Explore the first annotated songbird basal ganglia connectomes

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Two datasets are available, j0251 (256 × 256 × 384 µm) and j0126 (96 × 98 × 114 µm). Both were acquired from area X of adult male zebra finches, a basal ganglia region required for song learning that contains striatal- and pallidal-like cell types. For j0251, the version with the 2026 (v8) cell types is selected by default; the 2023 (v6) cell types used in the preprint remain available.

Quick start

Choose a dataset and version above and click Show data. The viewer opens with the cell segmentation, and the Segments tab on the right lists the cells with their properties (for j0251, all cells with a total path length above 150 µm). Double-click a cell in one of the cross-sectional views to select it; the hotkeys below then act on the selected cell. Names are given as they appear in the viewer.

  1. Cell properties (shown in the Segments tab)

    2. Cell-types

    Predicted cell type. The classes differ between datasets and versions:

    j0251, v8 cell types (2026) : DA, LMAN, HVC, MSN, STN, TAN, GPe, GPi, LTS, INT1, INT2, INT3, INT4, ASTRO, OLIGO, OPC, MICRO, MIGR, FRAG

    j0251, v6 cell types (2023) : DA, LMAN, HVC, MSN, STN, TAN, GPe, GPi, LTS, INT1, INT2, INT3, ASTRO, OLIGO, MICRO, MIGR, FRAG

    j0126 : exc, modulatory, MSN, LMAN, HVC, GP, INT

    HVC, LMAN and DA cells are axons that enter area X from other brain regions; FRAG marks fragments that could not be assigned to a cell.

    CellTypeCertainty

    Certainty of the cell-type prediction, in percent.

    Volume

    Cell volume in µm³.

    TotalPathLength

    Summed length of the cell's skeleton (axon, dendrites and soma) in µm.

    NSynapses

    Number of synapses of the cell.

    MeanSynapseArea

    Mean synapse area of the cell in µm² (only in j0251_rag_flat_Jan2019_v3).

  2. Segment queries (typed into the query field of the segmentation layer)

    3. By cell type

    Type a cell-type name, e.g. MSN or INT4, to list the cells of that type.

    By cell size

    Append a size condition in thousands of voxels (1 voxel = 10 × 10 × 25 nm), e.g. GPi_size>100000 for GPi cells larger than 108 voxels (250 µm³).

    Pages

    Long results are split into pages of 500 cells; append _pg2, _pg3, … to see further pages, e.g. MSN_pg2.

    Is there a property or feature you would like to see here? Please contact us.

  3. Connectivity actions (hotkeys, acting on the selected cell)

    4. show-synaptic-partner-with-largest-area

    Shows the partner cell connected to the selected cell by its largest synapse and moves the view to that synapse. Axo-dendritic and axo-somatic synapses in either direction are considered, with a synapse probability of at least 0.5.

    Hotkey: p

    show-presynaptic-partners

    Lists the cells that make synapses onto the selected cell (axo-dendritic and axo-somatic synapses, including en-passant and terminal boutons, synapse probability of at least 0.5). The list appears in the right panel; use cycle-synaptic-partners to step through the partners.

    Hotkey: ctrl + i

    show-postsynaptic-partners

    Like show-presynaptic-partners, but lists the cells that the selected cell makes synapses onto.

    Hotkey: ctrl + o

    cycle-synaptic-partners

    Steps through the partners found by the two actions above, starting with the largest synapse. Each key press shows the next partner and moves the view to its synapse. The hotkey becomes active once a partner list has been loaded.

    Hotkey: ctrl + u

    depth-first-search

    Follows the strongest output connection of the selected cell: each key press adds the postsynaptic partner with the largest summed synapse area and moves the view there, up to a depth of three steps. The chain of cells and their types is shown in the status message.

    Hotkey: ctrl + d

    share-viewer

    Creates a link to the current viewer state that can be shared with others.

    Hotkey: ctrl + l

    reset-viewer-state

    Returns the viewer to its initial state: removes the selected cells and any segment query, and recentres the view. Use it to clear partner lists. Note that Neuroglancer's own x key only clears the cells shown in the cross-sections and the 3D view.

    Hotkey: ctrl + x