Computational microscopy toolkit for label-free imaging
Project description
recOrder
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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file recOrder-napari-0.4.0rc3.tar.gz.
File metadata
- Download URL: recOrder-napari-0.4.0rc3.tar.gz
- Upload date:
- Size: 6.1 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.10.12
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 3c1432eb49fcf769a6f76f2497d4f59ccb2776577259f3c90914744e0079491f |
|
| MD5 | f67698d9c92216cfb53c512e266bad64 |
|
| BLAKE2b-256 | 7360a010b8e525dfd07014b2c9758e6168071507af93cc149ceb36e33945ba16 |
File details
Details for the file recOrder_napari-0.4.0rc3-py3-none-any.whl.
File metadata
- Download URL: recOrder_napari-0.4.0rc3-py3-none-any.whl
- Upload date:
- Size: 6.1 MB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.10.12
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | aecf2fd7fec862e556b9059050f75ffec22ee1ad7623efea596f2a9cee6ab639 |
|
| MD5 | 769ae12cc893eb49ebe11d534077fe89 |
|
| BLAKE2b-256 | 7f671118f27274d436c52d12c636aef04c54bb878578fc574abf84b2493a016a |
