Computational microscopy toolkit for label-free imaging

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This package provides a napari plugin for quantitative label-free microscopy.

In this repository you will find python tools and a napari plugin that allow the user to calibrate microscope hardware, acquire multi-modal data, reconstruct density and anisotropy, and visualize the results.

The acquisition, calibration, background correction, reconstruction, and applications of QLIPP (quantitative label-free imaging with phase and polarization) are described in the following E-Life Paper:

Syuan-Ming Guo, Li-Hao Yeh, Jenny Folkesson, Ivan E Ivanov, Anitha P Krishnan, Matthew G Keefe, Ezzat Hashemi, David Shin, Bryant B Chhun, Nathan H Cho, Manuel D Leonetti, May H Han, Tomasz J Nowakowski, Shalin B Mehta, "Revealing architectural order with quantitative label-free imaging and deep learning," eLife 2020;9:e55502 DOI: 10.7554/eLife.55502 (2020).

recOrder is to be used alongside a conventional widefield microscope fitted with a universal polarizer (Panel A below). The universal polarizer allows for the collection of label-free information including the intrinsic anisotropy of the sample and its relative phase (density). These measurements are collected by acquiring data under calibrated, polarization-diverse illumination followed by a computational reconstruction. The overall structure of recOrder is shown in Panel B, highlighting the structure of the graphical user interface (GUI) through a napari plugin.

Flow Chart


Slides and a dataset shared during a workshop on QLIPP and recOrder can be found on Zenodo.


Quick Start

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

conda create -y -n recOrder python=3.9
conda activate recOrder

Install recOrder-napari:

pip install recOrder-napari

Open napari with recOrder-napari:

napari -w recOrder-napari

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


  • 0.3.0

Last updated:

  • 19 April 2023

First released:

  • 19 April 2022


  • BSD 3-Clause License

Supported data:

  • Information not submitted

Plugin type:

Open extension:

GitHub activity:

  • Stars: 3
  • Forks: 3
  • Issues + PRs: 47

Python versions supported:

Operating system:


  • waveorder (==1.0.0rc0)
  • pycromanager (==0.24.1)
  • click (>=8.0.1)
  • natsort (>=7.1.1)
  • colorspacious (>=1.1.2)
  • pyqtgraph (>=0.12.3)
  • napari-ome-zarr (>=0.3.2)
  • importlib-metadata
  • iohub (==0.1.0.dev3)
  • napari ; "arm64" in platform_machine
  • PyQt6 ; "arm64" in platform_machine
  • napari[all] ; "arm64" not in platform_machine

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