Supported weights:
- [x] blending
- [x] content-based
- Supported fusion methods:
- [x] weighted average
- [ ] multi-view deconvolution
- [ ] fusion of overlapping label maps
- [ ] GPU compatibility
Data formats
- [x] zarr based intermediate file format for reading and writing, compatible with parallel dask workflows: multiscale-spatial-data
- [-] czi input
- [x] multi-positioning
- [ ] light-sheet
- [x] tif input
- [x] tif writing
Visualization
Napari
See napari-stitcher. - [x] 2D slice view: multiscale rendering - 3D rendered view: - [x] lowest scale - [ ] chunked rendering - [x] colormaps optimized for highlighting differences between overlapping views
Dimensionality
- [x] 2d
- [x] 3d
Supported usage modes
- [x] as a library to build custom reconstruction workflows
- [ ] predefined workflows/pipelines adapted to specific setups
- [(x)] napari plugin
- [ ] processing on HPC