recOrder-napari

recOrder-napari

Computational microscopy toolkit for label-free imaging

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recOrder is a collection of computational imaging methods. It currently provides QLIPP (quantitative label-free imaging with phase and polarization), phase from defocus, and fluorescence deconvolution.

Unveiling the invisible

Acquisition, calibration, background correction, reconstruction, and applications of QLIPP 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).

These are the kinds of data you can acquire with recOrder and QLIPP:

What do I need to use recOrder

recOrder is to be used alongside a conventional widefield microscope. For QLIPP, the microscope must be fitted with an analyzer and a universal polarizer:

For phase-from-defocus or fluorescence deconvolution methods, the universal polarizer is optional.

The overall structure of recOrder is shown in Panel B, highlighting the structure of the graphical user interface (GUI) through a napari plugin and the command-line interface (CLI) that allows users to perform reconstructions.

Flow Chart

Software 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.

Dataset

Slides and a dataset shared during a workshop on QLIPP and recOrder can be found on Zenodo, and the napari plugin's sample contributions (File > Open Sample > recOrder-napari in napari).

DOI DOI

Version:

  • 0.4.1

Last updated:

  • 06 October 2023

First released:

  • 19 April 2022

License:

  • BSD 3-Clause License

Supported data:

  • Information not submitted

Open extension:

GitHub activity:

  • Stars: 11
  • Forks: 4
  • Issues + PRs: 51

Python versions supported:

Operating system:

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