[ICML 2026] Autonomous AI agent for end-to-end spatial proteomics analysis, with SP-Bench for agentic multiplexed-imaging workflows.
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resolution.
Spatial biology processing suite
Scalable spatial omics in the browser for hundreds of samples at once | 10x, IMC, IF, H&E, CosMX, & more | https://rakaia.io/
AESTETIK: Convolutional autoencoder for learning spot representations from spatial transcriptomics and morphology data
DeepSpot2Cell: Predicting virtual single-cell spatial transcriptomics from H&E images using spot-level supervision
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.
Official repository for Characterization of tumor heterogeneity through segmentation-free representation learning on multiplexed imaging data
Browser-based OME-ZARR microscopy viewer. Open local files, annotate, overlay segmentation labels, share deep links. GPU-accelerated, privacy-first, zero-install.
A Dockerized R Shiny app for visualization of spatial single-cell data with cell masks
Executed cohort-, patient-, and biology-level benchmarks for Gaia
Python package for converting multiplex immunofluorescence single-cell exports from QuPath into AnnData objects for spatial analysis.
Interpretable Graph Neural Networks for Spatial Cell Biology. Learn complex, biologically meaningful cell-cell interaction functions with unprecedented interpretability.
📐 Cylindrical Bessel K0 biophysical transport solver for perivascular tumour cords & pharmacological sanctuary sleeves.
Bioimage registration and spatial data quality assessment for H&E histological images
Code and data associated with the manuscript "Engineering Programmable Tumor Microenvironment Interactions through Single-Cell Bioprinting of Spatially Defined Cell Microarrays"
Spatial transcriptomics investigation of immune-program colocalization, multicellular niches, and tissue organization in breast cancer using 10x Visium.
This repository bridges manual pathological annotation and reproducible computational feature extraction in MxIF WSI analysis.
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