search

mehta-lab / recOrder

3D quantitative label-free imaging with phase and polarization
BSD 3-Clause "New" or "Revised" License
12 stars 4 forks source link

readme

recOrder

PyPI - Python Version Python package index download statistics Python package index Development Status

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:

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.

Flow Chart

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).

DOI DOI