cbi_toolbox.simu.optics

The optics module provides simulations of the optics of imaging systems for microscopy

Conventions:

arrays follow the ZXY convention, with

  • Z : depth axis (axial, focus axis)

  • X : horizontal axis (lateral)

  • Y : vertical axis (lateral, rotation axis when relevant)

cbi_toolbox.simu.optics.create_wf_1d(wf_object, upsampling=1, scale=1, copy=False)[source]

Create a 1D wavefront object from an existing wavefront

Parameters:

  • wf_object (poppy.FresnelWavefront) – the original wavefront

  • upsampling (int, optional) – upsampling factor (does not change the field of view), by default 1

  • scale (int, optional) – zoom factor (changes the field of view), by default 1

  • copy (bool, optional) – return a new object, by default False

Returns:

a 1D wavefront full of 1 with same properties as the input

Return type:

poppy.FresnelWavefront

cbi_toolbox.simu.optics.gaussian_psf(npix_lateral=129, npix_axial=129, pixelscale=6.35e-07, wavelength=5e-07, numerical_aperture=0.5, refraction_index=1.33)[source]

Compute an approximate PSF model based on gaussian beam propagation

Koskela, O., Montonen, T., Belay, B. et al. Gaussian Light Model in Brightfield Optical Projection Tomography. Sci Rep 9, 13934 (2019).

Parameters:

  • npix_lateral (int, optional) – number of pixels in the lateral direction, by default 129

  • npix_axial (int, optional) – number of pixels in the axial direction, by default 129

  • pixelscale (float, optional) – pixelscale in meters per pixel, by default 1.3e-3/2048

  • wavelength (float, optional) – illumination wavelength in meters, by default 500e-9

  • numerical_aperture (float, optional) – objective NA, by default 0.5

  • refraction_index (float, optional) – imaging medium NA, by default 1.33

Returns:

the gaussian PSF

Return type:

array [ZXY]

cbi_toolbox.simu.optics.openspim_illumination(wavelength=5e-07, refr_index=1.333, laser_radius=0.0012, objective_na=0.3, objective_focal=0.018, slit_opening=0.01, pixelscale=6.35e-07, npix_fov=512, npix_z=None, rel_thresh=None, simu_size=2048, oversample=16)[source]

Compute the illumination function of an OpenSPIM device

Parameters:

  • wavelength (float, optional) – illumination wavelength in meters, by default 500e-9

  • refr_index (float, optional) – imaging medium refraction index, by default 1.333

  • laser_radius (float, optional) – source laser radius in meters, by default 1.2e-3

  • objective_na (float, optional) – illumination objective NA, by default 0.3

  • objective_focal (float, optional) – illumination objective focal length in meters, by default 18e-3

  • slit_opening (float, optional) – vertical slit opening in meters, by default 10e-3

  • pixelscale (float, optional) – target pixelscale in meters per pixel, by default 1.3e-3/2048

  • npix_fov (int, optional) – target size in pixels, by default 512

  • npix_z (int, optional) – target depth size in pixel, by default None (uses npix_fov)

  • rel_thresh (float, optional) – relative threshold to crop the beam thickness if a full row is below this theshold, all rows after are removed will be computed as compared to the maximum pixel

  • simu_size (int, optional) – size of the arrays used for simulation, by default 2048

  • oversample (int, optional) – oversampling used for the simulation (must be increased sith simu_size), by default 16

Returns:

the illumination function

Return type:

array [ZXY]

cbi_toolbox.simu.optics.resample_wavefront(wf, pixelscale, npixels)[source]

Resample 1D wavefront to new pixelscale (adapted from poppy.poppy_core._resample_wavefront_pixelscale)

Parameters:

  • wf (poppy.FresnelWavefront) – a 1D wavefront

  • pixelscale (astropy.units.[distance] / astropy.units.pixel) – target pixelscale

  • npixels (int) – target size in pixels

Returns:

resampled and resized 1D wavefront

Return type:

poppy.FresnelWavefront

cbi_toolbox.simu.optics.wf_mix(wf1, wf2, ref=None)[source]

Compute a 2D wavefront by multiplying 2 1D wavefronts (for separable propagation)

Parameters:

  • wf1 (poppy.FresnelWavefront) – a 1D wavefront

  • wf2 (poppy.FresnelWavefront) – a 1D wavefront

  • ref (poppy.FresnelWavefront, optional) – reference wavefront for the parameters of the output, by default None (wf1 will be used)

Returns:

the 2D mixed wavefront

Return type:

poppy.FresnelWavefront

Raises:

ValueError – if the input wavefronts have different pixelscales

cbi_toolbox.simu.optics.wf_to_2d(wf_object, npix=None, copy=False)[source]

Convert a 1D wavefront to 2D (for plotting only)

Parameters:

  • wf_object (poppy.FresnelWavefront) – the 1D wavefront

  • npix (int, optional) – crop to a size of npix, by default None

  • copy (bool, optional) – return a new object, by default False

Returns:

the 2D wavefront

Return type:

poppy.FresnelWavefront