recOrder-napari
Computational microscopy toolkit for label-free imaging
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.
Version:
- 0.4.0
Last updated:
- 31 August 2023
First released:
- 19 April 2022
License:
- BSD 3-Clause License
Supported data:
- Information not submitted
Plugin type:
GitHub activity:
- Stars: 4
- Forks: 3
- Issues + PRs: 38
GitHub activity:
- Stars: 4
- Forks: 3
- Issues + PRs: 38
Requirements:
- 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)