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@uw-loci

UW-Madison LOCI

Laboratory for Optical and Computational Instrumentation: the UW-Madison research lab of Kevin Eliceiri

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  1. curvelets curvelets Public

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

    MATLAB 28 19

  2. loci-scripts loci-scripts Public

    Scripts and macros for LOCI scientific problems

    Shell

  3. visbio-imagej visbio-imagej Public

    ImageJ plugins for 3D visualization using the VisAD toolkit

    Java 1

  4. misc-plugins misc-plugins Public

    Miscellaneous ImageJ plugins

    Java 2 1

  5. search-image-sc search-image-sc Public

    Image.sc search service

    Python

Repositories

Showing 10 of 159 repositories
  • qupath-extension-qpsc Public

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

    uw-loci/qupath-extension-qpsc's past year of commit activity
    Java 1 Apache-2.0 0 0 5 Updated Oct 18, 2026
  • microscope_command_server Public

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

    uw-loci/microscope_command_server's past year of commit activity
    Python 0 MIT 1 0 0 Updated Oct 18, 2026
  • microscope_control Public

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

    uw-loci/microscope_control's past year of commit activity
    Python 2 MIT 0 0 0 Updated Oct 18, 2026
  • qupath-catalog-mikenelson Public

    QuPath extensions by Mike Nelson at LOCI

    uw-loci/qupath-catalog-mikenelson's past year of commit activity
    Python 3 0 0 0 Updated Oct 17, 2026
  • qupath-extension-cell-analysis-tools Public

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

    uw-loci/qupath-extension-cell-analysis-tools's past year of commit activity
    Java 8 Apache-2.0 1 1 0 Updated Oct 17, 2026
  • qupath-extension-image-export-toolkit Public

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

    uw-loci/qupath-extension-image-export-toolkit's past year of commit activity
    Java 3 Apache-2.0 0 0 0 Updated Oct 17, 2026
  • microscope_configurations Public

    YAML configuration templates for QPSC microscope systems

    uw-loci/microscope_configurations's past year of commit activity
    Python 0 1 0 0 Updated Oct 17, 2026
  • qupath-extension-dl-pixel-classifier Public

    QuPath extension for deep learning pixel classification with Python training backend

    uw-loci/qupath-extension-dl-pixel-classifier's past year of commit activity
    Java 2 Apache-2.0 0 1 5 Updated Oct 17, 2026
  • flamingo-stitcher Public

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

    uw-loci/flamingo-stitcher's past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Oct 17, 2026
  • qupath-extension-wizard-wand Public

    Enhanced wand tool for QuPath with scroll-wheel sensitivity, dwell expansion, live smoothing, edge-aware selection, and more.

    uw-loci/qupath-extension-wizard-wand's past year of commit activity
    Java 0 GPL-3.0 0 1 0 Updated Oct 17, 2026
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