Cytognosis exists so no one else waits decades for answers.
Single source of truth for the 911 unique tools evaluated, adopted, deferred, or rejected across the Cytognosis Foundation infrastructure stack. Consolidated from six research archives plus the May 2026 connectomics review.
| Document | Lines | Purpose |
| --- | ---: | --- |
| tools-master-catalog.md | 2 022 | Full per-layer breakdown of all 911 tools with status, license, surface, org, and rejection rationale |
| tools-infrastructure-stack.md | 624 | Deep-dive on the infrastructure layers: storage → repos → meta → FAIR → provenance → workflow → KG, with Mermaid data-flow diagrams |
| tools-master-catalog.xlsx | — | Filterable spreadsheet with views by Layer, Surface, Status, Organization, plus Tag Glossary and Stats |
| Surface | Tool count | Description |
| --- | ---: | --- |
| 🌸 Cytonome | 200 | On-device navigator + empathic voice interviewer |
| 🟢 Cytoverse | 308 | AI map: knowledge graph + foundation-model platform + multi-omic data lake |
| 🟡 Spine | 396 | FAIR-compliant foundations: standards, repositories, lineage, reproducibility |
| # | Layer | Tools | Headline picks |
| --- | --- | ---: | --- |
| L1 | Storage | 81 | TileDB, Zarr v3, Parquet, Safetensors, GGUF |
| L2 | Preprocessing | 146 | fMRIPrep, Docling, GROBID, PLINK2, ComBat |
| L3 | Repositories | 69 | GitHub, HuggingFace, Zenodo, OpenNeuro, DANDI |
| L4 | Meta layer | 109 | Bioregistry, Hypothes.is, Zoekt, GitNexus, OAK |
| L5 | Zoos | — | HuggingFace Hub, MLflow Registry, WorkflowHub |
| L6 | FAIR packaging | 26 | RO-Crate, FAIRSCAPE, Zenodo, Model Cards |
| L7 | Provenance | 35 | LaminDB, redun, DVC, DataLad, MLflow, Aim |
| L8 | Workflow | 38 | Nextflow, Snakemake, redun, Nipype, Docker |
| L9 | Standards | 211 | LinkML, GA4GH, BIDS, NWB, HED, OBO, MCP |
| L10 | Knowledge graphs | 69 | BioCypher, Neo4j, KuzuDB, SemOpenAlex |
| L11 | UI / Frontend | 101 | Flutter, React 19, Tauri v2, Rive, Mermaid |
| L12 | AI / Models | 278 | Gemma 4, OLMo, BrainGFM, LangGraph, PyTorch |
| L13 | Networking | 21 | mDNS, NATS, Tailscale, Iroh CRDT, WireGuard |
| L14 | Scholarly | 59 | Zotero, OpenAlex, GROBID, CiteAs, arXiv |
| L15 | KM | 22 | Anytype, Mermaid, Excalidraw, tldraw |
| L16 | Cloud | — | Cloud Run, Vertex AI, GCS, GitHub Actions |
| Status | Count | Meaning |
| --- | ---: | --- |
| ✅ primary | 518 | Recommended pick, adopted in the stack |
| 🟡 alternative | 110 | Strong alternative, kept on radar |
| ⏸️ deferred | 16 | Revisit later (license, maturity) |
| ❌ rejected | 80 | Explicitly ruled out (rationale preserved) |
| • mentioned | 187 | Named but not actionable |
1. Open by default — every primary pick is permissively licensed (Apache 2.0 / MIT / BSD-3 / CC0)
2. Schema is the hub — LinkML compiles to Pydantic, JSON-Schema, GraphQL, OWL, ShEx, SHACL, SQL DDL, TypeScript
3. Local-first and privacy-preserving — edge inference, on-device persona, CRDT state, PHI never leaves phone
4. Interoperability through MCP — Model Context Protocol is the de-facto agent-to-tool standard
5. FAIR is operational, not aspirational — RO-Crate auto-emits from every workflow run; tri-identifier coverage
6. Dual-tier S2S, never single-process — phone (Tier 1, 90%) + supervisor (Tier 2, 8%) + cloud (Tier 3, 2%)
7. Reproducibility as system property — AST + data hashing via redun; provenance binds code, data, model, paper
This catalog informs and is referenced by several other infrastructure documents:
This catalog is the union of 6 sources, deduplicated by canonical tool name:
| Source | Tools | Description |
| --- | ---: | --- |
| master_unsorted.md | 508 | Unsorted union of all 19 research tabs |
| research_outline.md | 494 | April 2026 outline with rejection rationale |
| consolidated.md | 439 | May 2026 harmonised 11-component architecture |
| repos.md | 194 | 16 catalogued GitHub org directories |
| zotero-setup-guide.md | 60 | Reference manager + PDF annotation pipeline |
| connectomics/*.md | 148 | BIDS / HED / NWB triad + fMRI foundation-model review |