1. On the Analysis tab, in the Image Analysis tool, click and select New from the dropdown.
  2. In the Settings field, enter a name for your image analysis setting and click . Alternatively, enter the name and press Enter.
  3. A new image analysis setting is created and saved.
  4. For Method, click .
  5. The Segmentation Method Selection dialog opens.
  6. From the Method drop down menu, select 3D Segmentation and click OK.
  7. A dialog is displayed to ask if you want to overwrite existing settings to create the 3D setting.
  8. Click Yes.
  9. In the Image Analysis tool, click Edit Image Analysis Setting.
  10. The Image Analysis Wizard opens in the Classes step with a default class already created.
  11. If you want to extend the predefined list of classes, click Add Class to add a new class or Add Subclass to add a subclass to the currently selected class.
  12. If you want to change the name for the classes, select a class and change the text in the Name field.
  13. Select your class(es) and define the Channel you want to use for segmentation and define a Color for the segmentation mask.
  14. Click Next.
  15. The Frame step opens.
  16. If you only want to analyze a specific volume of the image, you can use the parameters in this step to create one or more measurement frames. For a description of the parameters, see Frame.
  17. Click Next.
  18. The Automatic Segmentation step opens.
  19. Select one of your classes and click Select.
  20. The Class Segmentation Method dialog opens.
  21. For Method, select the segmentation method you want to use for your current class and click OK.
  22. The dialog closes and the displayed parameters are updated according to the selected method. Parameters that work only on the 2D slices of the volume are grouped under 2D Parameters, whereas parameters that work on the 3D dataset are grouped under 3D Parameters. For a description of the parameters, see Automatic Segmentation.
  23. Additionally, the section for 3D Preview is displayed.
  24. Set the parameters for the segmentation of the currently selected class according to your needs.
  25. Repeat the previous three steps to select a segmentation method and set the parameters for each of your classes.
  26. To see your image in 3D, change to the 3D view in the center view of the wizard.
  27. Use the parameters in the 3D Preview section to generate three dimensional slices around the current z position.
  28. Click Next.
  29. The Region Filter step opens.
  30. If you want to use conditions to filter out unwanted segmented regions, you can use the parameters of this step. For a description of the parameters, see Region Filter.
  31. Click Next.
  32. The Features step opens.
  33. Select one of your classes and, under Features of Individual Regions, click Select.
  34. The dialog for measurement feature selection opens.
  35. In the list of features on the right, select a measurement feature you want to use and click .
  36. The feature is added to the Selected Features list on the left.
  37. Add all the measurement features you want to use for the regions of the current class and click OK.
  38. To define measurement features for all regions, under Features of All Regions, click Select.
  39. The feature selection dialog opens.
  40. In the list of features on the right, select a measurement feature you want to use and click .
  41. The feature is added to the Selected Features list on the left.
  42. Add all the measurement features you want to use for all the regions and click OK.
  43. Click Next.
  44. The Results Preview step opens.
  45. Check the preview and go back and adapt the parameters in previous steps, if necessary.
  46. Click Finish.
  47. The wizard closes and the changes to the setting are saved.