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    • IN-DEPTH

      Public
      Code for IN-DEPTH
      HTML
      Other
      1000Updated Apr 17, 2026Apr 17, 2026
    • Large-scale Quantitative Assessment of Tissue Preparation and Staining Conditions for Robust Multiplexed Imaging
      Jupyter Notebook
      MIT License
      1101Updated Mar 24, 2026Mar 24, 2026
    • PASTA

      Public
      Analysis code for PASTA: Versatile Tyramide-oligonucleotide Amplification for Multi-modal Spatial Biology
      Python
      0000Updated Feb 11, 2026Feb 11, 2026
    • Jupyter Notebook
      0100Updated Jan 30, 2026Jan 30, 2026
    • CRS

      Public
      Codes for analyzes in Distinct Immune and Epithelial Dysregulation in the Inflammatory Respiratory Nasal Tract
      Jupyter Notebook
      1000Updated Nov 13, 2025Nov 13, 2025
    • Tutorials

      Public
      Tutorials for various analysis
      Jupyter Notebook
      1200Updated Aug 29, 2025Aug 29, 2025
    • pycodex

      Public
      Co-detection by indexing (CODEX) analysis using Python
      Python
      GNU General Public License v3.0
      0000Updated May 31, 2025May 31, 2025
    • Tools for backup
      Python
      0100Updated Apr 26, 2025Apr 26, 2025
    • Python
      GNU General Public License v3.0
      1000Updated Mar 17, 2025Mar 17, 2025
    • pipeline

      Public
      Jupyter Notebook
      1000Updated Nov 6, 2024Nov 6, 2024
    • Probabilistic cell segmentation for in situ spatial transcriptomics
      Rust
      Other
      16000Updated Oct 11, 2024Oct 11, 2024
    • MCB-MIBI

      Public
      MATLAB
      0000Updated Mar 7, 2024Mar 7, 2024
    • Script to generate OME-TIFF
      Python
      1210Updated Sep 21, 2023Sep 21, 2023
    • A pipeline to run RAPID and generate a OMETiff for visualization
      Python
      0000Updated Mar 29, 2023Mar 29, 2023
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