Package: nanopyx
Actively being developed with stable releasesNanoscopy Python library (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imagingWhat is the NanoPyx 🔬 Library?NanoPyx is a library specialized in the analysis of light microscopy and super-resolution data.
It is a successor toNanoJ, 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 theHenriques Laboratory.
It will be distributed as a Python Library and also asCodeless Jupyter Notebooks, that can be run locally or on Google Colab, and as anapari plugin.You can read more about NanoPyx in ourpreprint.Currently it implements the following approaches:A reimplementation of the NanoJ image registration, SRRF and Super Resolution metricsMore to come soon™if you found this work useful, please cite:preprintandShort Video TutorialsWhat is NanoPyx?How to use NanoPyx in Google Colab?Codeless jupyter notebooks available:CategoryMethodLast testNotebookColab LinkRegistrationChannel Registration✅ by ADB (13/08/23)RegistrationDrift Correction✅ by ADB (13/08/23)Quality ControlImage fidelity and resolution metrics✅ by ADB (13/08/23)Super-resolutionSRRF✅ by ADB (13/08/23)Super-resolutioneSRRF✅ by BMS (11/08/23)TutorialNotebook with Example Dataset✅ by ADB (13/08/23)napari pluginNanoPyx is also available as a napari plugin, which can be installed via pip:pip install napari-nanopyxInstallationNanoPyxis 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 installNanoPyxviapip:pipinstallnanopyxIf you want to install with support for Jupyter notebooks:pipinstallnanopyx[jupyter]or if you want to install with all optional dependencies:pipinstallnanopyx[all]To install latest development version:pipinstallgit+https://github.com/HenriquesLab/NanoPyx.gitNotes for Mac usersIf you wish to compile the NanoPyx library from source, you will need to install the following dependencies:Homebrew fromhttps://brew.sh/gcc, llvm and libomp from Homebrew through the command:brewinstallgccllvmlibompRun in jupyterlab within a docker containerdockerrun--namenanopyx1-p8888:8888henriqueslab/nanopyx:latestUsageDepending on your preferences and coding proficiency you might be using NanoPyx differently.If you are using Jupyter Notebooks or Google Colab notebooks check out ourvideo tutorialIf you are using ournapari plugincheck out the officialnapari tutorialand 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 ourofficial documentation.Simple Liquid Engine templateshereandhereFully fledged Liquid Engine templateshereandhereContributingContributions are very welcome.
Please read ourContribution Guidelinesto know how to proceed.LicenseDistributed under the terms of theCC-By v4.0license,
"NanoPyx" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.Development at a glance/ Structure