Repositories list

• EBEAM_webmonitor

  Public
  Website for remote monitoring of ebeam experiment

  JavaScript

  •0•2•1•1•Updated Mar 21, 2026Mar 21, 2026

• Flamingo_Control

  Public
  Controlling a Flamingo microscope from Python

  Python

  •

  MIT License

  •2•2•0•0•Updated Mar 21, 2026Mar 21, 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

  •

  Apache License 2.0

  •0•0•0•5•Updated Mar 21, 2026Mar 21, 2026

• EBEAM_dashboard

  Public
  EBEAM System GUI

  Python

  •1•7•2•7•Updated Mar 20, 2026Mar 20, 2026

• microscope_command_server

  Public
  Socket-based command server for remote microscope control and QuPath integration

  Python

  •

  MIT License

  •1•0•0•0•Updated Mar 20, 2026Mar 20, 2026

• qupath-extension-tiles-to-pyramid

  Public
  An extension to allow the creation of a pyramidal image file from individual tiles, based on known tile positions.

  Java

  •

  Apache License 2.0

  •1•0•0•4•Updated Mar 20, 2026Mar 20, 2026

• cellcast

  Public
  A recast of cell segmentation models built on the Burn deep learning framework.

  Rust

  •

  MIT License

  •0•16•3•0•Updated Mar 20, 2026Mar 20, 2026

• knob-box

  Public
  EBEAM Knob Box firmware

  C++

  •1•2•2•0•Updated Mar 19, 2026Mar 19, 2026

• qupath-extension-ppm

  Public
  Polarized light microscopy (PPM) modality extension for QuPath/QPSC

  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

• tme-quant

  Public
  Python

  •1•1•23•1•Updated Mar 19, 2026Mar 19, 2026

• ppm_library

  Public
  Image processing library for polarized light microscopy (PPM) and general microscopy imaging

  Python

  •

  MIT License

  •1•0•1•0•Updated Mar 19, 2026Mar 19, 2026

• microscope_configurations

  Public
  YAML configuration templates for QPSC microscope systems

  1•0•0•0•Updated Mar 19, 2026Mar 19, 2026

• microscope_control

  Public
  Hardware control library for microscopes via Pycromanager (Micro-Manager)

  Python

  •

  MIT License

  •0•1•0•0•Updated Mar 19, 2026Mar 19, 2026

• Kepco-Dashboard

  Public
  A material-style Dashboard for control the Kepco. With waveform generation ability

  Python

  •0•1•1•1•Updated Mar 19, 2026Mar 19, 2026

• phasorkit

  Public
  A light weight Fiji plugin that offers a simple font end to phasor/FLIM libraries.

  Java

  •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

• 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 Mar 16, 2026Mar 16, 2026

• pmon_mini_dashboard

  Public
  Python

  •0•1•0•0•Updated Mar 12, 2026Mar 12, 2026

• beam-controller

  Public
  EBEAM Beam Controller firmware code

  C

  •1•1•0•0•Updated Mar 4, 2026Mar 4, 2026

• QPSC

  Public
  QuPath Scope Control - Annotation-driven targeted microscopy acquisition from within QuPath

  PowerShell

  •1•0•3•0•Updated Feb 27, 2026Feb 27, 2026

• curvelets

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

  MATLAB

  •

  Other

  •18•28•28•1•Updated Feb 13, 2026Feb 13, 2026

• shutter-interlock

  Public
  Arduino firmware for interlocked shutter switching

  C++

  •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

• waveAnalysis_GUI

  Public
  Python tools for batch analysis of oscillatory dynamics

  Python

  •4•0•1•0•Updated Jan 21, 2026Jan 21, 2026

• flim-metrics

  Public
  Jupyter Notebook

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

• flim-metrics-viewer

  Public
  Python

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

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

  Public
  MATLAB

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

• PhasorJ

  Public
  Java

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

• ast-net

  Public
  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
  Automated tests for LOCI websites

  Raku

  •

  The Unlicense

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