Neuroglancer Views

Using Neuroglancer

If this is your first time using MICrONS, you’ll need to accept the Terms of Service with a Google account to be able to view these links properly. You’ll then be prompted to sign in (make sure to use the same account) when opening one of the links below for the first time in a session.

Unfamiliar with Neuroglancer? More detail is available here.

Cell inputs

Layer 6 CT cell with annotated input synapses

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Layer 5 ET cell with annotated input synapses

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Basket cell with annotated input synapses

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Cell outputs

Layer 4 pyramidal cell with annotated output synapses

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Layer 5 IT pyramidal cell with annotated output synapses

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Basket cell with annotated output synapses

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Navigating by cell properties

Neuroglancer’s segment propoerties allow you to quickly select cells via a table of properties attached to each cell. Here, we’ve generated a segment properties table which includes information about cell type and some summary statistics about subcellular targeting for each cell in the curated “column” described in the paper. This allows you to quickly navigate to cells of interest based on their predicted properties.

Example selections using segment properties

Neuroglancer view of a basket cells with annotated output synapses

Selection of two basket cells with the highest soma-targeting output fraction.

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Selection of two Layer 2/3 pyramidal cells with the rate of multi-input spines on their dendrites.

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Using segment properties

To generate your own selection, access the segment properties view. Ctrl or right-click on the seg tab:

Type the name of a cell type to filter by type:

Use the sliders or type an expression to filter by cell properties. Available properties include a sample of the cell-level statistics available for curated cells as described in the paper. For instance, the selection above filters for the Layer 6 CT cells which most target spines:

Neuroglancer segment properties view with selection

Available properties

Numerical properties:

Name	Description
pre_p_spine_synapse	Proportion of output synapses to spines
pre_p_shaft_synapse	Proportion of outputs synapses to shaft
pre_p_soma_synapse	Proportion of output synapses to soma
pre_p_spine_site_is_multi	Proportion of contacted spines which are multi-input
pre_to_exc_p_spine_synapse	Proportion of output synapses to excitatory neurons which are to spines
pre_to_exc_p_shaft_synapse	Proportion of output synapses to excitatory neurons which are to shafts
pre_to_exc_p_soma_synapse	Proportion of output synapses to excitatory neurons which are to somas
pre_to_exc_p_spine_site_is_multi	Proportion of contacted spines on excitatory neuron spines which are to multi-input
post_p_spine_synapse	Proportion of input synapses to spines
post_p_shaft_synapse	Proportion of input synapses to shaft
post_p_soma_synapse	Proportion of input synapses to soma
post_p_spine_site_is_multi	Proportion of input spines which are multi-input

Cell types:

Name	Description
23P	Layer 2/3 intratelencephalic pyramidal neuron
4P	Layer 4 intratelencephalic pyramidal neuron
5P-IT	Layer 5 intratelencephalic pyramidal neuron
5P-ET	Layer 5 extratelencephalic pyramidal neuron
5P-NP	Layer 5 near-projecting pyramidal neuron
6P-IT	Layer 6 intratelencephalic pyramidal neuron
6P-CT	Layer 6 corticothalamic pyramidal neuron
BC	Basket cell
BPC	Bipolar cell
MC	Martinotti cell
NGC	Neurogliaform cell