GigaTIME: Multimodal AI generates virtual population for tumor microenvironment modeling (Cell)
[ICML 2026] Autonomous AI agent for end-to-end spatial proteomics analysis, with SP-Bench for agentic multiplexed-imaging workflows.
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Spatial biology processing suite
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)
A Python package for unsupervised analysis of spatial (prote)omics data.
Nextflow version of Sopa - spatial omics pipeline and analysis
A unifying bioinformatics framework for organelle proteomics
GRaph-based Analysis of Subcellular/Spatial Proteomics
Efficient tool to query spatial pattern of spatial-modalities data
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 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.
OME-Zarr whole-slide images to patch- and slide-level foundation-model embeddings - cloud-native, FAIR, model- and backend-agnostic.
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
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
Custom software written for analysis of spatial proteomics data from fetal lung acquired in the HDCA project.
Analysis pipelines for paper Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures
Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry
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