End-to-end workflow from tissue preparation to published connectome.
Biological tissue is prepared for electron microscopy imaging through fixation, staining, and embedding.
Serial section electron microscopy captures high-resolution images of the tissue volume.
Raw images are stitched, aligned, and corrected to create a contiguous 3D volume.
Machine learning models identify and label individual neurons and cellular structures in the volume.
Human annotators correct segmentation errors—splits and mergers—to produce accurate neuron reconstructions. Primary tracer team activity.
Synapses, cell types, and other biological features are labeled on the proofread segmentation. Primary tracer team activity.
Connectivity data is queried, analyzed, and visualized to understand neural circuits.
Findings are documented and shared through papers, preprints, and public data releases.
| Tool | Stage | Purpose |
|---|---|---|
| WebKnossos | 5, 6 | Volume annotation, proofreading, segmentation correction |
| Neuroglancer | 5, 6 | 3D visualization, synapse annotation, data viewing |
| CAVE | 6, 7 | Annotation database, versioned data queries |
| tracer_tools | 7 | Python API for CAVE queries, batch processing, ID management |
| Tampermonkey | 5, 6 | Browser scripts for WebKnossos workflow enhancement |
| Dataset | Organism | Datastack | Status |
|---|---|---|---|
| FlyWire FAFB | Drosophila (whole brain) | flywire_fafb_production |
Active |
| BANC | Drosophila (brain + nerve cord) | brain_and_nerve_cord |
Active |