3D environment overview

• Somas
• Trees
• Spines
• Varicosities
• Puncta (e.g., synaptic puncta)

• Split large and/or complex images into Subvolumes to facilitate analysis.
• Select a color Channel for display onscreen and to associate with structures as you model them.
• Define Contours (regions of interest)
• Place Markers

• Create video clips.
• Export your 3D representations as vector or image files.

• Drag to rotate (3D view only).
• Scroll the mouse wheel to zoom.
• Hold down the SHIFT key and drag to pan (3D only).
• Drag to pan (projection views only).

To spin a stack to change its orientation, use the 2D rotation tool.

1. Click the button in the toolbar.
2. Drag to rotate clockwise or counterclockwise.

To change the rotation axis, use the move-pivot-point tool.

1. Click the button in the toolbar.
2. Click a point in the image.
3. Drag to rotate relative to the new rotation point.

Click the icon.

Use the Channel panel on the left side of the window to select and work in specific color channels in multichannel images.

• Click any color button(s) to be displayed.
• When a single color channel is selected, any structures traced or detected will be associated with that color channel.
• To change the color channel, click to select a different one.
• To show all color channels present in the image, click the All button. If All channels are selected, structures traced are not assigned to a channel.
• Use the Trace Opacity slider to control the visibility of structures traced in other channels. This does not affect the appearance of structures traced in the currently selected channel.

To adjust gamma, black point and white point in your images, use the Image Adjustment panel, accessible from the Image and Workspace Ribbons (outside of the 3D environment).

3D Volume is the default but you can switch to the Image Slice mode:

1. Click the Image button to access the Change Image Display dialog box.
2. Under Display Image as, select Image Slice.