Repositories list

• holdenlab.github.io

  Public
  Holden Lab website

  JavaScript

  •

  MIT License

  •1•0•1•0•Updated Nov 24, 2024Nov 24, 2024

• FastAcquisition2

  Public
  Fast acquisition plugin for Micromanager 2.0gamma

  Java

  •

  GNU General Public License v3.0

  •0•0•4•0•Updated Aug 13, 2024Aug 13, 2024

• DeepAutoFocus

  Public
  Autofocus by live infra-red brightfield image cross correlation

  Java

  •0•2•0•0•Updated Jul 15, 2024Jul 15, 2024

• lipowskiModel

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 4, 2024Jun 4, 2024

• shadowlessTIRF

  Public
  Shadowless TIRF Galvo Driver

  Python

  •

  MIT License

  •1•0•0•0•Updated Jan 23, 2024Jan 23, 2024

• LifeHackWebsite

  Public
  Website for LifeHack microscope system

  HTML

  •0•0•0•0•Updated Dec 23, 2023Dec 23, 2023

• septal_constriction_analysis

  Public
  Contains functions for fitting septal images and analysing constriction vs. time data

  MATLAB

  •1•0•0•0•Updated Dec 20, 2023Dec 20, 2023

• microscope-focus-lock

  Public
  Arduino-based microscope autofocus control

  C++

  •1•15•0•0•Updated Sep 18, 2023Sep 18, 2023

• LifeHack

  Public
  Open source SMLM microscope designs

  C++

  •

  Other

  •0•11•0•0•Updated May 31, 2023May 31, 2023

• Kymograph-spt-analysis

  Public
  All the code needed to reproduce Stu's single molecule MreB data analysis

  Jupyter Notebook

  •0•0•0•0•Updated May 18, 2023May 18, 2023

• VerCINI_nanofab

  Public
  Code for nanofabrication of silicon micropillars

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 21, 2021Oct 21, 2021

• VerciniAnalysisJ

  Public
  ImageJ analysis of Vertical Imaging by Nanostructured Immobilization (VerCINI) microscopy data

  Python

  •

  GNU General Public License v3.0

  •0•0•2•0•Updated Jul 26, 2021Jul 26, 2021

• ring-fitting2

  Public
  VerCINI image analysis software

  MATLAB

  •

  GNU General Public License v3.0

  •0•0•4•0•Updated Jul 26, 2021Jul 26, 2021

• list-of-update-sites

  Public
  The update sites ImageJ knows about automatically

  Python

  •92•0•0•0•Updated Mar 18, 2021Mar 18, 2021

• violinplusDABEST-Matlab

  Public
  MATLAB package to generate contrast plots

  MATLAB

  •

  GNU General Public License v3.0

  •20•0•0•0•Updated Mar 2, 2021Mar 2, 2021

• ring-simulator

  Public
  ring simulation

  MATLAB

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 2, 2021Mar 2, 2021

• microscope-incubation-box

  Public
  Microscope incubation box for home built single molecule microscope.

  Other

  •3•8•1•1•Updated Feb 23, 2021Feb 23, 2021

• ij-trajectory-classifier

  Public
  This plugin segments and classify diffusion trajectories

  Java

  •

  MIT License

  •4•0•0•0•Updated Jul 18, 2019Jul 18, 2019

• Violinplot-Matlab

  Public archive
  Violin Plots for Matlab

  MATLAB

  •103•0•0•0•Updated Jul 17, 2019Jul 17, 2019

• micro-manager

  Public
  Microscope control and image acquisition integrated with ImageJ.

  C++

  •231•0•0•0•Updated Feb 27, 2019Feb 27, 2019

• TrackMate

  Public
  TrackMate is your buddy for your everyday tracking.

  Java

  •76•0•0•0•Updated Aug 10, 2018Aug 10, 2018

• ring-fitting-bisson2017

  Public
  Microhole ring fitting (circular kymograph analysis) code associated with Bisson-Filho et al Science 2017

  MATLAB

  •

  Other

  •0•0•0•0•Updated Mar 28, 2018Mar 28, 2018