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@mehta-lab Computational Microscopy Platform (Mehta Lab), CZ Biohub

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    26 repositories

    • waveorder

      Public
      Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.
      simulationopticsphasescatteringpolarizationlabel-freepermittivityreconstruction-algorithmqlippmipolscope
      Python
      •
      Other
      •7•40•63•4•Updated Feb 12, 2026Feb 12, 2026

    • VisCy

      Public
      computer vision models for single-cell phenotyping
      machine-learningcomputer-visionrepresentation-learningimage-translationbioimage-analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•87•38•17•Updated Feb 11, 2026Feb 11, 2026

    • recOrder

      Public
      3D quantitative label-free imaging with phase and polarization
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•18•1•4•Updated May 15, 2025May 15, 2025

    • dynacontrast

      Public archive
      Image-based phenotyping of single cells using self-supervised contrastive learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•2•0•Updated Sep 3, 2024Sep 3, 2024

    • pycro-manager

      Public
      Python control of micro-manager for customized data acquisition
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •54•0•0•1•Updated Apr 19, 2024Apr 19, 2024

    • NDViewer

      Public
      N-D multichannel multiresolution image viewer for Micro-Manager
      Java
      •6•0•0•0•Updated Apr 19, 2024Apr 19, 2024

    • NDTiffStorage

      Public
      N-dimensional, multiresolution file format for Micro-Manager
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •14•0•0•0•Updated Apr 19, 2024Apr 19, 2024

    • AcqEngJ

      Public
      Java-based acquisition engine for Micro-manager
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •7•0•0•0•Updated Apr 19, 2024Apr 19, 2024

    • mmCoreAndDevices

      Public
      Micro-Manager's device control layer, written in C++
      C++
      •130•0•6•0•Updated Apr 10, 2024Apr 10, 2024

    • TriggerScopeMM

      Public
      Micro-Manager-specific firmware for the TriggerScope
      C++
      •
      Other
      •5•0•0•0•Updated Apr 5, 2024Apr 5, 2024

    • .github

      Public
      0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • micro-manager

      Public
      Microscope control and image acquisition integrated with ImageJ.
      Java
      •247•1•0•1•Updated Aug 3, 2023Aug 3, 2023

    • microDL

      Public archive
      3D virtual staining with 2D and 2.5D U-Nets
      deep-learningpytorchphasepolarizationlabel-freeu-net-pytorchvirtual-stainingu-net-keras
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•31•4•3•Updated Jul 29, 2023Jul 29, 2023

    • multiSero

      Public
      serological measurements from multiplexed ELISA assays
      pythonimagingelisacovid-19covid19covid19-serologyantigen-arrays
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•6•3•4•Updated Jun 14, 2023Jun 14, 2023

    • instantPolScope-matlab

      Public
      Imaging molecular order in live cells using fluorescence polarization.
      MATLAB
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•0•Updated Jun 4, 2023Jun 4, 2023

    • tensor-visualization

      Public
      Visualization of uniaxial permittivity tensors measured with polarization microscopy in 2D and 3D space
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 4, 2023Jun 4, 2023

    • microlith

      Public
      Image simulation for microscopy and lithography systems
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •7•26•0•0•Updated Jun 4, 2023Jun 4, 2023

    • reconstruct-order

      Public
      Label-free measurement of density and anisotropy from polarization-resolved images
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•12•2•1•Updated Jun 4, 2023Jun 4, 2023

    • MM_meadowlarkLC_opensource

      Public archive
      Open source micro-manager adapter for Meadowlark Liquid Crystal controllers.
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Apr 25, 2023Apr 25, 2023

    • dynamorph

      Public archive
      Learn morphological states of dynamic cells
      dimensionality-reductionvq-vaecell-state
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•12•11•2•Updated Apr 16, 2023Apr 16, 2023

    • micro-manager.github.io

      Public
      Micro-Manager website source
      JavaScript
      •51•0•0•0•Updated Apr 14, 2023Apr 14, 2023

    • miPolScope

      Public
      miPolScope: rapid label-free imaging across wavelegnths
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 6, 2022Aug 6, 2022

    • napari-glyphs

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 2, 2022Jun 2, 2022

    • napari-allencell-segmenter

      Public
      A plugin that enables image segmentation provided by Allen Institute for Cell Science
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•0•0•0•Updated Feb 9, 2022Feb 9, 2022

    • octopi-research

      Public
      Python
      •49•0•0•0•Updated Apr 8, 2021Apr 8, 2021

    • aicsimageio

      Public archive
      Delayed Parallel Image Reading for Microscopy Images in Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •50•0•0•0•Updated Feb 2, 2021Feb 2, 2021