CBI Toolbox

CBI Toolbox is a collection of algorithms used for computational bioimaging and microscopy.

CBI Toolbox is suitable for large scale 3D simulations to reproduce realistic sample sizes and sampling resolution thanks to hardware acceleration (both GPU and multithreading) and optimized implementation of the algorithms. It is flexible enough to emulate different acquisition geometries, and also contains a set of tools used for quantitative evaluation of imaging methods. The framework can also be used for experiment design, as geometries can be virtually tested before being implemented on real acquisition devices.

Copyright (c) 2020 Idiap Research Institute, http://www.idiap.ch/

Written by François Marelli <francois.marelli@idiap.ch>

View the source on github

Documentation

• CBI Toolbox
• Installation
• About
• Experiments

API Reference

• cbi_toolbox
  • cbi_toolbox.bsplines
    • bspline()
  • cbi_toolbox.parallel
    • cbi_toolbox.parallel.mpi
      • compute_vector_extent()
      • create_slice_view()
      • create_vector_type()
      • distribute_mpi()
      • distribute_mpi_all()
      • gather_full_shape()
      • get_rank()
      • get_size()
      • is_root_process()
      • load()
      • redistribute()
      • save()
      • to_mpi_datatype()
      • wait_all()
    • distribute_bin()
    • distribute_bin_all()
    • parallelize()
  • cbi_toolbox.reconstruct
    • cbi_toolbox.reconstruct.fpsopt
      • deconvolve_sinogram()
      • inverse_psf_rfft()
    • cbi_toolbox.reconstruct.preprocess
      • erase_corners()
      • remove_background_illumination()
      • transmission_to_absorption()
    • cbi_toolbox.reconstruct.vhf
      • argsort_tsp()
      • average_frequency()
      • estimate_di()
      • l_curve()
      • orient_phases()
      • phase_correction()
      • phase_diff()
      • phase_error()
      • sample_video()
      • unfold_phases()
      • vhf_phase_naive()
      • vhf_phase_uncorrected()
    • mse()
    • mutual_information()
    • normalize()
    • psnr()
    • scale_to_mse()
  • cbi_toolbox.simu
    • cbi_toolbox.simu.dynamic
      • sample_phases()
      • sigsin()
      • sigsin_beat()
    • cbi_toolbox.simu.imaging
      • fps_opt()
      • fss_opt()
      • noise()
      • opt()
      • quantize()
      • spim()
      • widefield()
    • cbi_toolbox.simu.optics
      • create_wf_1d()
      • gaussian_psf()
      • openspim_illumination()
      • resample_wavefront()
      • wf_mix()
      • wf_to_2d()
    • cbi_toolbox.simu.primitives
      • ball()
      • boccia()
      • fiber()
      • forward_ellipse()
      • phantom()
      • quadrant_symmetry()
      • quadrant_to_volume()
      • torus_boccia()
    • cbi_toolbox.simu.textures
      • forward_simplex()
      • simplex()
      • spheres()
  • cbi_toolbox.splineradon
    • iradon()
    • iradon_inner()
    • iradon_post()
    • iradon_pre()
    • is_cuda_available()
    • radon()
    • radon_inner()
    • radon_post()
    • radon_pre()
  • cbi_toolbox.utils
    • cbi_toolbox.utils.ome
      • load_ome_tiff()
      • save_ome_tiff()
    • cbi_toolbox.utils.plotting
      • AnimImshow
        • AnimImshow.save_to_gif()
      • trace_points()
    • fft_size()

Index

• Index