Repositories list

• microscope_command_server

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

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 24, 2026Jul 24, 2026

• microscope_control

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

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 24, 2026Jul 24, 2026

• flamingo-stitcher

  Public
  Standalone light-sheet tile stitching (CLI + GUI) for Flamingo T-SPIM data, extracted from py2flamingo.

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 24, 2026Jul 24, 2026

• Kepco-Dashboard

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

  Python

  •00 forks•22 stars•00 issues•11 pull request•Updated Jul 24, 2026Jul 24, 2026

• EBEAM_dashboard

  Public
  EBEAM System GUI

  Python

  •11 fork•88 stars•2020 issues•2323 pull requests•Updated Jul 23, 2026Jul 23, 2026

• Flamingo_Control

  Public
  Controlling a Flamingo microscope from Python

  Python

  •

  MIT License

  •22 forks•22 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• EBEAM_webmonitor

  Public
  Website for remote monitoring of ebeam experiment

  JavaScript

  •00 forks•44 stars•33 issues•33 pull requests•Updated Jul 23, 2026Jul 23, 2026

• tme-quant

  Public
  Python

  •11 fork•11 star•2727 issues•33 pull requests•Updated Jul 23, 2026Jul 23, 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

  •11 fork•11 star•00 issues•55 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-catalog-qpsc

  Public
  QuPath extension catalog for QPSC microscope control system

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-qpsc

  Public
  Java based extension for QuPath allowing control of a microscope through MicroManager

  Java

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•55 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-dialog-manager

  Public
  QuPath extension for managing dialog window positions with persistence and off-screen recovery

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•44 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-class-distribution

  Public
  Live pie chart of annotation class distribution across a QuPath project, with over/under-representation highlighting for training-data hygiene.

  Java

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-channel-names-viewer

  Public
  QuPath extension: always-visible legend window for currently selected fluorescence channels. Discoverable via toolbar button, menu, and Cmd/Ctrl+Shift+C; window…

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-project-metadata-browser

  Public
  Browse, filter, and edit metadata for all images in a QuPath project.

  Java

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-cell-analysis-tools

  Public
  Python-powered clustering and phenotyping for highly multiplexed imaging data in QuPath

  Java

  •

  Apache License 2.0

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-catalog-mikenelson

  Public
  QuPath extensions by Mike Nelson at LOCI

  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-ocr4labels

  Public
  A QuPath extension for OCR on slide label images with metadata extraction

  Java

  •

  Apache License 2.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-image-export-toolkit

  Public
  QuIET - QuPath Image Export Toolkit: batch export images for publication or model training

  machine-learningmicroscopybioimage-analysis+ 5

  machine-learningmicroscopybioimage-analysisqupathimage-exportpublication-figuresqupath-extensionquarep-limi

  Java

  •

  Apache License 2.0

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-ppm

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

  Java

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-classify-object-subset

  Public
  Apply a saved QuPath object classifier to a subset of objects (by class, by measurement, or from selection).

  Java

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• qupath-extension-dl-pixel-classifier

  Public
  QuPath extension for deep learning pixel classification with Python training backend

  Java

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•55 pull requests•Updated Jul 23, 2026Jul 23, 2026

• microscope_configurations

  Public
  YAML configuration templates for QPSC microscope systems

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 23, 2026Jul 23, 2026

• cellcast

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

  Rust

  •

  MIT License

  •11 fork•2323 stars•44 issues•00 pull requests•Updated Jul 22, 2026Jul 22, 2026

• pump-down-analyzer

  Public
  Pump down analyzer app for examining what happened during an ebeam vacuum chamber pump down

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 21, 2026Jul 21, 2026

• ppm_library

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

  Python

  •

  MIT License

  •11 fork•00 stars•11 issue•00 pull requests•Updated Jul 20, 2026Jul 20, 2026

• VTRX_firmware

  Public
  C++

  •00 forks•11 star•00 issues•11 pull request•Updated Jul 18, 2026Jul 18, 2026

• beam-controller

  Public
  EBEAM Beam Controller firmware code

  Python

  •11 fork•11 star•22 issues•11 pull request•Updated Jul 14, 2026Jul 14, 2026

• ebeam-laser-monitor

  Public
  Laser monitor systems specifically for e-beam experiment

  C++

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 13, 2026Jul 13, 2026

• HighSpeedBubbleAnalysis

  Public
  A quick analysis of high-speed images from LINK, for Aarushi's lab

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 10, 2026Jul 10, 2026