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Inspecting circuits

Aim

To learn about the options available in RTNeuron for inspecting circuits.

Individual cells

Each cell can be isolated by clicking on its soma. This isolates the cell and displays its soma, dendrites, and axon.

../_images/isolated.png

Return to the view of the whole circuit by clicking on the soma again.

Slice planes

Creation

Slice planes can be added to the view by expanding the Slice tab and clicking Add.

../_images/add.png

This displays a pair of planes in the view which restrict the geometry displayed.

Adjustment

You can adjust the width of the slice by changing the width parameter in the Slice tab.

../_images/change_width.png

The slice can be moved clicking and dragging on the widget centred between the planes.

../_images/move.png

The slice can be rotated by clicking the widget centered between the planes so that it changes to the rotation widget.

../_images/change_widget.png

Clicking and dragging the widget will rotate the slice.

../_images/rotate.png

The planes can be hidden by clicking Hide in the Slice tab. This will hide the planes but retain their effect on the displayed geometry.

../_images/hide.png

Removing

To remove the planes and their effect, click Clear.

../_images/clear.png

Background color

The background color of the view can be adjusted under the Options tab.

../_images/color_swatch.png

Click in the color swatch to the right of the Background color label. This will show a color selector that you can use to change the background color.

../_images/set_color.png

The default color is white.

../_images/changed_color.png

Cell dyes

Cell dyes are not currently compatible with Sonata data.

Extra models

You can load your own .obj models into the view by selecting Add model under the Extra models tab.

Congratulations

You can now change how you visualize your data in RTNeuron!