State reconstruction

Fluorescence emission state reconstruction from microscopic fluorescence images of atoms on a lattice.

Includes the following functionalities:

• Simulate noisy fluorescence images
• Extract subpixel point spread functions
• Extract lattice vectors
• Reconstruct single-site occupation

The full documentation can be found here.

Installation

Clone this repository:

git clone https://www.github.com/david-wei/state_reconstruction.git

Install the library:

pip install ./state_reconstruction

Dependencies

• libics

Getting started

The package API is defined in the file api.py.

Tutorials are provided as Jupyter notebooks in the directory scripts:

• The notebook image_generation demonstrates how to
  • set up coordinate transformations between site and image coordinates,
  • define point spread function generator objects,
  • generate noisy fluorescence images.
• The notebook psf+trafo_estimation uses the files generated in image_generation to demonstrate how to
  • estimate a pixel-supersampled point spread function,
  • fit an affine transformation between site and image coordinates.
• The notebook state_reconstruction uses the files generated in image_generation to demonstrate how to set up the reconstruction process, including
  • image preprocessing for outlier removal,
  • image-to-site-space projector generation,
  • histogram analysis,
  • usage of the main StateEstimator object.