PSICS - the Parallel Stochastic Ion Channel Simulator
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Under development
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Cells and channels

The main display shows the contents of the model folder on the far left. The selected morphology is shown in the middle with details of the selected cell properties specification (one or more channel populations) at the bottom.


As well as the channels, the effect of a given discretization parameter can also be shown on the morphology. This is independent of any channel allocation: the channels are positioned on the cell according to the supplied distribution rules and only allocated to compartments when the calculation is run with a particular spatial resolution.

Channel display

In the standard view, channels are shown as dots or circles depending on the scale. The structure can be moved, resized and rotated with the mouse.

Depending on the zoom factor, not all the channels are shown. The display keeps the same color intensity independent of the scale, so if the corresponding channel size is less than one pixel, then only a subset of channels is shown.

Region labelling

All the normal PSICS channel distribution options are available through the user interface. In particular, labels attached to the morphology can be used as part of the specification for region constraints. Here channels are applied uniformly to all parts of the cell distal to label1. The labels can be pulled off and re-attached with the mouse.

Distribution specification

Both the density and region specifications can contain expressions. Here channels are applied to five micron segments of dendrite every 20 micron with the "(p % 20) < 5" condition.

3D Visualization

As well as the projection view, a shaded 3D view can be opened in a separate window. The pan, zoom and roll controls are the same.

3D Channels

Each channel has an exact position on the cell.

Display styles

Three levels of display resolution are available depending on the available memory and graphics hardware.

High resolution channels

The most detailed display can require many millions of triangles to show all the channels on the cell. This may give poor interactive performance for the whole cell, though smaller sections of the cell can typically be manipulated without trouble.

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