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@HenriquesLab AI-driven Optical Biology Laboratory

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    51 repositories

    • vlab4mic-jupyter

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 30, 2026Apr 30, 2026

    • VLab4Mic

      Public
      Python
      •
      MIT License
      •0•0•7•1•Updated Apr 29, 2026Apr 29, 2026

    • mAIcroscopysandbox

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • mAIcrobe

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•10•0•0•Updated Apr 22, 2026Apr 22, 2026

    • homebrew-formulas

      Public
      Homebrew formulas for Henriques Lab tools
      Just
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • TaskRepo

      Public
      Python
      •
      MIT License
      •0•2•0•2•Updated Apr 20, 2026Apr 20, 2026

    • PythonImageAnalysis

      Public
      So You Want To Do Image Analysis With Python
      HTML
      •0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • PythonPackageCookiecutter

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 17, 2026Apr 17, 2026

    • ReScale4DL

      Public
      ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation
      Jupyter Notebook
      •
      MIT License
      •1•3•0•0•Updated Apr 16, 2026Apr 16, 2026

    • NanoPyx

      Public
      Nanoscopy library for Python (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •13•90•2•2•Updated Apr 14, 2026Apr 14, 2026

    • ZeroCostDL4Mic

      Public
      ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy
      Jupyter Notebook
      •
      MIT License
      •143•639•53•6•Updated Mar 29, 2026Mar 29, 2026

    • DL4MicEverywhere

      Public
      Bringing the ZeroCostDL4Mic experience running everywhere via easy-to-install docker images
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •17•86•13•1•Updated Mar 28, 2026Mar 28, 2026

    • rxiv-maker

      Public
      Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. It automates scientific preprint generation with a focus on reprodu…
      publishingpreprintsarticle-template
      publishingpreprintsarticle-templatepreprint
      Python
      •
      MIT License
      •5•31•3•4•Updated Mar 25, 2026Mar 25, 2026

    • vscode-rxiv-maker

      Public
      A vscode plugin for rxiv-maker
      TypeScript
      •
      MIT License
      •0•4•0•7•Updated Mar 25, 2026Mar 25, 2026

    • napari-NanoPyx

      Public
      Python
      •
      Creative Commons Attribution 4.0 International
      •1•11•2•0•Updated Mar 3, 2026Mar 3, 2026

    • folder2md4llms

      Public
      Combine files in a folder structure into a single text file suitable for use by LLMs, inspired by gpt-repository-loader
      llm
      llm
      Python
      •
      MIT License
      •2•9•0•0•Updated Feb 2, 2026Feb 2, 2026

    • EZInput

      Public
      EZInput is a Python library that simplifies the creation of graphical user interfaces (GUIs) both in the terminal and in Jupyter notebooks. It provides a conven…
      Python
      •
      MIT License
      •0•3•1•0•Updated Jan 30, 2026Jan 30, 2026

    • manuscript-rxiv-maker

      Public
      Rxiv-Maker preprint source code
      Python
      •
      Other
      •0•2•0•0•Updated Dec 24, 2025Dec 24, 2025

    • henriqueslab-updater

      Public
      Centralized update checking library for HenriquesLab Python packages
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • LiquidEngine

      Public
      Standalone Liquid Engine Python Package
      Python
      •
      Creative Commons Attribution 4.0 International
      •2•8•0•0•Updated Dec 2, 2025Dec 2, 2025

    • docker-rxiv-maker

      Public
      Docker image building infrastructure for rxiv-maker with weekly and on-demand builds
      Shell
      •
      MIT License
      •0•0•0•0•Updated Nov 17, 2025Nov 17, 2025

    • DeepBacs

      Public
      Python
      •
      Creative Commons Zero v1.0 Universal
      •6•32•0•0•Updated Nov 11, 2025Nov 11, 2025

    • SReD

      Public
      Structural Repetition Detector (SReD) - Quantitative mapping of molecular complexes
      Java
      •
      MIT License
      •0•3•2•0•Updated Sep 29, 2025Sep 29, 2025

    • PhotoFiTT

      Public
      Computational workflows to assess phototoxicity in live-cell microscopy experiments
      Jupyter Notebook
      •
      MIT License
      •0•11•1•0•Updated Sep 15, 2025Sep 15, 2025

    • Code-of-Conduct

      Public
      The Unlicense
      •0•1•0•0•Updated Sep 15, 2025Sep 15, 2025

    • EZInput-rxiv-maker

      Public template
      Python
      •
      MIT License
      •5•1•0•0•Updated Jul 22, 2025Jul 22, 2025

    • gptrepo

      Public
      Python
      •
      MIT License
      •233•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • NanoJ-eSRRF

      Public
      Java
      •
      Apache License 2.0
      •1•24•11•0•Updated May 30, 2025May 30, 2025

    • PublicationsHeatmap

      Public
      Python Jupyter notebook used to generate heatmap of publication records for Roadmap on Deep Learning in Microscopy
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 27, 2025Feb 27, 2025

    • easy-gui-jupyter

      Public
      Python
      •
      MIT License
      •1•0•1•0•Updated Feb 5, 2025Feb 5, 2025
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