Change image display panel (3D)

Show surface as (drop-down menu)

• Min projection: Recommended when the image foreground is brighter than the structures (e.g., brightfield images).
• Max projection:  Recommended when the image background is darker than the structures (e.g., fluorescence & confocal images).
• Alpha composite: Adds 3D depth and more detail.

Partial projection (check box)

• Check the box to display a subset of the data in X, Y or Z. This can be helpful in visually dense and/or complicated images.

• Use the slider on the left to navigate the portion of the image to display (click to view a short demonstration).

• The Center position and Thickness of the partial projection display you specify using the slider is reported in the Image stack settings portion of the window.

• Clip tracing (check box): When partial projection is active, you can check the box to Clip tracing so that the display of traced structures and/or markers is clipped to match the portion of the image being displayed

Note that image transparency settings are applied to all color channels in multi-color channel images.

Simple

Click the Simple radio button and adjust the transparency using the slider. Simple transparency is applied evenly to the image.

Intensity Based

Click the Intensity Based radio button and the Map button to specify transparency settings for dark, midrange, and bright intensity values in the image.

Click Done to apply the settings or Cancel to exit without applying the settings.

The 3D slice scroll panel opens when you display images as an Image Slice in the 3D Environment window.

• Check/uncheck XY, XZ or YZ to display/hide slices (planes).
• To move along an axis, drag the slider for that axis OR click a slider and use the PageUp/PageDown keys to move one plane at a time (click to view a short demonstration).

• Click or clear the Clip Tracing on Slices checkbox to hide the display of tracings on all slices (planes) apart from the one selected.

• Click a radio button to select a slice (see previous bullet).

• Drag the slider to display the image with even transparency across intensities (simple transparency).

• Click or clear the Show Border checkbox to display or clear a box around the image slices
• Use the Line Color color picker to select a color for the slice borders.
• Adjust the Thickness slider to set the line weight for the slice borders.

Show Bounding Box

• Click or clear the Show Bounding Box checkbox to display or clear a box around the image.
• Use the Line Color color picker to select a color for the bounding box.

Click the Undo Changes button to discard the image display settings.

Click to open/close the Image Adjustment panel that includes options for image-data adjustment.