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@HMS-IAC Image Analysis Collaboratory

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    20 repositories

    • NoRI-Visualizer

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 3, 2026Feb 3, 2026

    • NoRI

      Public
      Pipeline for kidney tissue segmentation & quantification using Normalized Raman Imaging (NoRI) with SAM & Ilastik.
      Python
      •1•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • bobiac

      Public
      Teaching materials for Boston Bioimage Analysis Course (BoBiAC).
      pythonimage-analysis-and-processing
      pythonimage-analysis-and-processing
      Jupyter Notebook
      •7•6•0•0•Updated Jan 16, 2026Jan 16, 2026

    • Bioimage-Analysis-on-O2

      Public
      Documentation page
      HTML
      •0•2•0•0•Updated Nov 25, 2025Nov 25, 2025

    • GBI-india

      Public
      Global BioImaging Image Data 2025 Course - Pune, India
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

    • stroma-spatial-analysis-web

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•1•0•Updated Jun 11, 2025Jun 11, 2025

    • bobiac-juv-notebook

      Public
      Teaching materials for Boston Bioimage Analysis Course (BoBiAC).
      Jupyter Notebook
      •1•0•0•0•Updated May 12, 2025May 12, 2025

    • diffusion_microscopy

      Public
      Diffusion models for microscopy image generation
      Python
      •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • quantify_edema

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • image_analysis_pancreatitis

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 19, 2025Feb 19, 2025

    • qupath-workshop

      Public
      Materials supporting the QuPath workshop at Harvard Medical School.
      teachingimage-analysisintroduction
      teachingimage-analysisintroductionqupath
      Creative Commons Attribution 4.0 International
      •1•4•0•0•Updated Feb 10, 2025Feb 10, 2025

    • dashai

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 1, 2025Feb 1, 2025

    • fiji-macro-workshop

      Public
      Materials supporting the Fiji Macro workshop at Harvard Medical School.
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • fiji-exercises-collection

      Public
      This is a collection of exercises for the open-source Fiji software.
      JavaScript
      •1•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • fiji-workshop

      Public
      Materials supporting the ImageJ/Fiji workshop at Harvard Medical School.
      imagejfijiteaching
      imagejfijiteachingimage-analysis
      Creative Commons Attribution 4.0 International
      •2•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • SAM-using-Python-for-Microscopy-Data

      Public
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • BIA-QC

      Public
      Quality control for bioimage analysis
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 19, 2024Oct 19, 2024

    • workshop-template

      Public template
      Sphinx template to host workshop materials with versioning support.
      templatesphinxversioning
      templatesphinxversioning
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • stroma-spatial-analysis

      Public
      An image analysis pipeline for quantifying the spatial distribution of cell markers in stroma-rich tumors
      image-analysiswhole-slide-imagingqupath
      image-analysiswhole-slide-imagingqupathfluorescence-microscopy
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Sep 18, 2024Sep 18, 2024

    • .github

      Public
      About
      0•2•0•0•Updated Jun 15, 2024Jun 15, 2024
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