A Claude Code workspace for querying Virtual Fly Brain (VFB) and Drosophila neuroscience resources using natural language.
Ask questions about neurons, neuroanatomy, synaptic connectivity, gene expression, transcriptomics and the literature — and get back structured answers, tables, and image reports, all linked directly to VFB.
"What is MBON-γ3?" "Show me term info for the mushroom body" "Find all GABAergic neurons in VFB with images"
Retrieves term info (description, classification, relationships) from the VFB knowledge graph and hyperlinks all results to the VFB browser.
"Show me thumbnails for 5 MBON neurons" "Make a markdown report with images of Kenyon cells"
Fetches neuron morphology thumbnails from VFB and produces markdown reports with embedded images and 3D browser links.
"What are the downstream targets of Kenyon cells with weight ≥ 10?" "Show class-level connectivity from DANs to MBONs" "What inputs does the mushroom body output neuron receive?"
Queries the VFB connectomics graph via vfb-connect for upstream/downstream partners, synapse weights, and class-level aggregations. Supports filtering by weight threshold and database source.
"What is the FBbt term for the mushroom body calyx?" "Show me subclasses of sensory neuron"
Searches and traverses the Drosophila anatomy ontology (FBbt) and other OBO ontologies via the OLS4 MCP.
"Find recent papers on MBON function in memory" "Get the full text of PMC3737249"
Searches Europe PMC and retrieves full-text content or PDF-converted markdown for use in analysis.
- Claude Code (CLI)
- Python 3.9–3.13
- The following MCP servers configured in your Claude Code settings:
virtual-fly-brainartl-mcpols4
git clone https://github.com/your-org/ask-vfb.git
cd ask-vfbbash setup_venv.shThis auto-detects your highest available Python (3.9–3.13), creates .venv/, and installs:
vfb-connect— VFB Python client for connectomics queriespsycopg— PostgreSQL adapter
Ensure the following MCP servers are registered in your Claude Code MCP settings (~/.claude/mcp_settings.json or equivalent):
| Server name | Purpose |
|---|---|
virtual-fly-brain |
Neuron/anatomy search, term info, connectivity |
artl-mcp |
Europe PMC literature retrieval |
ols4 |
OBO ontology search and traversal |
claudeThe CLAUDE.md in this directory configures the assistant's persona and output conventions automatically.
Skills are slash commands that implement multi-step workflows.
Query synaptic connectivity between neuron classes.
Examples:
/vfb-connectivity what does the Kenyon cell connect to downstream?
/vfb-connectivity inputs to mushroom body output neuron, weight >= 10
/vfb-connectivity class-level summary of DAN → MBON connectivity
Supports:
- Upstream / downstream / bidirectional queries
- Minimum synapse weight threshold (default: 5)
- Per-neuron or class-aggregated output
- Database filtering (e.g. exclude Hemibrain)
- All neurons and anatomy terms are hyperlinked to the VFB browser
- Image reports embed morphology thumbnails with links to the 3D viewer
- Connectivity results include VFB IDs for every neuron listed
Results are drawn from:
| Source | Content |
|---|---|
| Virtual Fly Brain | Neuron morphology, anatomy ontology, connectomics |
| FAFB | Full adult female brain EM (Otto et al. 2020) |
| Europe PMC | Literature and full-text articles |
| OLS4 | OBO ontologies (FBbt, GO, etc.) |