Activating images for processing

When you activate multiple images for batch processing in ZEN, make sure to exactly click on the respective checkbox of the entry. If you click outside the checkbox, all activated images are deselected and only the last clicked entry is activated.

Using the same method and parameters for multiple images

When you want to use the same method with the exact same parameters for multiple or all images in the list, you need to ensure the following conditions for meaningful results:

  1. The images need to have the same characteristics, including the same image dimensions, number of channels or phases, and need to be acquired with the same imaging modality.
  2. If the processing method relies on particular metadata, the necessary metadata needs to be identical as well. An example are the PSF parameters for deconvolution, which are based on image acquisition metadata.

Batch processing in ZEN allows you to apply a specific processing method automatically to a batch of images. For each image you can use identical or different settings.

  1. You have a folder with CZI-images you want to process.
  1. Go to the Processing tab and click Batch.
  2. The Batch Processing view opens.
  3. Open the Batch Method tool and select the method you want to use.
  4. The method is selected.
  5. In the Center Screen Area, click + Add.
  6. A file explorer opens.
  7. Open your folder, select all images you want to process, and click Open.
  8. The list of images is displayed in the Batch Processing view.
  9. Per default the currently selected method is defined for all images.
  10. Activate Use Input Folder as Output Folder to save the processed images in the folder of the original images. Alternatively, deactivate the option and select an output folder for each of your images by selecting them and clicking .
  11. You defined the output folder.
  12. Select an image in the list and define the settings in the Parameters tool. Alternatively, select a settings file from the Settings dropdown list. If you use a settings file, the file must have been created with the same method.
  13. You have defined the settings for the image. The settings are only valid for the selected image but can be copied to further images in the list.
  14. To copy the parameter settings of the current image, click Copy Parameters.
  15. You have copied the parameters.
  16. Select the image with identical dimensions in the list and click Paste Parameters.
  17. You have added the previously copied parameter settings to the selected image.
  18. Continue with all other images of the list. Use Copy Parameters and Paste Parameters, select a settings file, or define the settings for each image individually in the Parameters tool. You can also use different methods for each of the images.
  19. You have defined parameter settings for all images.
  20. Click Check All.
  21. All images are checked if they are suitable for the selected method. They are tagged with a green marker in the list, if they have a suitable setting.
  22. Activate the checkbox for each image you want process and click Apply.
  1. All selected images in the list are processed and put into the defined output folder.