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    35 repositories

    • merfish3d-analysis

      Public
      GPU accelerated post-processing for 2D or 3D imaging spatial transcriptomics data.
      gpu-accelerationspatial-dataimage-analysis
      gpu-accelerationspatial-dataimage-analysismicroscopyspatial-transcriptomicsmerfish
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•9•4•2•Updated Apr 20, 2026Apr 20, 2026

    • opm-processing-v2

      Public
      Code for fast deconvolution, deskewing, registration, and fusion of OPM/diSPIM/LLSM data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•7•1•1•Updated Apr 13, 2026Apr 13, 2026

    • opm-v2

      Public
      GUI and code for controlling an oblique plane microscope with projection imaging, sensorless adaptive optics, and integrated microfluidics.
      microscopyadaptive-opticsfluidics
      microscopyadaptive-opticsfluidicslightsheetpymmcore-plus
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•1•2•Updated Apr 13, 2026Apr 13, 2026

    • merfish3d-wfacq

      Public
      Microscope and fluidics control suite for 2D or 3D imaging spatial transcriptomics experiments.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 8, 2026Apr 8, 2026

    • SN2N

      Public
      Official PyTorch implementation of the "SN2N"
      Python
      •
      Open Data Commons Open Database License v1.0
      •8•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • mcSIM

      Public
      Code for running a multicolor structured illumination microscopy (SIM) experiment using a DLP6500 digital micromirror device (DMD) and performing SIM reconstruc…
      experimentsimulationphysics
      experimentsimulationphysicssimimagingdmdmicromanager
      Python
      •
      GNU General Public License v3.0
      •14•71•1•1•Updated Feb 14, 2026Feb 14, 2026

    • navigate

      Public
      navigate - open source light-sheet microscope controls
      Python
      •
      Other
      •15•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • BaSiCPy

      Public
      Python
      •
      MIT License
      •33•1•0•0•Updated Oct 18, 2025Oct 18, 2025

    • SPIM_model

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 16, 2025Oct 16, 2025

    • warpfield

      Public
      GPU-based 3D non-rigid volumetric registration
      Python
      •
      MIT License
      •4•0•0•0•Updated Sep 3, 2025Sep 3, 2025

    • 2025-CBP-SummerSchool

      Public
      2025 ASU Center for Biological Physics Summer School
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • deeds-registration

      Public
      Python wrapper around DEEDS - efficient algorithm for 3D discrete deformable image registration, reaching the highest accuracy in several benchmarks
      C
      •
      MIT License
      •4•0•0•0•Updated Jul 24, 2025Jul 24, 2025

    • dpc-3d

      Public
      Python
      •
      Other
      •0•0•0•1•Updated Jul 14, 2025Jul 14, 2025

    • U-FISH

      Public
      Deep learning based spot detection for FISH images.
      Jupyter Notebook
      •
      MIT License
      •8•1•0•0•Updated Jun 10, 2025Jun 10, 2025

    • trackastra

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •28•0•0•1•Updated Apr 25, 2025Apr 25, 2025

    • OPM

      Public archive
      Archived: control, reconstruction, and analysis code for oblique plane microscopy.
      experimentphysicsgpu-acceleration
      experimentphysicsgpu-accelerationimagingtimelapsemicromanagerlightsheet
      Python
      •
      GNU General Public License v3.0
      •7•22•0•2•Updated Apr 1, 2025Apr 1, 2025

    • pycrofluidics

      Public
      A Python module for controlling Elveflow microfluidic devices
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Dec 14, 2024Dec 14, 2024

    • napari-micromanager

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •25•0•0•0•Updated Sep 28, 2024Sep 28, 2024

    • instanseg

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •39•0•0•0•Updated Sep 10, 2024Sep 10, 2024

    • rlgc

      Public
      Richardson-Lucy deconvolution with local stopping given by gradient consensus
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Sep 1, 2024Sep 1, 2024

    • ray_trace_pb

      Public
      Simple ray tracing in Python
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • sparse-deconv-py

      Public
      Official Python implementation of the 'Sparse deconvolution'-v0.3.0
      Python
      •
      Open Data Commons Open Database License v1.0
      •20•1•0•0•Updated Jul 16, 2024Jul 16, 2024

    • localize-psf

      Public
      Code for localizing diffraction limited fluorescent objects and fitting the results to various different point-spread function (PSF) models.
      python
      python
      Python
      •
      GNU General Public License v3.0
      •2•6•0•0•Updated Jul 3, 2024Jul 3, 2024

    • napari-spot-detection

      Public
      Detect diffraction limited spots in 2D and 3D, in standard or skewed microscopy images.
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Feb 28, 2024Feb 28, 2024

    • ProjectionSimulation

      Public
      Simple simulation to compare standard and projection imaging
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2023Oct 9, 2023

    • Gpufit

      Public
      GPU-accelerated Levenberg-Marquardt curve fitting in CUDA
      Cuda
      •
      MIT License
      •102•1•0•0•Updated Aug 11, 2023Aug 11, 2023

    • napari-mcsim

      Public
      Napari plugin automating structured illumination microscopy (SIM) reconstruction and diagnostics from the mcSIM package
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 2, 2023Aug 2, 2023

    • npy2bdv

      Public
      Fast writing of numpy 3d-arrays into HDF5 and N5 Fiji/BigDataViewer files.
      Python
      •
      GNU General Public License v3.0
      •12•0•0•0•Updated May 17, 2023May 17, 2023

    • rDL-SIM

      Public
      A Tensorflow implementation of rationalized deep learning (rDL) based image denoising for microscopy images
      Python
      •
      MIT License
      •6•0•0•0•Updated Oct 12, 2022Oct 12, 2022

    • I2K2022-SIM

      Public
      I2K 2022 mcSIM tutorial
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated Jun 8, 2022Jun 8, 2022
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