What's it do for me?

This package provides a python wrapper and convenience functions for cudaDeconv, which is a CUDA/C++ implementation of an accelerated Richardson Lucy Deconvolution algorithm1, suitable for general applications, but designed particularly for stage-scanning light sheet applications such as Lattice Light Sheet. cudaDeconv was originally written by Lin Shao and modified by Dan Milkie, at Janelia Research campus. This package makes use of a cross-platform shared library interface that I wrote for cudaDecon while developing LLSpy (a Lattice light-sheet post-processing utility), that adds a couple additional kernels for affine transformations and camera corrections. The code here is mostly extracted from that package and cleaned up to allow it to be used independently of LLSpy.

 

The main features are:

  • radially averaged OTF generation
  • OTF interpolation for voxel size independence between PSF and data volumes
  • CUDA accelerated deconvolution with a handful of artifact-reducing features.
  • Deskew, Rotation, and general affine transformations
  • CUDA-based camera-correction for sCMOS artifact correction
  • a few context managers for setup/breakdown of GPU-I/O-heavy tasks and convenience functions
    windows, linux, mac
Created by

Talley Lambert, Harvard Medical School

Is it open source?

Yes