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Research Areas

Computational BiologySingle-cell, bulk RNA-seq, spatial, and biomarkers
CardiologyCardiovascular signals, cohorts, and interpretationImmunologyImmune cell states, signaling networks, and repertoire dynamicsNeurologyBrain connectivity, functional imaging, and electrophysiologyOncologyTumor microenvironment, immune response, mutations, and survivalPathologyWhole-slide imaging, tissue quantification, and spatial pathology

Application

Documentation

Documentation

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FAQ

Is Immunology separate from Computational Biology?

Yes. Immunology owns immune-specific interpretation layers such as repertoire analysis, communication, immune state scoring, disease context, and multi-modal immune profiling. General single-cell and spatial infrastructure still belongs to Computational Biology where appropriate.

Does CellTypist run today?

The pipeline detects whether CellTypist is installed and records CellTypist status. True CellTypist model execution needs a configured model asset/path. Until then, celltypist_model_version is null.

Why are some visualizations tables instead of full plots?

The initial app surfaces computed outputs in stable table/card views. Figure specs and table-based views are available now; richer chart renderers can be added later without changing the backend artifacts.

Can I use binary FCS files?

Binary FCS parsing is feature-gated behind FlowUtils or flowutils. CSV/TSV cytometry event tables are supported today.

Is this clinical decision support?

No. Immunology outputs are research-use only. AI interpretation includes a research disclaimer and must cite computed metrics.

Which AI model is used?

When configured, the backend uses Ollama cloud with gpt-oss:120b, following the same pattern documented in ai.md. If the service is unavailable, interpretation uses a deterministic fallback and records that status in the audit artifact.