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    26 repositories

    • mcSIM

      Public
      Code for running a multicolor structured illumination microscopy (SIM) experiment using a DLP6500 digital micromirror device (DMD) and performing SIM reconstruction.
      experimentphysicssimimagingdmdmicromanagersimulation
      Python
      •
      GNU General Public License v3.0
      •13•55•0•0•Updated Nov 29, 2024Nov 29, 2024

    • merfish3d-analysis

      Public
      3D MERFISH data processing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•4•0•Updated Nov 22, 2024Nov 22, 2024

    • navigate

      Public
      navigate - open source light-sheet microscope controls
      Python
      •
      Other
      •7•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • napari-micromanager

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •21•0•0•0•Updated Sep 28, 2024Sep 28, 2024

    • instanseg

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •14•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
      •2•0•0•0•Updated Sep 1, 2024Sep 1, 2024

    • SPIM_model

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 30, 2024Aug 30, 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

    • pycrofluidics

      Public
      A Python module for controlling Elveflow microfluidic devices
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 8, 2024Aug 8, 2024

    • OPM

      Public
      Control, reconstruction, and analysis code for oblique plane microscopy.
      experimentphysicsgpu-accelerationimagingtimelapsemicromanagerlightsheet
      Python
      •
      GNU General Public License v3.0
      •7•21•0•0•Updated Aug 4, 2024Aug 4, 2024

    • sparse-deconv-py

      Public
      Official Python implementation of the 'Sparse deconvolution'-v0.3.0
      Python
      •
      Open Data Commons Open Database License v1.0
      •17•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
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Jul 3, 2024Jul 3, 2024

    • U-FISH

      Public
      Deep learning based spot detection for FISH images.
      Jupyter Notebook
      •
      MIT License
      •5•1•0•0•Updated Apr 7, 2024Apr 7, 2024

    • spots3d

      Public
      GPU accelerated spot finding and localization for both skewed (diSPIM, lattice, OPM) and standard geometry (widefield, confocal) 3D microscopy data.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 30, 2024Mar 30, 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
      •93•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

    • MVRegFus

      Public
      Python module for registering and fusing multi-view microscopy data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•0•0•Updated May 16, 2021May 16, 2021

    • IDT-using-Annular-Illumination

      Public
      This is the MATLAB Implementation for Annular Illumination Intensity Diffraction Tomography (aIDT).
      MATLAB
      •
      BSD 3-Clause "New" or "Revised" License
      •9•0•0•0•Updated May 12, 2020May 12, 2020

    • cruzdb

      Public
      python access to UCSC genomes database
      Python
      •
      MIT License
      •42•0•0•0•Updated Mar 12, 2020Mar 12, 2020

    • storm-control

      Public
      Microscope control software
      Python
      •
      Other
      •68•0•0•0•Updated Mar 5, 2020Mar 5, 2020

    • 2019-Kim-BiologyOpen

      Public
      Image processing and analysis code for Kim et al 2019
      Jupyter Notebook
      •0•0•0•0•Updated Oct 4, 2019Oct 4, 2019