Route:
Problems

P6 · Transcriptomics

What's this cell type's expression profile and marker genes?

The connectomics–transcriptomics bridge — the through-line of the workshop.

Key question: What’s this cell type’s expression profile and marker genes?

Route A: Python API

Query transcriptomics data linking cell types to scRNAseq clusters and expressed genes.

from vfb_connect import vfb

# Get expression profile for a cell type
expression = vfb.get_transcriptomic_profile("DA1 lPN")
print(expression[['gene', 'expression_level', 'cluster']])

# Find marker genes
markers = vfb.get_marker_genes("DA1 lPN")
print(markers)

Route B: MCP Tool

Ask about expression data and marker genes.

Example Prompt

For cell type 'DA1 lPN', what scRNAseq / expression data does VFB have, and which marker genes are associated with it?

Route C: VFB Chat

Chat can survey what expression data exists for a cell type.

Optimized prompt: Ask for both expression profile and marker genes with IDs.

VFB Chat
Open in new tab

Tip: End your questions with "and give me the VFB IDs" to get identifiers you can use in Python.

Route D: 3D Circuit Browser

The Circuit Browser can overlay expression data on neurons.
Open in Circuit Browser

When to Reach for Which Route

  • API to join expression data to connectivity for analysis
  • MCP/Chat to survey what expression data exists
  • 3D Browser to visualize expression patterns spatially