Computational microscopy toolkit for label-free imaging

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recOrder is a napari plugin and command-line tool for quantitative label-free microscopy that depends on a computational optics library, waveorder, and an I/O library, iohub.

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.


  • 0.4.0

Last updated:

  • 31 August 2023

First released:

  • 19 April 2022


  • BSD 3-Clause License

Supported data:

  • Information not submitted

Open extension:

GitHub activity:

  • Stars: 4
  • Forks: 3
  • Issues + PRs: 38

Python versions supported:

Operating system:


  • waveorder (==2.0.0rc3)
  • pycromanager (==0.27.2)
  • click (>=8.0.1)
  • natsort (>=7.1.1)
  • colorspacious (>=1.1.2)
  • pyqtgraph (>=0.12.3)
  • napari-ome-zarr (>=0.3.2)
  • napari[pyqt6_experimental]
  • importlib-metadata
  • iohub (==0.1.0.dev5)
  • wget (>=3.2)

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