recOrder-napari

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.

Dataset¶

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.