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    15 repositories

    • gen575

      Public
      Gen 575: Fundamentals of Biomedical Instrumentation
      Jupyter Notebook
      •0•4•0•0•Updated Apr 16, 2026Apr 16, 2026

    • PaintSHOP_pipeline

      Public
      A scalable machine learning pipeline for probe specificity prediction.
      HTML
      •
      MIT License
      •9•14•5•0•Updated Mar 26, 2026Mar 26, 2026

    • OligoMiner2

      Public
      Python package for genome-scale DNA/RNA FISH oligo probe set design
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 25, 2026Mar 25, 2026

    • lightsheet-analysis-pipeline

      Public
      An image analysis pipeline for performing image alignment, nuclear instance segmentation, and morphological feature extraction from terabyte-scale lightsheet fl…
      Python
      •0•3•2•0•Updated Jan 2, 2026Jan 2, 2026

    • uw-keck-center

      Public
      (temporary?) website for the W.M. Keck Imaging Center at UW Seattle
      0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • spatialbio

      Public template
      Jekyll Template for Spatial Biology Website
      HTML
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • PaintSHOP_resources

      Public
      A collection of downloadable resources accompanying the PaintSHOP application.
      MIT License
      •1•10•3•0•Updated Feb 21, 2024Feb 21, 2024

    • TigerFISH

      Public
      Tigerfish
      fishgenomicsmicroscopy
      fishgenomicsmicroscopyrepetitive-dna
      HTML
      •
      MIT License
      •2•13•1•0•Updated Jan 30, 2024Jan 30, 2024

    • PaintSHOP

      Public
      Shiny App for interactive oligo probe design.
      R
      •1•7•5•0•Updated Oct 13, 2023Oct 13, 2023

    • SABER-Spot-Quant

      Public
      Python scripts to segment/quantify smFISH spots and local proteome labeling from SABER and peroxidase-SABER microscopy images.
      Jupyter Notebook
      •0•1•0•0•Updated Feb 14, 2023Feb 14, 2023

    • gen559.2023

      Public
      Support for WI 2023 GEN559
      MIT License
      •0•0•0•0•Updated Jan 3, 2023Jan 3, 2023

    • Decode-PAINT

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 18, 2022Oct 18, 2022

    • Fluidics-system-for-FISH-1

      Public
      C++
      •
      MIT License
      •1•0•0•0•Updated Mar 9, 2022Mar 9, 2022

    • OligoMiner

      Public
      Genome-scale design tool for oligo hybridization probes
      Python
      •
      MIT License
      •27•71•2•0•Updated May 19, 2021May 19, 2021

    • example_repo_559

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 13, 2020Nov 13, 2020
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