Computational microscopy toolkit for label-free imaging
Project description
recOrder
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.
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:
https://user-images.githubusercontent.com/9554101/271128301-cc71da57-df6f-401b-a955-796750a96d88.mov
https://user-images.githubusercontent.com/9554101/271128510-aa2180af-607f-4c0c-912c-c18dc4f29432.mp4
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:
https://user-images.githubusercontent.com/9554101/273073475-70afb05a-1eb7-4019-9c42-af3e07bef723.mp4
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.
Software Quick Start
(Optional but recommended) install anaconda and create a virtual environment:
conda create -y -n recOrder python=3.10
conda activate recOrder
Install recOrder-napari with acquisition dependencies
(napari and pycro-manager):
pip install recOrder-napari[acq]
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).
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