spatial-biology

[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

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

Spatial One

AESTETIK: Convolutional autoencoder for learning spot representations from spatial transcriptomics and morphology data

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

DeepSpot2Cell: Predicting virtual single-cell spatial transcriptomics from H&E images using spot-level supervision

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

Interpretable Graph Neural Networks for Spatial Cell Biology. Learn complex, biologically meaningful cell-cell interaction functions with unprecedented interpretability.

Python package for converting multiplex immunofluorescence single-cell exports from QuPath into AnnData objects for spatial analysis.

Code and data associated with the manuscript "Engineering Programmable Tumor Microenvironment Interactions through Single-Cell Bioprinting of Spatially Defined Cell Microarrays"

Agent skill to retrieve, analyze, and visualize Human Protein Atlas (HPA) data—featuring 3D subcellular organelle mapping, 10-system anatomical IHC heatmaps, RNA-to-protein concordance, cancer pathology profiling, and standalone HTML5 dashboards.

A geometry-aware framework for prioritizing biologically meaningful ligand–receptor interactions in spatial transcriptomics.

Bioimage registration and spatial data quality assessment for H&E histological images

Code associated with the manuscript "A Single-Cell Bioprinting Approach with Subcellular Resolution to Reconstruct Native Cellular Microenvironments"