nrefocus documentation

Nrefocus is a Python 3 library that allows to numerically refocus (including autofocusing) complex wave fields. This is the documentaion of nrefocus version 0.8.0.

Contents:

• Introduction
  • Obtaining nrefocus
  • Citing nrefocus
  • Acknowledgments
  • References
• Getting started
  • Basics of nrefocus
  • Setting the NDArray Backend
    • Controlling the ndarray backend
    • Example use of ‘cupy’ backend for Field Refocussing
  • 3D stacks
  • Input and Output Domains
    • Default: spatial input, spatial output
    • Fourier input: skip the forward FFT
    • Fourier output: skip the inverse FFT
    • Combining both: no transforms at all
• Theory
  • Optical transfer function
  • Fresnel approximation
  • Transfer functions in nrefocus
• Examples
  • 2D Refocusing of an HL60 cell
  • Compare available Metrics for Refocusing
  • Refocus a stack of 2D fields (3D array input).
  • Specifying input_domain / output_domain in nrefocus.
• Code reference
  • Refocus interface
    • get_best_interface()
    • RefocusPyFFTW
    • RefocusNumpy
    • RefocusNumpy1D
  • Metrics
    • metric_average_gradient()
    • metric_med_gradient()
    • metric_rms_contrast()
    • metric_spectrum()
    • metric_std_gradient()
    • METRICS
  • Minimizers
    • minimize_legacy()
    • minimize_lmfit()
    • MINIMIZERS
  • Legacy methods
    • Refocusing
    • Autofocusing

• Changelog
• Bilbliography

Indices and tables

• Index

• Module Index

• Search Page