waveorder

waveorder is a collection of computational imaging methods. It currently provides QLIPP (quantitative label-free imaging with phase and polarization), phase from defocus, and fluorescence deconvolution.

These are the kinds of data you can acquire with waveorder and QLIPP:

What do I need to use waveorder

waveorder is to be used alongside a conventional widefield microscope. For QLIPP, the microscope must be fitted with an analyzer and a universal polarizer:

For phase-from-defocus or fluorescence deconvolution methods, the universal polarizer is optional.

The overall structure of waveorder is shown in Panel B, highlighting the structure of the graphical user interface (GUI) through a napari plugin and the command-line interface (CLI) that allows users to perform reconstructions.

Software Quick Start

(Optional but recommended) install anaconda and create a virtual environment:

conda create -y -n waveorder python=3.12
conda activate waveorder

Install waveorder with acquisition dependencies (napari with PyQt6 and pycro-manager):

pip install waveorder[all]

Install waveorder without napari, QtBindings (PyQt/PySide) and pycro-manager dependencies:

pip install waveorder

Open napari with waveorder:

napari -w waveorder

For more help, see waveorder’s documentation. To install waveorder on a microscope, see the microscope installation guide.

Dataset

Slides and a dataset shared during a workshop on QLIPP can be found on Zenodo, and the napari plugin’s sample contributions (File > Open Sample > waveorder in napari).