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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