File Types

Bio Applications can only be applied to suitable image files. If you try to use them with an unsuitable image type, a message is displayed. The following types of images are not supported for this application:

  1. Z-Stacks
  2. Unprocessed Airyscan data
  3. Unprocessed Apotome data
  4. Multi-phase images
  5. Multi-block images
  6. PSF images
  1. You have opened an image which is typical for the analysis scenario.
  2. You have set up a general setting for your application, see Creating a General Bio Application Setting.
  1. On the Analysis tab, in the Bio Applications tool, click Confluency.
  2. The parameters are displayed.
  3. Select your created setting and click Create Setting.
  4. The Bio Applications wizard opens.
  5. Enter a Name for the class you want to segment,
  6. In the channel control, select the channel which contains the necessary information for the analysis. For multi-channel images, which contain a channel out of the list (Bright, Oblique, DIC and PGC), this channel is automatically preselected.
  7. Select a Color for the resulting masks.
  8. Per default, the Segmentation Type is set to Manual to use a manual variance-based segmentation.
  9. Select if you want to segment the Structure in your image or the Background (this inverts the applied threshold values).
  10. Define the Threshold for the variance calculated from one pixel with the neighboring pixels and adjust the Kernel Size for this calculation.
  11. If you want to use machine learning for segmentation, click AI-based (the prerequisite is that you have installed the 3rd party Python Tools during the installation of ZEN).
  12. A dropdown to select your model is displayed. It contains your own trained and imported networks if they have been trained on one channel.
  13. In the AI Model dropdown, select the model you want to use for segmentation.
  14. Select the Model Class that should be used for segmentation and set a Min. Confidence.
  15. Set the Min. Object Size to define the minimum area in pixel that an object must have to be segmented.
  16. Activate Fill all holes if you want to close the holes in the segmented masks. Otherwise leave Fill all holes deactivated.
  17. Set the Min. Hole Size to define minimum area in pixel of the holes in the detected objects.
  18. Click Finish.
  1. You have created a setting for Confluency which can now be used to analyze images by clicking Run Analysis, see Running Bio Applications.