Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Integrated pipeline for multiplexed image analysis

astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨

Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications

Probabilistic topic model for identifying cellular micro-environments.

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

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

A workflow designed to perform multiplexed image analysis, specialising in (but not limited to) analysis of metal distribution in LA-ICP-TOFMS data.

Rust library for reading imaging mass cytometry (IMC) data stored in .mcd files.

High-dimensional image preparation module for MIAAIM

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.

Multi-omics image alignment and analysis by information manifolds (MIAAIM)

High-dimensional image registration workflow as part of the MIAAIM framework. Hdi-reg is written in Python, and utilizes the Elastix library for computations.

Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

General importing and utility functions for high-dimensional image data

Perform RESTORE normalization on multiplexed imaging data.