Optics

This is a small package of microscopy data processing. Can be used in combination with InControl package or for data analysis.
Author: danustc
Required package:

• matplotlib
• numpy
• libtim
• scipy
• skimage

---

Package Instruction by Folders

PR(Phase Retrieval)

Contains codes for phase retrieval. Methods based on Hanser et al., "Phase-retrieved pupil functions in wide-field fluorescence microscopy", J. Microscopy, 216, 32--48, 2004.

Oblique_aberration.py: the main program for processing .mat data sets of the oblique SPIM. All the retrieved pupil functions are stored in a dictionary and saved as an .npz file.

• group_retrieval: (kinda) the main program that processes all the .mat files in a selected folder. Returns a list of Strehl ratios and retrieved pupils. The core algorithm is contained in the class PSF_PF, which must take the microscope parameters upon initialization.

• load_mat: load a .mat file (file name mat_path) and convert it into an numpy array. Notice that 3D arrays in matlab and python have different orders of dimensions, which requires a transposition in one of them to match the two.

Phase_retrieval.py: Adapted from the phase-retrieval codes in Ryan's InControl package.

• PSF_PF: the class of phase-retrieval. Users should provide a PSF (3-D numpy array), pixel size, z-step size, fluorescence wavelength (all in microns), refractive index (by default, water), numerical aperture (by default 1.0), focal length of objective (f(tube lens)/Manification) and number of iterations. Once the PSF is loaded, the pupil function (complex numpy 2-D array) can be retrieved by calling the function retrievePF and result would be saved in the class member PF. The unwrapped phase part can be acquired by calling the function get_phase.

• _PupilFunction: A private class tracking the properties of a pupil function.

psf_tools.py: some mini tools for slicing/visualizing PSF stacks.

pupil.py: called by retrievePF in Phase_retrieval.py. The core of the core :).

• Pupil: class that defines a pupil function. Contains a bunch of redundant functions and properties which are useless but harmless.
• Simulation: the class containing the algorithms for conversions between a psf and its associated pupil function.

visualization.py: functions that plots pupil functions and zernike components.

src (raw codes) ---- to be filled up