Computational microscopy toolkit for label-free imaging
Project description
recOrder
This package provides a napari plugin and a command line interface 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
View command-line help by running
recOrder.help
For more help, see recOrders documentation.
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