nanopyx 0.2.0

Nanoscopy Python library (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging

Under Development, currently in beta stage

Nanoscopy Python library (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging

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What is the NanoPyx 🔬 Library?

NanoPyx is a library specialized in the analysis of light microscopy and super-resolution data. It is a successor to NanoJ, which is a Java library for the analysis of super-resolution microscopy data.

NanoPyx focuses on performance, by heavily exploiting cython aided multiprocessing and simplicity. It implements methods for the bioimage analysis field, with a special emphasis on those developed by the Henriques Laboratory. It will be distributed as a Python Library and also as Codeless Jupyter Notebooks, that can be run locally or on Google Colab, and as a napari plugin.

Currently it implements the following approaches:

• A reimplementation of the NanoJ image registration, SRRF and Super Resolution metrics
• More to come soon™

if you found this work useful, please cite:

Short Video Tutorials

What is NanoPyx?	How to use NanoPyx in Google Colab?

Codeless jupyter notebooks available:

Category	Method	Last test	Notebook	Colab Link
Registration	Channel Registration	✅ by BMS (20/04/23)
Registration	Drift Correction	✅ by BMS (20/04/23)
Quality Control	Image fidelity and resolution metrics	✅ by BMS (20/04/23)
Super-resolution	SRRF	✅ by BMS (20/04/23)
Tutorial	Notebook with Example Dataset	✅ by BMS (20/04/23)

napari plugin

NanoPyx is also available as a napari plugin, which can be installed via pip:

pip install napari-nanopyx

Installation

You can install NanoPyx via pip:

pip install nanopyx

or if you want to install with all optional dependencies

pip install 'nanopyx[all]'

To install latest development version :

pip install git+https://github.com/HenriquesLab/NanoPyx.git

Notes for Mac users

If you wish to compile the NanoPyx library from source, you will need to install the following dependencies:

• Homebrew from https://brew.sh/
• gcc, llvm and libomp from Homebrew through the command:

brew install gcc llvm libomp

Run in jupyterlab within a docker container

docker run --name nanopyx1 -p 8888:8888 henriqueslab/nanopyx:latest

Contributing

Contributions are very welcome. Please read our Contribution Guidelines to know how to proceed.

License

Distributed under the terms of the GNU GPL v2.0 license, "NanoPyx" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Development at a glance

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