recOrder-napari 0.3.0rc3

Computational microscopy toolkit for label-free imaging

recOrder

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 two different usage modes and their features: graphical user interface (GUI) through a napari plugin, and a command line interface (CLI).

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

Apple Silicon users please use:

CONDA_SUBDIR=osx-64 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.