Actively being developed with stable releases

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

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.

You can read more about NanoPyx in our preprint.

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: preprint and

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 ADB (13/08/23)
Registration	Drift Correction	✅ by ADB (13/08/23)
Quality Control	Image fidelity and resolution metrics	✅ by ADB (13/08/23)
Super-resolution	SRRF	✅ by ADB (13/08/23)
Super-resolution	eSRRF	✅ by BMS (11/08/23)
Tutorial	Notebook with Example Dataset	✅ by ADB (13/08/23)

napari plugin

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

pip install napari-nanopyx

Installation

NanoPyx is compatible and tested with Python 3.9, 3.10, 3.11 in MacOS, Windows and Linux. Installation time depends on your hardware and internet connection, but should take around 5 minutes.

You can install NanoPyx via [pip]:

pip install nanopyx

If you want to install with support for Jupyter notebooks:

pip install nanopyx[jupyter]

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

Usage

Depending on your preferences and coding proficiency you might be using NanoPyx differently.

• If you are using Jupyter Notebooks or Google Colab notebooks check out our video tutorial
• If you are using our napari plugin check out the official napari tutorial and stay tuned for more!
• If you prefer to use the Python library and take full advantage of the Liquid Engine flexibility, check out our Liquid Engine templates and our official documentation.
  • Simple Liquid Engine templates here and here
  • Fully fledged Liquid Engine templates here and here

Contributing

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

License

Distributed under the terms of the [CC-By v4.0] 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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