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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 18

  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 157 repositories
  • 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 Sep 10, 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 Sep 10, 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 7 Apache-2.0 1 3 0 Updated Sep 10, 2026
  • multiplex-synthetic-data Public

    Small, fully-labelled synthetic tumor-microenvironment dataset for testing and teaching cell clustering, phenotyping, classification, and spatial analysis in QuPath / QP-CAT. Data ships as release assets.

    uw-loci/multiplex-synthetic-data's past year of commit activity
    0 CC0-1.0 0 0 0 Updated Sep 10, 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 Sep 10, 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 1 Apache-2.0 0 1 5 Updated Sep 10, 2026
  • microscope_imageprocessing Public
    uw-loci/microscope_imageprocessing's past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 10, 2026
  • qupath-catalog-qpsc Public

    QuPath extension catalog for QPSC microscope control system

    uw-loci/qupath-catalog-qpsc's past year of commit activity
    Python 0 0 0 0 Updated Sep 9, 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.

    uw-loci/qupath-extension-class-distribution's past year of commit activity
    Java 1 Apache-2.0 0 0 0 Updated Sep 8, 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).

    uw-loci/qupath-extension-classify-object-subset's past year of commit activity
    Java 1 Apache-2.0 0 0 0 Updated Sep 8, 2026
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