Repositories list

• cellcast

  Public

  uw-loci/cellcast’s past year of commit activity
  A recast of cell segmentation models built on the Burn deep learning framework.

  Rust

  •

  MIT License

  •0•5•2•0•Updated Jan 9, 2026Jan 9, 2026

• microscope_command_server

  Public

  uw-loci/microscope_command_server’s past year of commit activity
  Socket-based command server for remote microscope control and QuPath integration

  Python

  •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

• QPSC

  Public

  uw-loci/QPSC’s past year of commit activity
  QuPath Scope Control - Annotation-driven targeted microscopy acquisition from within QuPath

  PowerShell

  •1•0•3•0•Updated Jan 9, 2026Jan 9, 2026

• ppm_library

  Public

  uw-loci/ppm_library’s past year of commit activity
  Image processing library for polarized light microscopy (PPM) and general microscopy imaging

  Python

  •0•0•1•0•Updated Jan 9, 2026Jan 9, 2026

• microscope_control

  Public

  uw-loci/microscope_control’s past year of commit activity
  Hardware control library for microscopes via Pycromanager (Micro-Manager)

  Python

  •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

• Flamingo_Control

  Public

  uw-loci/Flamingo_Control’s past year of commit activity
  Controlling a Flamingo microscope from Python

  Python

  •

  MIT License

  •2•2•0•0•Updated Jan 8, 2026Jan 8, 2026

• flim-metrics

  Public

  uw-loci/flim-metrics’s past year of commit activity
  Jupyter Notebook

  •0•0•1•0•Updated Jan 8, 2026Jan 8, 2026

• flim-metrics-viewer

  Public

  uw-loci/flim-metrics-viewer’s past year of commit activity
  Python

  •1•0•0•0•Updated Jan 8, 2026Jan 8, 2026

• qupath-extension-tiles-to-pyramid

  Public

  uw-loci/qupath-extension-tiles-to-pyramid’s past year of commit activity
  An extension to allow the creation of a pyramidal image file from individual tiles, based on known tile positions.

  Java

  •

  MIT License

  •1•0•0•0•Updated Jan 8, 2026Jan 8, 2026

• qupath-extension-qpsc

  Public

  uw-loci/qupath-extension-qpsc’s past year of commit activity
  Java based extension for QuPath allowing control of a microscope through MicroManager

  Java

  •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

• microscope_configurations

  Public

  uw-loci/microscope_configurations’s past year of commit activity
  YAML configuration templates for QPSC microscope systems

  0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

• waveAnalysis_GUI

  Public

  uw-loci/waveAnalysis_GUI’s past year of commit activity
  Python tools for batch analysis of oscillatory dynamics

  Python

  •4•0•2•1•Updated Jan 7, 2026Jan 7, 2026

• EBEAM_dashboard

  Public

  uw-loci/EBEAM_dashboard’s past year of commit activity
  EBEAM System GUI

  Python

  •1•7•0•5•Updated Jan 5, 2026Jan 5, 2026

• data-and-code-for-improved-interface-paper

  Public

  uw-loci/data-and-code-for-improved-interface-paper’s past year of commit activity
  MATLAB

  •0•0•0•0•Updated Dec 23, 2025Dec 23, 2025

• knob-box

  Public

  uw-loci/knob-box’s past year of commit activity
  EBEAM Knob Box firmware

  C++

  •1•1•0•2•Updated Dec 12, 2025Dec 12, 2025

• curvelets

  Public

  uw-loci/curvelets’s past year of commit activity
  Curvelet-Transform based fibrillar collagen quantification (CurveAlign and CT-FIRE)

  MATLAB

  •

  Other

  •18•25•26•1•Updated Dec 9, 2025Dec 9, 2025

• tme-quant

  Public

  uw-loci/tme-quant’s past year of commit activity
  Python

  •0•1•13•1•Updated Dec 9, 2025Dec 9, 2025

• EBEAM_webmonitor

  Public

  uw-loci/EBEAM_webmonitor’s past year of commit activity
  Website for remote monitoring of ebeam experiment

  JavaScript

  •0•1•0•0•Updated Dec 5, 2025Dec 5, 2025

• PhasorJ

  Public

  uw-loci/PhasorJ’s past year of commit activity
  Java

  •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

• ast-net

  Public

  uw-loci/ast-net’s past year of commit activity
  A deep learning network trained to classify bacterial species from label-free data.

  Rust

  •

  The Unlicense

  •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

• website-tests

  Public

  uw-loci/website-tests’s past year of commit activity
  Automated tests for LOCI websites

  Raku

  •

  The Unlicense

  •1•0•0•0•Updated Nov 13, 2025Nov 13, 2025

• cbmark_logger

  Public

  uw-loci/cbmark_logger’s past year of commit activity
  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

• 4d-software-suite

  Public archive
  LOCI 4D Software Suite [DISCONTINUED]

  Java

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

• flim-metrics-multiplexing

  Public
  separation of bead lifetime's using variational autoencoder

  Jupyter Notebook

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

• search-image-sc

  Public
  Image.sc search service

  Python

  •

  The Unlicense

  •0•0•0•0•Updated Jun 3, 2025Jun 3, 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•1•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