Bridging connectomes and transcriptomics across the Drosophila CNS
Interactive workshop materials from Virtual Fly Brain for NeuroFly 2026 — the 21st Biennial European Drosophila Neurobiology Conference, University of Cologne, Germany, 7–11 September 2026.
This is the 2026 successor to our 2024 "Bridging connectomics and transcriptomics" session and the earlier "Hacking the connectome" workshop (training / natworkshop). It covers the same core skills — finding, bridging, visualising and analysing neurons across datasets — updated for the connectomes and tools we've added since, and now shows every task three ways.
The workshop is built around real research questions. For each one we show the same answer via three routes, so you can pick whichever fits your workflow — from a quick natural-language question to a fully scripted analysis:
| Route | What it is | Best for |
|---|---|---|
A · vfb_connect |
Python API returning pandas DataFrames | Reproducible, scriptable analysis and figures |
| B · VFB MCP tool | vfb3-mcp.virtualflybrain.org inside an LLM (e.g. Claude) | Exploratory, conversational analysis with data-grounded answers |
| C · VFB chat | chat.virtualflybrain.org (guardrailed, no setup) | Zero-install natural-language lookups; great for teaching & non-coders |
The MCP tool and chat are woven into every module, not treated as an add-on. A short "when to reach for which" box closes each problem.
The questions each module asks, the exemplar data behind them and the results you should expect are
specified in DESIGN.md.
Nothing to install — open a notebook in Google Colab:
| Module | Topic | Open |
|---|---|---|
| 00 | Setup & the 2026 data landscape |  |
| 01 | Discovery — finding neurons across datasets | |
| 02 | Bridging datasets & identity | |
| 03 | Visualisation | |
| 04 | Connectomics | |
| 05 | Similarity & NBLAST | |
| 06 | Transcriptomics | |
| 07 | Putting it together | |
No-code track: start at no-code/ — set up the MCP tool, or just open
chat.virtualflybrain.org and work through
no-code/example_prompts.md.
R / natverse track: see R/ (mirrors the Python modules; published after the Python track).
Run it yourself / self-host: pip install -r requirements.txt, or use the
Dockerfile / Binder config for a hosted JupyterLab. See
Self-hosting.
The fly CNS is now covered by whole-CNS and sex-specific connectomes that didn't exist (or weren't integrated) at the last workshop. Current connectomes on VFB:
- BANC (Brain And Nerve Cord) — whole adult CNS
- FAFB–FlyWire (v783) — adult brain
- male-CNS — adult male CNS
- Optic Lobe (JRC_Optic-Lobe v1.0.1)
- MANC (v1.2.1) — male adult nerve cord
- Hemibrain (v1.2.1)
- FAFB-CATMAID and L1 larval CNS (CATMAID)
Plus the VFB MCP tool (2026, preprint), the
chat.virtualflybrain.org interface, the Circuit Browser, and an updated
vfb_connect. See PLAN.md for the full design
and a 2024 → 2026 diff.
vfb_connect— Python client for the VFB knowledge basenavis— neuron visualisation & morphometricsneuprint-python— neuPrint connectomespymaid(python-catmaid) — CATMAID datasetsnavis-flybrains— template-space transforms- VFB MCP tool & VFB chat
- R: the natverse (
nat,neuprintr,rcatmaid,nat.nblast)
git clone https://github.com/VirtualFlyBrain/neurofly2026-workshop.git
cd neurofly2026-workshop
pip install -r requirements.txt
jupyter labOr build the container: docker build -t vfb-workshop . && docker run -p 8888:8888 vfb-workshop.
A Binder config is included for a free hosted session.
Materials released under the GNU GPL v2, consistent with the VFB training repo.
If VFB helps your work, please cite
Court et al. (2023); for the MCP tool cite
McLachlan et al. (2026).
Questions during or after the workshop: VFB contact page · GitHub issues · community Google group / support.