To design and run a 3D experiment:

1. Manually acquire images of your specimen and adjust acquisition parameters and settings until you are satisfied with the images.

2. Use the Z Slider on the right side of the Resolve3D window to find and center the object of interest. Drag the slider up to find the top of your sample. (When you release the mouse button, an image is acquired and displayed in the Data Collection window.) Drag the slider and acquire images until you are satisfied. Then press the  button to mark that location. Next, use the slider to find the bottom of the sample. When you are satisfied, press the  button to mark that location.

3. Click the Experiment icon to open the Design/Run Experiment window. Then click the Design tab.

4. Click the Sectioning tab and specify the focus point of the microscope at the start of the experiment as follows:

   Choose one of the following *focus points in the Focus point when scan starts list.	Then click the corresponding  button in the Resolve3D window to move the stage to that focus point
   Top of the sample
   Middle of the sample
   Bottom of the sample
   * For most applications, the Middle of the sample provides the best results.

5. In the Optical section spacing field, specify the separation (in microns) between each optical section.

6. Specify either the thickness or the number of sections as follows:

   To get the thickness of the specimen, as defined in Step 2, click Get thickness. softWoRx adjusts the number of sections to span the specimen thickness.
   -or-

   To specify the number of sections, enter the number of sections in the Number of optical sections field.

7. Click the Channels tab and select a check box for each filter used. (The most recent value for exposure time is automatically set for each filter.)

8. If you are repeating an experiment with new exposure times, click Refresh exposure conditions.

9. Save the experiment as follows:

   To save the current experiment, choose File | Save.
   -or-

   To change the experiment name, Choose File | Save As and enter the new name.

10. Click the Run tab. In the Image file name field, enter the file name.

11. In the Image title field, enter pertinent information or a description of the experiment.

12. Click the Start Scan button.

    If the Launch viewer after experiment option is selected, the file automatically opens when the experiment is through.

13. When data collection is finished, choose File | Quit from the Design/Run Experiment dialog box menu.

    Notes The Data Collection window remains on the screen but it only contains the last 20 images that were collected. To view the complete data file, go to the directory you specified for the file and open the file. For more complete instructions, see the softWoRx Imaging Workstation User's Manual. softWoRx appends the _R3D.dv extension to your file name. (For example, if you enter your_file, the resulting file name is your_file_R3D.dv.) If Auto-increment file names is selected on the Resolve3D Settings window Files tab, this same file name is used until it is changed. A sequential number is added to the file name (e.g., your_file_01_R3D.dv).