Repositories list

• swc-advanced-microscopy.github.io

  Public
  facility webpage

  SCSS

  •

  MIT License

  •27k27k forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• multiphoton-qc

  Public
  Multi-photon quality control tools

  imagingpoint-spread-functionscanimage

  imagingpoint-spread-functionscanimage

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •77 forks•3737 stars•4747 issues•22 pull requests•Updated Apr 22, 2026Apr 22, 2026

• StitchIt

  Public
  Stitching of large tiled datasets

  tilematlabneuroscience+ 5

  tilematlabneurosciencestitchingmicroscopyimaginganatomystitched-images

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •88 forks•2323 stars•7373 issues•11 pull request•Updated Apr 21, 2026Apr 21, 2026

• BakingTray

  Public
  Serial-section automated anatomy extension for ScanImage

  matlabneurosciencetomography+ 7

  matlabneurosciencetomographymicroscopyimaginganatomyneuroanatomy2-photonscanimageserial-section

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •55 forks•1818 stars•172172 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• ScanImageTools

  Public
  MATLAB tools for running imaging experiments with ScanImage

  data-acquisitionmicroscopyscanimage

  data-acquisitionmicroscopyscanimage

  MATLAB

  •

  GNU General Public License v3.0

  •33 forks•44 stars•33 issues•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• MATLAB_DAQmx_examples

  Public
  DAQmx Examples using MATLAB

  hardwareexamplesmatlab+ 5

  hardwareexamplesmatlabneurosciencedata-acquisitiondaqscanimageni-daqmx

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •1212 forks•3131 stars•88 issues•00 pull requests•Updated Feb 2, 2026Feb 2, 2026

• Python_DAQmx_examples

  Public
  DAQmx Examples using Python with NI's nidaqmx package

  pythonhardwareexamples+ 4

  pythonhardwareexamplesneurosciencedata-acquisitiondaqni-daqmx

  Python

  •

  GNU General Public License v3.0

  •44 forks•1515 stars•11 issue•00 pull requests•Updated Nov 6, 2025Nov 6, 2025

• SimplePyScanner

  Public
  Simple Python scanning software for demo purposes

  pythonexampleslaser+ 6

  pythonexampleslaserdata-acquisitionneuroimagingscanningmicroscopy2-photonni-daqmx

  Python

  •

  GNU General Public License v3.0

  •22 forks•77 stars•11 issue•00 pull requests•Updated Nov 6, 2025Nov 6, 2025

• standard_source_to_photons

  Public
  Repo to develop protocols for converting a standard fluorescent source to photons

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•11 issue•00 pull requests•Updated Feb 14, 2025Feb 14, 2025

• noise-practical

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 14, 2024Nov 14, 2024

• laser_calculator

  Public
  Laser safety calculator for 3b lasers

  00 forks•00 stars•00 issues•00 pull requests•Updated May 22, 2024May 22, 2024

• SWC_Optics_Course_Practicals

  Public
  Rich Text Format

  •

  The Unlicense

  •00 forks•00 stars•33 issues•00 pull requests•Updated May 14, 2024May 14, 2024

• btpytools

  Public
  Python-based BakingTray and StichIt helper tools

  Python

  •

  GNU Affero General Public License v3.0

  •11 fork•22 stars•1010 issues•00 pull requests•Updated May 3, 2024May 3, 2024

• SimpleMScanner

  Public
  Simple MATLAB scanning software for demo purposes

  exampleslasermatlab+ 6

  exampleslasermatlabdata-acquisitionneuroimagingscanningmicroscopy2-photonni-daqmx

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •22 forks•66 stars•1010 issues•00 pull requests•Updated Oct 16, 2023Oct 16, 2023

• 2p_crosssection_viewer

  Public
  Webpage with interactive plot of commonly used 2p dye cross-sections

  HTML

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 6, 2023Oct 6, 2023

• volView

  Public
  Simple image stack visualizer for MATLAB

  guiviewermatlab+ 1

  guiviewermatlabvolume

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •11 fork•33 stars•00 issues•00 pull requests•Updated Oct 6, 2023Oct 6, 2023

• image-analysis-python

  Public
  Materials for the SWC course on Image Analysis in Python

  JavaScript

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 31, 2023May 31, 2023

• linux_cli_intro

  Public
  Presentation for intro to Linux CLI using the Linux CLI

  Shell

  •

  Creative Commons Attribution 4.0 International

  •11 fork•44 stars•33 issues•00 pull requests•Updated May 2, 2023May 2, 2023

• diffuserwavefrontsensor

  Public
  Implements a diffuser-based wavefront sensor

  matlabopticswavefront-sensing

  matlabopticswavefront-sensing

  MATLAB

  •22 forks•33 stars•77 issues•00 pull requests•Updated Oct 26, 2021Oct 26, 2021

• LaserControl

  Public
  MATLAB control classes for lasers

  hardwarelasermatlab+ 3

  hardwarelasermatlabmicroscopy2-photonaom

  MATLAB

  •

  GNU General Public License v3.0

  •11 fork•66 stars•55 issues•00 pull requests•Updated Sep 2, 2020Sep 2, 2020

• HiLo_SIM

  Public
  Basic implementation of HiLo structured illumination algorithm in MATLAB

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •00 forks•55 stars•00 issues•00 pull requests•Updated Dec 14, 2019Dec 14, 2019

• ScanImageAPI_Examples

  Public
  ScanImage API Examples

  apiexamplesneuroscience+ 3

  apiexamplesneurosciencescanningmicroscopyimaging

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •22 forks•44 stars•00 issues•00 pull requests•Updated Dec 14, 2019Dec 14, 2019

• ScanImageTileScan

  Public
  MATLAB-based ScanImage tile scanner

  neurosciencemicroscopyimaging+ 2

  neurosciencemicroscopyimagingtime-lapsemotion-control

  MATLAB

  •

  GNU Lesser General Public License v3.0

  •11 fork•44 stars•11 issue•00 pull requests•Updated Dec 14, 2019Dec 14, 2019

• lensdistort

  Public
  Correct barrel and pincushion distortion

  matlabimage-processing

  matlabimage-processing

  MATLAB

  •33 forks•33 stars•00 issues•00 pull requests•Updated Jun 18, 2018Jun 18, 2018

• beamAligner

  Public
  MATLAB tool for aligning mesoscope beam.

  MATLAB

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 3, 2017Nov 3, 2017

• MesoscopeLoader

  Public
  Basic tools to load mesoscope stacks in Matlab

  MATLAB

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 25, 2017Sep 25, 2017