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3D Image Analysis

This module offers functionality to analyze and quantify 3D image data. The image analysis wizard, optimized for 3D functionality, guides you through the segmentation steps to setup a fast and easy-to-use quantification of segmented objects. The resulting objects are visualized using the 3D viewer and with the help of a table, the objects can be sorted and exported. You need a valid license for the 3D Toolkit.

Backwards compatibility of 3D analysis results

The results of a 3D analysis are saved in the image but are not backwards compatible. Older versions of ZEN cannot read and display 3D analysis results produced by ZEN 3.13 or newer.

Creating a 3D Image Analysis Setting

  1. On the Analysis tab, in the Image Analysis tool, click Dark rounded square icon with white four-point sparkle at top-left and white gear on right and select New from the dropdown.
  2. In the Settings field, enter a name for your image analysis setting and click Small save floppy disk icon. Alternatively, enter the name and press Enter.
  3. A new image analysis setting is created and saved.
  4. For Method, click Black pencil icon slanted on blue rounded square background.
  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 Small dark button showing a white plus sign.
  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 Small dark button showing a white plus sign.
  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.

Performing and Saving a 3D Analysis

  1. You have created an analysis setting for a 3D analysis, see Creating a 3D Image Analysis Setting.
  2. You have opened the image you want to analyze.
  1. On the Analysis tab, open the Image Analysis tool.
  2. For Setting, select the setting you have created for your 3D analysis.
  3. Click Start Analysis.
  4. Your image is analyzed based on your setting.
  5. The 3D view opens to display your 3D volume and the objects resulting from the image analysis, with the Analysis Objects Table containing the data for the analyzed objects. The objects are displayed in the color that was assigned to the respective class in the analysis wizard.
  6. Click File > Save. Alternatively, press Ctrl + S.
  7. The analyzed image is saved under its current name. The resulting objects are saved in the czi file as well.

Viewing and Exporting the Results of a 3D Analysis

Backwards compatibility of 3D analysis results

The results of a 3D analysis are saved in the image but are not backwards compatible. Older versions of ZEN cannot read and display 3D analysis results produced by ZEN 3.13 or newer.

  1. You have opened an image where a 3D analysis has been performed, see Performing and Saving a 3D Analysis.
  1. Open the 3D view for your image.
  2. The 3D view opens to display your 3D volume and the objects resulting from the image analysis, with the Analysis Objects Table containing the data for the analyzed objects. The objects are displayed in the color that was assigned to the respective class in the analysis wizard.
  3. If you do not see the result table, in the Analysis tab below the image, activate Show Analysis Objects Table. To be able to see the objects, also make sure that Light gray cube icon on dark blue rounded square is activated in the bottom tool bar of the viewer, see Tool Bar (Bottom).
  4. The result table and objects are displayed.
  5. In the Analysis Objects Table on the right, in the Classes dropdown, select the object class you want to examine.
  6. The table and view are updated accordingly.
  7. To highlight certain objects in the view, activate the checkbox for the respective entry in the Analysis Objects Table.
  8. The objects are highlighted.
  9. Use the controls of the tool bars and 3D specific view options to interact with the image. To export your result table, in the Analysis Objects Table, click Export Table.
  10. A file browser opens.
  11. Navigate to the desired location and click Save.
  12. The currently displayed entries of the Analysis Objects Table are exported and saved as a .csv file.
  13. To export the image to arivis Pro, in the bottom tool bar, click Blue hexagon outline with small white cube icon on dark blue rounded square.
  14. The image is exported to arivis Pro and is displayed with almost identical rendering settings.

Analysis Tab

This tab is only available if you have opened an image with objects from the 3D Image Analysis.

Parameter

Description

Show Analysis Objects Table

Activated: Displays the analysis objects table on the right side of the 3D view.

Delete Analysis Results

Deletes the analysis results of the image.

Analysis Objects Table

This table is only available if you have opened an image with objects from the 3D Image Analysis, or if you have run an 3D image analysis and is displayed by default. It can be switched off by deactivating Show Analysis Objects Table in the Analysis tab. The table displays the resulting objects of an image analysis and allows you to manipulate, filter and export the objects. The table can be sorted by one column when clicking into the table header. A little arrow in the header indicates if the sorting order is ascending or descending.

When you select an entry, the respective object is highlighted in the 3D view, and vice versa. You can also select multiple entries when pressing the Ctrl key while clicking, or you can select a range of entries by pressing the Shift key while clicking on the first and last entry of the range. All corresponding objects are highlighted in the viewer. You can also undock the table by clicking the undock icon in the top right and then move the table freely on your screen.

Parameter

Description

Classes

Selects the class for which the objects are displayed in the table.

Export Table

Opens a file browser to export the objects table.

Objects Table

–

Checkbox

Activated: Highlights the respective analysis object in the 3D view. If you activate the checkbox in the table header, all objects are activated and highlighted.

–

ID

Displays the ID of the respective object.

–

Features

The various features you added in the Features step of the analysis wizard are displayed in this table, like the Volume and Parent ID.

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