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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

3.0.0 - 2024-01-22

Added

  • fp_recover now takes a learning_rate rate parameter to adjust the learning rate of the gradient descent method for pupil recovery.
  • There is a now a command line tool called calibrate_ptycho for acquiring FP calibration datasets. The acquisition engine is pymmcore-plus.
  • There is now a Metadata typed dictionary for use by acquisition scripts and dataset loading logic.
  • A StackType.LEB dataset type has been added so that load_dataset works with stacks acquired by the new calibrate_ptycho script.
  • FPDataset now has save and load methods for saving the dataset to and reading it from disk.
  • FPDataset.save supports saving to both a pickled and a MATLAB format.
  • A Jupyter notebook was added to demonstrate how to create HDR dataset.
  • MATLAB scripts were added to the misc folder for running FP reconstructions through the algorithm of Jiang, et al. Nature Protocols 18, 2051 (2023). This is used to cross-check the Python code.

Changed

  • Renamed the Python package to leb.ptycho.
  • The default number of Zernike coefficients to use in fp_recover is now 10, which includes all of the Zernike modes up to radial degree 3.
  • fp_recover now returns a FPResults object that contains, in addition to the object and pupil reconstruction, the gradients and Zernike coefficients from each iteration of the recovery process if the gradient descent pupil recovery method is used.
  • calibrate_rectangular_matrix now accounts for refraction by the microscope slide when determining the wave vector corresponding to each LED.

Fixed

  • Pupil recovery by gradient descent is now working.
  • Fixed the default value for the axial_offset_mm keyword argument to the function calibrate_rectangular_matrix. It was likely assumed to be in microns and not millimeters.

Removed

  • Removed flip_yz argument from calibrate_rectangular_matrix because it was confusing and not really used.

2.0.0 - 2023-08-07

Added

  • Test data for the Jupyter notebooks are now part of the repository.
  • Implemented gradient descent pupil recovery in fp_recover reconstruction.
  • Added a show_progress parameter to fp_recover to toggle a progress bar during reconstruction.
  • Added a function hdr_combine to combine low dynamic range images into a single HDR image. This can be used for calibrations.
  • Added a function hdr_stack to combine multiple, low dynamic range FPDatasets into a single HDR FPDataset.
  • Pupil objects now contain a Zernike instance that can be used for pupil calculations during Fourier Ptychographic recovery routines.
  • Added a phase_contrast.bsh script to the Micro-Manager scripts folder to acquire differential phase contrast images.
  • Added brightfield, darkfield, and several phase contrast patterns and their corresponding commands to the Arduino control code.

Changed

  • The default pixel size in fp_simulation and Pupil.from_system_params is now 5.86 um to match the pixel size of the new Flir Grasshopper 3 camera.
  • The max_radial_degree parameter to the Zernike class is now called radial_degree.
  • The calibrate.bsh Micro-Manager script now takes one acquisition for each of several sets of exposure times and camera gains.

Fixed

  • Fixed pupil recovery using the PupilRecoveryMethod.rPIE method by zeroing values outside the pupil radius.

1.1.1 - 2023-07-10

Fixed

  • Fixed a residual bug in calibrate.bsh from renaming row/col to x/y.

1.1.0 - 2023-07-10

Added

  • A detailed discussion about the coordinate systems used to transform LED indexes to wavevectors is now included in calibration.py.

Changed

  • FPDataset images can now be rectangular instead of requiring them to be square. This change was made to make it easier to import datasets from cameras with non-square sensors.
  • fp_recover now raises a FPRecoveryError instead of an AssertionError if dataset images are not square.

Fixed

  • The spiral generator in calibrate.bsh now returns (x, y) coordinates instead of (row, col).
  • clockwise and counterclockwise spiral directions in calibrate.bsh are now correct.
  • calibrate_rectangular_matrix now accounts for the fact that the LED matrix coordinate system's z-axis points in the opposite direction of the z-axis of the global coordinate system.

1.0.0 - 2023-07-06

Added

  • Added a Zernike class and routines to compute Zernike polynomials for aberrated pupils to leb-freeze.
  • The calibrate.bsh Micro-Manager script now appends the LED indexes to the image metadata.
  • The calibrate.bsh Micro-Manager script now appends the center LED indexes to the image metadata.
  • FPDataset instances can now be sliced, e.g. dataset[:42].
  • A new FPDataset.crop method allows images to be cropped.

Changed

  • The leb-freeze simulation now returns an unaberrated pupil to use in reconstructions and a ground truth pupil.
  • fp_recover() now returns the reconstructed object and pupil, not just the object.

Fixed

  • Fixed the pupil_radius_px calculation for the Pupil class in leb-freeze.
  • Fixed a bug when printing the status in calibrate.bsh.
  • Fixed a bug related to serial command variable naming in calibrate.bsh.
  • Fixed scaling factors for FFTs in fp_recover function.

leb-freeze-0.0.0

Added

  • Added leb-freeze Python package to analyze Fourier ptychography data.
  • Created a Fourier Pytchographic reconstruction routine called fp_recover that is based on https://doi.org/10.1038/s41596-023-00829-4.
  • Created a simulation routine to generate simulated FP datasets to verify the recovery process.

LED-Matrix-Controller-0.0.0

Added

  • Responses from the Arduino to the PC are now terminated with the linefeed \n character.

uManager-Unreleased

Added

  • Added a calibrate.bsh script to run the Fourier ptychography calibration routine.