PSF-Extractor

A Python software package to characterize the Point Spread Function of an optical setup.

Created by Daan Boltje, Ernest van der Wee
Made presentable by Ryan Lane
Input from Yoram Vos

Installation

• Create a new conda environment (assumes Anaconda or Miniconda is already installed) from the terminal

$ conda create -n psf -c conda-forge numpy scipy pandas matplotlib scikit-image jupyterlab trackpy xarray

• Activate environment

$ conda activate psf

• Install directly from github repository (assumes git is installed and in PATH)

(psf) $ pip install git+https://github.com/hoogenboom-group/PSF-Extractor.git

To run in a Jupyter notebook

• (Optional) environment setup for enlightened folk

(psf) $ conda install -c conda-forge nodejs
(psf) $ pip install tqdm ipympl ipywidgets imagecodecs mpl_interactions

• Start jupyter lab session

(psf) $ cd /path/to/PSF-Extractor/
(psf) $ jupyter lab

• Run walkthrough.ipynb