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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. cellcast cellcast Public

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

    Rust 25 2

  3. loci-scripts loci-scripts Public

    Scripts and macros for LOCI scientific problems

    Shell

  4. visbio-imagej visbio-imagej Public

    ImageJ plugins for 3D visualization using the VisAD toolkit

    Java 1

  5. misc-plugins misc-plugins Public

    Miscellaneous ImageJ plugins

    Java 2 1

  6. search-image-sc search-image-sc Public

    Image.sc search service

    Python

Repositories

Showing 10 of 161 repositories
  • cellcast Public

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

    uw-loci/cellcast's past year of commit activity
    Rust 25 MIT 2 5 1 Updated Nov 6, 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 Nov 6, 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 9 Apache-2.0 1 3 0 Updated Nov 6, 2026
  • 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 Nov 6, 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 Nov 6, 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 Nov 6, 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 Nov 6, 2026
  • fiji-curvealign Public

    Fiji plugin integrating tme-quant workflows

    uw-loci/fiji-curvealign's past year of commit activity
    0 0 0 0 Updated Nov 5, 2026
  • tme-quant Public
    uw-loci/tme-quant's past year of commit activity
    Python 3 1 27 4 Updated Nov 5, 2026
  • interactive-microscopy-courseware Public

    Interactive, self-contained HTML teaching pages for microscopy (UW-LOCI).

    uw-loci/interactive-microscopy-courseware's past year of commit activity
    HTML 0 0 0 0 Updated Nov 5, 2026
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