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@ComputationalPathologyLab Computational Pathology Lab

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    13 repositories

    • .github

      Public
      0•0•0•0•Updated Sep 18, 2026Sep 18, 2026

    • resources

      Public
      Foundational learning resources for Python, GitHub, Linux shell, and high-performance computing.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2026Aug 1, 2026

    • VeSpA_benchmarking

      Public
      Benchmarking the VeSpA pipeline with groundtruth and other available tools
      Python
      •0•0•0•0•Updated Jul 9, 2026Jul 9, 2026

    • AI_pathology_research_kit

      Public
      Python
      •0•0•0•0•Updated Jul 9, 2026Jul 9, 2026

    • qupath-extension-catalog

      Public
      QuPath extension catalog for ComputationalPathologyLab extensions
      MIT License
      •0•0•0•0•Updated Jul 6, 2026Jul 6, 2026

    • VeSpA

      Public
      VeSpA (Vessel Spatial Analysis) is a QuPath extension for performing annotation based vessel segmentation directly within the QuPath environment.
      HTML
      •
      MIT License
      •0•0•2•0•Updated Jul 6, 2026Jul 6, 2026

    • ComputationalPathologyLab.github.io

      Public
      HTML
      •0•1•0•0•Updated Jun 3, 2026Jun 3, 2026

    • hpc-slurm-job-generator

      Public
      Tkinter-based Python GUI for generating self-contained Slurm bash scripts to run IMC Steinbock segmentation pipelines on HPC, with CPU/GPU resource configuratio…
      Python
      •
      MIT License
      •0•0•0•0•Updated May 26, 2026May 26, 2026

    • agentimc

      Public
      Python
      •0•0•0•0•Updated May 8, 2026May 8, 2026

    • imc-nextflow-pipeline

      Public
      A reproducible Nextflow pipeline for Imaging Mass Cytometry (IMC) data processing, including channel stacking, panel generation, Steinbock-based segmentation, a…
      Nextflow
      •0•0•0•0•Updated May 2, 2026May 2, 2026

    • complete-imc-analysis-workflow

      Public
      A complete end to end workflow for Imaging Mass Cytometry (IMC) data analysis
      Jupyter Notebook
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • IMC-Data-Analysis

      Public
      IMC (Imaging Mass Cytometry) data analysis workflows, including cell phenotyping and spatial biology analysis using R and Python.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • qupath-vessel-segmentation-plugin

      Public
      A QuPath plugin for vessel segmentation and annotation generation from images loaded in QuPath.
      HTML
      •
      MIT License
      •0•0•0•0•Updated Mar 25, 2026Mar 25, 2026
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