Select a dataset and version from the dropdowns and click the Submit button to launch the viewer.
There are two datasets available:
- j0251
- j0126
More information is available here.
There are icons at the top right of the page that can be clicked to open the different panels.
- ? : help panel (displays all the key and mouse bindings for the viewer)
: layer settings panel (displays the data source, rendering options, segment list and annotations)
: layer list panel (displays all the layers for archiving or toggling visibility)
Neuroglancer can be used with the mouse and the keyboard shortcuts come in handy to quickly jump through layers. A full range of these shortcuts is available in the help panel.
Neuroglancer has four viewports visible by default. Starting from the left, in the clockwise-direction, these are the XY, XZ and YZ cross-sectional views and the 3D view. A segment (from the segmentation layer) is a coloured area visible in the three cross-sectional views that can be selected to retrieve the segmentation objects (if available). Use the following to retrieve cells:
- left-click to select the segment
- double-click to request the cell objects (skeleton, cell mesh and organelle meshes)
- x to clear all segments
- ctrl+x to reset the viewer state
With the layer toggling, one can choose to see individual or combinations of ultrastructures.
One way to select a segment is to click it in one of the cross-sectional views. The other is to open the layer side panel and head to the Seg. tab. There will be a segment list at the bottom. Any segment can be selected by checking the box left to the id column. This segment list can be modified based on some properties . Currently, we support the following properties (more information is available here):
- Cell type
- Volume (µm³)
- Total path length of the cell (µm).
- Mean synapse mesh area per cell (µm²).
- Number of synapses per cell.
For example, cells of the HVC cell type can be selected by clicking the left to #HVC. Alternatively, segment ids of all the cell types except HVC can be selected by clicking the left to #HVC. Multiple cell types can be excluded.
Filtering by the other properties can be performed by clicking the numerical properties toggle. For each numerical property, checking the property box allows to display the property value as a column in the segment list. The slider bar below the property can be adjusted to set the filter range.
Multiple properties can be modified concurrently according to the requirement.
In addition to the inline properties, there are dynamic properties that can be triggered with a hotkey. One such property is the show-synaptic-partner-with-largest-area that retrieves the synaptic partner of the currently selected cell based on the following criteria:
- Synapse should be either axo-dendritic or axo-somatic
- Synapse probability should be greater than 50%
- Synaptic partner with the largest synapse area is retrieved
This property can be triggered by pressing p. The resulting synapse is seen immediately in the 4 viewports and additional information is shown in the status message on the bottom left side.
Additionally, there are two useful dynamic properties—show-presynaptic-partners and show-postsynaptic-partners that are based on the following criteria:
- Synapse should be either axo-dendritic or axo-somatic (with en-passant boutons and terminal boutons)
- Synapse probability should be greater than 50%
- Both pre- and postsynaptic partners with total path length of the cell less than 150µm are filtered out.
The presynaptic partners can be triggered by pressing ctrl+i while the postsynaptic partners are triggered by pressing ctrl+o. In this case as well, the status message shows information about the property.
To view the pre- or postsynaptic partners, press ctrl+u. This cycles through the list of retrieved partners and displays the synapse in decreasing order of synapse area.