Nanoscopy Python library (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging
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:
| Category | Method | Last test | Notebook | Colab Link |
|---|---|---|---|---|
| Registration | Channel Registration | ✅ by BMS (20/04/23) |  |
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| Registration | Drift Correction | ✅ by BMS (20/04/23) | |
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| Quality Control | Image fidelity and resolution metrics | ✅ by BMS (20/04/23) | |
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| Super-resolution | SRRF | ✅ by BMS (20/04/23) | |
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| Tutorial | Notebook with Example Dataset | ✅ by BMS (20/04/23) |  |
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NanoPyx is also available as a napari plugin, which can be installed via pip:
pip install napari-nanopyx
You can install NanoPyx via pip:
pip install nanopyxor 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.gitIf 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 libompdocker run --name nanopyx1 -p 8888:8888 henriqueslab/nanopyx:latestContributions are very welcome. Please read our Contribution Guidelines to know how to proceed.
Distributed under the terms of the GNU GPL v2.0 license, "NanoPyx" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
