GigaTIME: Multimodal AI generates virtual population for tumor microenvironment modeling (Cell)
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Spatial omics in the browser for hundreds of images at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/
Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)
ICML 2026 autonomous AI agent for end-to-end spatial proteomics analysis, with SP-Bench for agentic multiplexed-imaging workflows.
Nextflow version of Sopa - spatial omics pipeline and analysis
A Python package for unsupervised analysis of spatial (prote)omics data.
A unifying bioinformatics framework for organelle proteomics
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
GRaph-based Analysis of Subcellular/Spatial Proteomics
Efficient tool to query spatial pattern of spatial-modalities data
A curated collection of papers, codes, and resources for cross-modal translation/prediction/generation between histopathological imaging and omics (genomics, proteomics, etc.), including histopathology-to-mIF image generation, histopathology-to-genomic prediction, etc.
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
Custom software written for analysis of spatial proteomics data from fetal lung acquired in the HDCA project.
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
spora [bench] is a benchmark for spatial proteomics foundation models.
A modular and interactive spatial proteomic image analysis workflow with individual containerized steps, consisting of cell segmentation, unsupervised clustering with optional batch correction, validation of clusters on the image, and cell type clustering results visualization
Distinct mesenchymal cell states mediate prostate cancer progression
Multi-modal integration of single-cell and spatial proteomics data
R package for analyzing and visualizing single-cell spatial data
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