With the processing function Cut Out Regions you can define a region in your z-stack and cut it out as a volume.

  1. You have opened your z-stack in ZEN.
  1. On the Processing tab, select the Method Cut Out Regions.
  2. Under Parameters, click on Define Regions.
  3. The Define Regions Setup opens.
  4. In the Dimensions tab, use the Z-Position slider to go to the first z-slice where you want to mark your region of interest.
  5. In the Region Edit Section on the left, click on Draw and select the type of region you want to use (rectangular, circular, polygonal,...).
  6. In the image, draw your so-called support region to mark the structure of interest.
  7. Repeat the previous steps for the last slice where your structure of interest appears as well as for those slices in between where significant changes (in shape and/or position) of this structure take place.
  8. Click on Interpolate.
  9. Interpolated regions are created for all slices between the support regions. The interpolated regions are displayed with a slightly darker color.
  10. Use the Z-Position slider to move through your stack and examine whether the interpolated regions satisfyingly cover the structure of interest in your stack.
  11. If you find a slice where the interpolated region does not cover your structure of interest, draw a new support region on this slice and click on Interpolate again.
  12. When the entire structure is marked satisfyingly by the interpolated regions, click on Finish.
  13. The Define Region setup closes and your image with the newly created regions is displayed in the Analysis view.
  14. On the Processing tab, click on Apply.
  1. Your marked structure is now cut out of the z-stack and opened as a new image.