Repositories list

• Flamingo_Control

  Public
  Controlling a Flamingo microscope from Python

  Python

  •

  MIT License

  •2•2•0•0•Updated Oct 30, 2025Oct 30, 2025

• tme-quant

  Public
  Python

  •0•1•12•0•Updated Oct 30, 2025Oct 30, 2025

• waveAnalysis_GUI

  Public
  Python tools for batch analysis of oscillatory dynamics

  Python

  •4•0•1•1•Updated Oct 30, 2025Oct 30, 2025

• EBEAM_dashboard

  Public
  EBEAM System GUI

  Python

  •1•6•0•9•Updated Oct 30, 2025Oct 30, 2025

• curvelets

  Public
  Curvelet-Transform based fibrillar collagen quantification (CurveAlign and CT-FIRE)

  MATLAB

  •

  Other

  •17•25•25•1•Updated Oct 29, 2025Oct 29, 2025

• EBEAM_webmonitor

  Public
  Website for remote monitoring of ebeam experiment

  JavaScript

  •0•1•0•0•Updated Oct 28, 2025Oct 28, 2025

• cbmark_logger

  Public
  Data logger for cathode benchmarking experiment for the e-beam system. Logs and displays select data from experiment.

  Jupyter Notebook

  •0•1•0•0•Updated Oct 17, 2025Oct 17, 2025

• PhasorJ

  Public
  Java

  •0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

• 4d-software-suite

  Public archive
  LOCI 4D Software Suite [DISCONTINUED]

  Java

  •0•1•0•0•Updated Aug 18, 2025Aug 18, 2025

• knob-box

  Public
  EBEAM Knob Box firmware

  C++

  •1•1•0•1•Updated Jul 10, 2025Jul 10, 2025

• search-image-sc

  Public
  Image.sc search service

  Python

  •

  The Unlicense

  •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

• website-tests

  Public
  Automated tests for LOCI websites

  Raku

  •

  The Unlicense

  •1•0•0•0•Updated May 19, 2025May 19, 2025

• he_shg_synth_workflow

  Public
  Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis

  Python

  •6•10•3•1•Updated Apr 25, 2025Apr 25, 2025

• MultivariateAnalysis_FLIM

  Public
  Determination of Coefficient of Variation in complex FLIM datasets under different imaging conditions

  MATLAB

  •

  MIT License

  •0•0•0•0•Updated Apr 24, 2025Apr 24, 2025

• beam-controller

  Public
  EBEAM Beam Controller firmware code

  C

  •1•1•0•0•Updated Apr 18, 2025Apr 18, 2025

• spieosamadison.org

  Public
  spieosamadison.org -> spieopticamadison.org

  HTML

  •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

• laser-monitor

  Public
  Code for laser monitoring system

  C++

  •0•1•0•0•Updated Apr 15, 2025Apr 15, 2025

• qp-scope

  Public
  Controlling a microscope through some sort of python control interface (Pycromanager) and MicroManager

  Groovy

  •

  MIT License

  •1•1•0•0•Updated Apr 15, 2025Apr 15, 2025

• EBEAM_scoreboard

  Public
  E-beam project management scoreboard for team

  JavaScript

  •0•1•0•0•Updated Apr 13, 2025Apr 13, 2025

• collagen-fiber-metrics

  Public
  Deep generative models for collagen fiber centerline segmentation and extraction in cancer tissue

  deep-learninggenerative-adversarial-networkimage-segmentation+ 4variational-autoencodercomputational-pathologyhistopathologycollagen-fibers

  Jupyter Notebook

  •3•11•0•0•Updated Feb 5, 2025Feb 5, 2025

• VTRX_firmware

  Public
  C++

  •0•1•0•0•Updated Jan 3, 2025Jan 3, 2025

• 972b

  Public
  Arduino library for the 972B Vacuum Pressure Transducer.

  C++

  •0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

• spieopticamadison.org

  Public
  UW SPIE/Optica website

  HTML

  •1•0•3•0•Updated Nov 26, 2024Nov 26, 2024

• basic-stitching

  Public
  Based on QuPath extension template - for basic tiling with no overlap resolution

  Groovy

  •

  MIT License

  •0•0•0•0•Updated May 15, 2024May 15, 2024

• BasicStitching

  Public
  Mike's test for 0.4.x extension

  Groovy

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jan 30, 2024Jan 30, 2024

• optogensim

  Public
  MATLAB

  •

  BSD 2-Clause "Simplified" License

  •2•4•0•0•Updated Jan 19, 2024Jan 19, 2024

• PaQuO_test

  Public
  Testing Python control of QuPath projects

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 22, 2023Nov 22, 2023

• RT-FLIM

  Public
  This is the Real Time FLIM Estimation project.

  MATLAB

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 17, 2023Oct 17, 2023

• dashboardsforMM

  Public
  Jupyter Dashboards for MicroManager OpenScan-TimeTagger Operation and SmartMicroscope Modules

  Jupyter Notebook

  •1•0•0•0•Updated Aug 17, 2023Aug 17, 2023

• eliceirilab.org

  Public
  eliceirilab.org -> loci.wisc.edu

  HTML

  •0•0•0•0•Updated Jun 21, 2023Jun 21, 2023