Spatial transcriptomics analysis via ToolUniverse — gene expression mapping in tissue architecture for 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms.
Targets tooluniverse-spatial-transcriptomics agentic workflow. Performs spatial clustering, domain identification, cell-cell proximity analysis, spatially variable gene detection, tissue architecture mapping, and integration with single-cell data. Use for spatial expression patterns, tumor microenvironment spatial structure, or tissue organization studies.
ToolUniverse wrapper — pip package doesn't bundle the agentic workflow. Script detects and reports this.
cd spatial-transcriptomics
python3 -m venv .venv && source .venv/bin/activate && pip install tooluniverse pyyaml -qNone for --list-workflows.
python3 scripts/run.py --help
python3 scripts/run.py --list-workflows
python3 scripts/run.py --query "Map spatial gene expression in Visium breast cancer"tooluniverse, pyyaml
--help: ✅- Agno agent (Claude Haiku 4.5): ✅ Described spatial clustering, domain ID, cell-cell proximity, SVG detection, tissue architecture
Perfect for understanding how cells organize in tissue and how their spatial relationships drive biological processes. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms.