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 |
|---|---|---|
| Ultramicrotome + diamond knife | 1 | Cutting the resin-embedded block into serial ultrathin (~40 nm) sections |
| TEMCA (TEM Camera Array) | 2 | High-throughput serial-section transmission EM imaging (the modality behind FAFB and BANC) |
| SEAMLeSS / AlignTK | 3 | Stitching and elastic alignment of the section images into a contiguous 3D volume |
| CloudVolume | 3, 4 | Chunked volume storage and multi-resolution pyramid generation (precomputed format) |
| Flood-filling networks (FFN) | 4 | Automated machine-learning segmentation of neurons into supervoxels |
| PyChunkedGraph | 4, 5 | Editable segmentation graph that makes proofreading splits and merges possible |
| 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 userscripts for WebKnossos, Neuroglancer, and Spelunker 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 |