Sectioning Options

Use the Sectioning tab fields to specify parameters for 3D experiment macros. (The Sectioning tab is under the Design tab on the Design/Run Experiment window.) Like other macros, Sectioning Setup (3D) experiments should be designed after you have manually acquired images of your specimen and adjusted exposure and other parameters until you are satisfied with the images.

Once your microscope is focused near the middle of the vertical zone of interest of your sample, you can use the parameters under the Sectioning tab to control the optical sectioning process.

Use	To...
Z Sectioning	When check box is activated, enable Z Sectioning. This involves moving the microscope vertically to change the focal point of imaging in carefully controlled steps. Deselect this option if you are only interested in imaging a single focal plane.
Z Scan Options	Apply backlash removal and choose backlash distance. This minimizes Z sectioning errors.
Focus point when scan starts	Specify the location of the focus plane when the experiment starts. The Experiment Designer generates the sectioning commands based on this relative starting point, so make sure that you set up the focus to be consistent with this setting when the experiment starts. The focus point is returned to this position at the end of the scan. The focus point can be: Middle of Sample: Focus point is midway between the top and bottom of the sample. This is the default and is usually the "plane of best focus" for the sample. Bottom of Sample: The Z stage is farthest away from the objective. This involves the least stage motion at the start of a scan. Top of Sample: The Z stage is closest to the objective. This involves the most stage motion at the start of a scan.
Optical section spacing	Specify the separation (in microns) between each optical section. The focal point is changed by this value after each image is collected. The choice of section spacing should be based on the size of structures that are being imaged and the Numerical Aperture of the lens. The Lens Info tool suggests an appropriate Optical section spacing for a given lens.
Number of optical sections	Enter the number of sections to be collected (for each wavelength) for the experiment. softWoRx automatically calculates and displays this value if the Sample thickness and Optical section spacing are entered. If you specify this value, the Sample thickness value is changed.
Sample thickness	View the sample thickness. This value is the Number of optical sections multiplied by the Optical section spacing.
Get thickness	Calculate the Sample thickness, based on the locations defined with the and buttons in the Resolve3D window. Note: To determine sample thickness, the top and bottom of the sample must be marked in the Resolve3D window.
Enable OAI Scan	When check box is activated, acquire a 3D Z projection of the interval defined by the marked top and bottom of the sample. Note: OAI is available only for DeltaVision systems.