recOrder-napari
Computational microscopy toolkit for label-free imaging
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 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:
- 0.3.0
Last updated:
- 19 April 2023
First released:
- 19 April 2022
License:
- BSD 3-Clause License
GitHub activity:
- Stars: 3
- Forks: 3
- Issues + PRs: 47
GitHub activity:
- Stars: 3
- Forks: 3
- Issues + PRs: 47
Python versions supported:
Requirements:
- waveorder (==1.0.0rc0)
- pycromanager (==0.24.1)
- click (>=8.0.1)
- natsort (>=7.1.1)
- colorspacious (>=1.1.2)
- pyqtgraph (>=0.12.3)
- napari-ome-zarr (>=0.3.2)
- importlib-metadata
- iohub (==0.1.0.dev3)
- napari ; "arm64" in platform_machine
- PyQt6 ; "arm64" in platform_machine
- napari[all] ; "arm64" not in platform_machine