Integrated pipeline for multiplexed image analysis
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Updated
Sep 20, 2024 - Jupyter Notebook
Integrated pipeline for multiplexed image analysis
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Probabilistic topic model for identifying cellular micro-environments.
Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
MIAAIM: Multi-omics Image Alignment and Analysis by Information Manifolds
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
SpatialVisVR is a VR platform tailored for advanced visualization and analysis of medical images in immuno-oncology. It allows real-time capture and comparison of mIF and mIHC images via mobile devices. Leveraging deep learning, it matches and displays similar images, supporting up to 100 protein channels.
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
High-dimensional image registration workflow as part of the MIAAIM framework. Hdi-reg is written in Python, and utilizes the Elastix library for computations.
Rust library for reading imaging mass cytometry (IMC) data stored in .mcd files.
Multi-omics image alignment and analysis by information manifolds (MIAAIM)
A workflow designed to perform multiplexed image analysis, specialising in (but not limited to) analysis of metal distribution in LA-ICP-TOFMS data.
General importing and utility functions for high-dimensional image data
Perform RESTORE normalization on multiplexed imaging data.
High-dimensional image preparation module for MIAAIM
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