Data

j0251 – adult zebra finch area X

EM data acquisition: J. Kornfeld
Alignment: J. Kornfeld & A. Pope (V. Jain's team, Google Research)
SyConn processing: P. Schubert, A. Rother, H. Ahmad, J. Kornfeld
Cell & ultrastructure segmentation: M. Januszewski (V. Jain's team, Google Research)

j0126 – adult zebra finch area X

EM data acquisition: J. Kornfeld
Alignment: J. Kornfeld & A. Pope (V. Jain's team, Google Research)
SyConn processing: P. Schubert, J. Kornfeld, S. Dorkenwald
Cell & ultrastructure segmentation: M. Januszewski (V. Jain's team, Google Research), S. Dorkenwald, P. Schubert

Please note that neuron reconstructions, synapse predictions, and cell-type classifications are best‑effort. We welcome feedback if you think you have discovered a systematic issue that deserves more attention. If you use this data in your work, please cite Rother et al., 2025 (see also songbird-connectomics.org/publications). The full connectome is available below as a public REST API and as direct downloads of the underlying arrays.

The currently available datasets, j0251 (256 × 256 × 384 µm) and j0126 (96 × 98 × 114 µm), were acquired from adult male zebra finch area X, a basal ganglia area responsible for song learning that contains striatal- and pallidal‑like cell types. Both datasets were acquired in the department of Winfried Denk at the MPI for Medical Research, Heidelberg.

Connectome analysis

The j0251 connectome (~18.36 M synapses, ~4.26 M neurons) can be queried in three ways: an interactive browser notebook, a public REST API, and direct downloads of the underlying NumPy arrays. For interactive analyses, see the API notebook; for programmatic access, the endpoints and downloads below.

REST API

Four endpoints. The two JSON endpoints accept rich filters (cell type, probability, synapse size, post-morphology, skeleton lengths) and tolerate concurrent clients. Skeleton and mesh fetches return binary blobs. Full parameter reference is in the API notebook and the agent guide (below).

GET /j0251/synapses/json
Filter synapses by pre/post cell type, neuron IDs, probability, size, post-morphology, and skeleton lengths. Returns selected fields (size, x, y, z, prob, pre_id, post_id, post_morph, pre_celltype, post_celltype). Results are randomly sampled when max_results is given. 
curl "https://syconn.esc.mpcdf.mpg.de/j0251/synapses/json?pre_celltype=MSN&post_celltype=GPi&return_fields=x,y,z,size,prob&max_results=100"
GET /j0251/neurons/json
Find neurons by cell type, connectivity criteria (target cell type, direction, minimum synapse count), and skeleton-length thresholds. Returns a list of neuron IDs. 
curl "https://syconn.esc.mpcdf.mpg.de/j0251/neurons/json?celltype=HVC&target_celltype=MSN&direction=outgoing&min_synapses=50"
GET /j0251/skeleton?neuron_id=<id>
Binary skeleton (vertices in nm, edges as index pairs). Format: uint32 num_vertices, uint32 num_edges, float32×3×N vertices, uint32×2×M edges. 
curl "https://syconn.esc.mpcdf.mpg.de/j0251/skeleton?neuron_id=930416054" -o skeleton.bin
GET /notebook/j0251/<version>/sv/<id>:0:<id>_mesh
Binary mesh (vertices in nm). Format: uint32 num_vertices, float32×3×N vertices. Subsample by 20–30× for browser rendering. 
curl "https://syconn.esc.mpcdf.mpg.de/notebook/j0251/72_seg_20210127_agglo2_syn_20220811_celltypes_20230822/sv/930416054:0:930416054_mesh" -o mesh.bin

Note: HVC, LMAN, and DA are axon-only in this dataset and cannot be used as post_celltype. Default prob_min is 0.6.

Raw data downloads

The full filtered j0251 connectome as NumPy structured arrays, plus the two label mappings. Loadable with np.load(..., mmap_mode='r'); field schema is documented in the agent guide. All four files belong to dataset version 72_seg_20210127_agglo2_syn_20220811_celltypes_20230822.

Agent guide

Cookbook-style markdown for AI coding agents (Claude and similar): REST endpoint schemas with concrete curl examples, common filter pitfalls, and how to load the raw .npy arrays in Python.
/connectome/connectome-guide.md

Connectome viewer