linumpy.psf.extract#

Extract PSF parameters (focal depth, Rayleigh length) from a stitched mosaic.

Functions#

extract_psf_parameters_from_mosaic(vol[, f, ...])

Compute the confocal PSF from a slice.

Module Contents#

linumpy.psf.extract.extract_psf_parameters_from_mosaic(vol, f=0.01, n_profiles=10, zr_0=610.0, res=6.5, n_iterations=15)[source]#

Compute the confocal PSF from a slice.

Parameters:

  • vol (ndarray) – A stitched tissue slice with axes in order (x, y, z).

  • f (float) – Smoothing factor (in fraction of image size).

  • n_profiles (int) – Number of intensity profile to use.

  • zr_0 (float) – Initial Rayleigh length to use in micron (default=%(default)s for a 3X objective)

  • res (float) – Z resolution (in micron).

  • n_iterations (int) – Number of fitting iterations.

Returns:

Focal depth (zf) and Rayleigh length (zr) in micron

Return type:

(2,) tuple