multiplexed-imaging 开源项目推荐（30 个）

prism-oncology /sopa

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

angelolab /ark-analysis

Integrated pipeline for multiplexed image analysis

camlab-bioml /rakaia

Scalable spatial omics in the browser for hundreds of samples at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/

mahmoodlab /MAPS

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

camlab-bioml /astir

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

nf-core /mcmicro

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

calico /spatial_lda

Probabilistic topic model for identifying cellular micro-environments.

nadeemlab /smprofiler

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io) [NeurIPS'26]

Mmasoud1 /HistoJS

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

complextissue /spatiomic

A Python package for unsupervised analysis of spatial (prote)omics data.

deMirandaLab /PENGUIN

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

JoshuaHess12 /miaaim-python

MIAAIM: Multi-omics Image Alignment and Analysis by Information Manifolds

deMirandaLab /PENGUIN_fork

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

liulabspatial /Omics-cycleHCR-QuAC

Analysis pipelines for paper Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures

KoellenspergerLab /MeXpose

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

marta-seq /PENGUIN

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

AlanRace /imc-rs

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

ajortizg /codex_preprocessing

该项目在 GitHub 上没有填写描述

theislab /sprotmetrics

Quality metrics for imaging-based spatial proteomics: segmentation, signal-to-background, normalization, marker distribution and technical-covariate diagnostics.

JoshuaHess12 /hdi-prep

High-dimensional image preparation module for MIAAIM