Explore the first annotated songbird basal ganglia connectomes

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The currently available data sets, j0251 (256 x 256 x 384 µm) and j0126 (96 x 98 x 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.

Quick start

The connectomic queries currently utilize the properties listed below. The names are specified here as they appear in a syconn-neuroglancer viewer instance.

  1. Neuroglancer inline properties

    2. Cell-types

    The following (putative) cell types are available from the latest j0251 (version 72_seg_20210127_agglo2_syn_20220811_celltypes_20230822) and j0126 (areaxfs_v10), labeled as:

    j0251 : DA, LMAN, HVC, MSN, STN, TAN, GPe, GPi, LTS, INT1, INT2, INT3, ASTRO, OLIGO, MICRO, MIGR, FRAG

    j0126 : STN, modulatory, MSN, LMAN, HVC, GP

    Volume

    Cell volume in µm³

    TotalPathLength

    Perimeter of the cell. Sum of the compartment (axon and its terminals, dendrite and soma) path lengths in µm

    MeanSynapseArea
    Mean mesh area of the synapses for each cell in µm²
    NSynapses

    Number of synapses for each cell

    Note that not all the properties listed above are available in the different datasets. Have a property or a feature in mind that you would like to add here? Please contact us.

  2. Dynamic properties

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

    Retrieve the synaptic partner associated with the selected cell, specifically focusing on the one with the largest synapse area and a synapse probability equal to or greater than 0.5. This property takes into account both axo-dendritic and axo-somatic synapses.

    Hotkey: p

    show-presynaptic-partners

    Fetch the presynaptic partners associated with the selected cell, considering synapse probability equal to or greater than 0.5. This feature encompasses both axo-dendritic and axo-somatic synapses, including axon terminals such as en-passant and terminal boutons. Activating the hotkey results in the presentation of a list of presynaptic partners for the currently selected cell in the right panel. Subsequently, a cycle-synaptic-partners call should be made to sequentially display the synaptic partners.

    Hotkey: ctrl + i

    show-postsynaptic-partners

    Similar to show-presynaptic-partners but fetches the postsynaptic partners associated with the selected cell, considering synapse probability equal to or greater than 0.5. This feature also encompasses both axo-dendritic and axo-somatic synapses, including en-passant and terminal boutons. Activating the hotkey results in the presentation of a list of postsynaptic partners for the currently selected cell in the right panel. Subsequently, a cycle-synaptic-partners call should be made to sequentially display the synaptic partners.

    Hotkey: ctrl + o

    cycle-synaptic-partners

    This action is a direct follow-up of the show-presynaptic-partners and show-postsynaptic-partners actions. Iterate through the obtained pre- or postsynaptic partners and present the partner cells at the synapse location. The cycling initiates from the synapse with the largest synaptic area. Each activation of the hotkey reveals a pair of synaptic partners in the order of their synaptic area.

    Hotkey: ctrl + u

    depth-first-search

    Conduct a depth-first search within the biological neural network, commencing from the chosen cell. Select the synaptic partner exhibiting the most robust connection with the presently chosen cell. Each activation of the hotkey corresponds to advancing 1 level in the depth-first search. The maximum allowable depth is set at 3 levels.

    Hotkey: ctrl + d

    reset-viewer-state

    Restore the viewer state to its initial configuration. This action removes selected segments and segment IDs in the segment query (if any). It also centers the viewer position, resembling the initial launch view. This feature is useful for clearing lists of presynaptic or postsynaptic partners. It's important to note that pressing the x key (natively provided in neuroglancer) only clears segments in the cross-section and 3D viewport.

    Hotkey: ctrl + x