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ZEN Workflows

 

ZEN Workflows is released as a Beta-Version through ZEN Early Access Program

You can learn more about ZEN Early Access Program, request a ZEN Early Access license, and share your feedback about the preview features here: https://zeiss.ly/zen-preview

ZEISS (Licensor) may offer a ZEN user (Licensee) an opportunity to use a beta version of the ZEN Software Features (“Beta Features”) for a limited period of time, for demonstration, testing, evaluation, or other nonproduction purposes. Beta Versions are covered by the provisions of the End User License Agreement, except that all Beta Features are provided “AS IS” and without warranty and support of any kind, express or implied.
By requesting a ZEN Preview license, you agree that such ZEN Beta Features: (i) may only be used in a production environment at the licensee's own risk; (ii) is not expected to function with the same reliability as generally available ZEISS Software and may contain defects that are not found in generally available Software Products; (iii) will not be subject to any obligation by ZEISS correct defects or offer support; and (iv) may not be made generally available.

This module allows you to define automated workflows in ZEN. You can load your data, acquire images, combine individual processing steps and the image analysis to create a workflow, and also have the possibility to create a loop, for example for batch processing. Note that this workflow functionality is currently only available for ZEN desk, ZEN pro, and ZEN system.

User Interface for Workflows in ZEN

Switching to the Workflow tab in the Left Tool Area changes the view to display the dedicated functionality for workflows. To the right of the Left Tool Area, you have a second column which displays the controls for a workflow step, including tools, and the Center Screen Area contains the Workflow container.

1

Workflow Tab

The tab is the central control to select, set up, and run your workflows, see Workflow Tab. The list on this tab displays and defines the steps of your workflow.

2

Workflow Step Header

Each step of a workflow has its own work area, where you can see and define which tool is used for the step, see Workflow Steps. Some steps also have tools that are added by default and cannot be removed, others only allow a limited number of tools to be added in parallel.

3

Tool

Here you have the tools which you added to your step. The tool window displays parameters which can be set for the current workflow step. Note that there is no Show All mode for tools in the workflow environment, instead you can define the visibility of individual parameters, see Customizing Steps and Tools. To remove a tool from the step, use the X in the top right corner of the tool.

4

Workflow Container

The Workflow container looks different depending on the current actions. It is the place where you see your data during a workflow run, it displays the available tools if you add a tool to the step, and it displays the available steps if you add a new one. The area can also be empty when you perform other actions like adapting the visibility of the tool parameters.

Creating a Workflow

  1. Open the Workflow tab.
  2. The Workflow tab is displayed and the view changes, see User Interface for Workflows in ZEN.
  3. To the right of the Workflow dropdown list, click Dark blue rounded square icon with a white gear and a small white sparkle to its right and select New.
  4. The dropdown is changed to a text field.
  5. Enter a name for your new workflow and press Enter. Alternatively, enter the name and click small floppy disk icon with metallic top.
  6. A new empty workflow is created.
  7. Check the file path for Output Folder. To change the path where your results are saved, click Dark rounded square button with three white horizontal dots.
  8. A file browser opens.
  9. In the file browser, select the folder where you want to save your workflow results and click Select Folder.
  10. You have updated the location where the result data is saved.
  11. To add a step to your workflow, go down to the list on the tab and click White plus sign centered on dark blue rounded-square icon. Alternatively, click + Add Step.
  12. The Workflow container on the right displays a view to select a step. They are ordered into different categories.
  13. Select the category. Alternatively, use the search field to search for a step. If it is the first step of your workflow, you need one to load input data or acquire an image.
  14. The respective steps are displayed.
  15. Select the step and click Add. Alternatively, double click the entry.
  16. A new step is added to the workflow and is visible in the list on the Workflow tab. The corresponding step is also displayed in the column to the right of the Workflow tab.
  17. In the step header, click +Tool.
  18. The Workflow container on the right displays all tools available for this step.
  19. Double click the entry for the tool.
  20. The tool is added and its parameters are displayed in a tool window below the step header.
  21. To a pause at a step during a workflow run, right click the step in the list. By default, each newly added step is set to run automatically.
  22. The context menu is displayed.
  23. Select Add Pause Marker.
  24. A pause marker is added to the step.
  25. To repeat certain steps of your workflow, you can add a loop, see Adding a Loop to a Workflow.
  26. You have defined a loop.
  27. To group certain steps together, see Adding a Group to a Workflow.
  28. You have defined a group of steps.
  29. Repeat these points to add all steps you want to use in your workflow.
  30. You have added steps to your workflow.
  31. Next to the Workflow dropdown list, click Dark blue rounded square icon with a white gear and a small white sparkle to its right and select Save.
  32. You have saved your workflow.
  1. You have created a workflow. You can now run your workflow, see Running a Workflow Stepwise or Running a Workflow Automatically.

Opening a Workflow

  1. You have workflows available.
  2. You are on the Workflow tab.
  1. In the Workflow dropdown list, select the workflow you want to display.
  2. The selected workflow with all its steps are displayed in table.

Adding a Loop to a Workflow

If you want to repeat certain steps of a workflow, you can create a loop.

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  1. In the workflow list, select the entry after which you want to add the loop, and click White plus sign centered on dark blue rounded-square icon.
  2. The Workflow container on the right displays a view to select a step.
  3. Select the category Workflow.
  4. The available steps are displayed.
  5. For the Loop entry, click Add. Alternatively, double click the entry.
  6. A loop is added to the list and is displayed. Per default, the Loop step has the Settings tool.
  7. Use the Settings tool to set up your loop. You can define an exact number of iterations, a range, or you can select Batch processing where each step of the loop is iterated once for each input document.
  8. You have defined an empty loop.
  9. You can now add steps and tools inside the loop as described for the workflow creation, see Creating a Workflow. When adding the first step of the loop, you have to select the Loop entry in the workflow list before clicking White plus sign centered on dark blue rounded-square icon. For all subsequent steps of the loop, you must not select the Loop entry when adding it. You have to select an entry inside the loop.
  10. You have added steps and tools inside your loop. All steps belonging to the loop have a color marker to indicate that they belong to the loop.
  11. To a pause at a step during a workflow run, right click the step in the list. By default, each newly added step is set to run automatically.
  12. The context menu is displayed.
  13. Select Add Pause Marker. Alternatively, select Add Pause Marker for First Loop Iteration if the step should be paused during the first time and then automatically run for all following iterations of the loop.
  14. You have defined a loop in your workflow. All steps of the loop are displayed below the Loop entry in the list and the view can be minimized with the expander arrow of the Loop entry.

Adding a Group to a Workflow

 

Locked Groups

Some functionality, like Image Analysis, is automatically added to the workflow as a group with a predefined set of steps. In those cases, you cannot change individual steps, only the whole group. Locked groups are displayed with a lock icon in the list on the Workflow tab and buttons or context menu entries are disabled, if the respective action cannot be performed for the selected step of the group.

You can group multiple steps of your workflow and define which outputs of the individual steps of the group are saved.

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  1. In the workflow list, select the entry after which you want to add the group, and click White plus sign centered on dark blue rounded-square icon.
  2. The Workflow container on the right displays a view to select a step.
  3. Select the category Workflow.
  4. The available steps are displayed.
  5. For the Group entry, click Add. Alternatively, double click the entry.
  6. A group is added to the list and is displayed.
  7. You can now add steps and tools inside the group as described for the workflow creation, see Creating a Workflow. When adding the first step of the group, you have to select the Group entry in the workflow list before clicking White plus sign centered on dark blue rounded-square icon. For all subsequent steps of the group, you must not select the Group entry when adding it. You have to select an entry inside the group.
  8. You have added steps and tools inside your group.
  9. To a pause at a step during a workflow run, right click the step in the list. By default, each newly added step is set to run automatically.
  10. The context menu is displayed.
  11. Select Add Pause Marker.
  12. A pause marker is added to the step.
  13. To define which output of the group's steps should be kept, you need the Define Output tool. Select the Group entry in the list, go to the step on the right, and click +Tool.
  14. The Workflow container on the right displays all tools available for this step.
  15. Double click the Define Outputs entry.
  16. The Define Outputs tool is added to the Group step.
  17. In the tool, activate the checkbox for each step where the output should be saved.
  18. You have defined a group in your workflow. All steps of the group are displayed below the Group entry in the list and the view can be minimized with the expander arrow of the Group entry.

Duplicating and Replacing a Workflow Step

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  1. Select the entry in the workflow list you want to duplicate and click Dark blue square icon with white floppy disk symbol. Alternatively, right-click the entry and select Duplicate.
  2. The entry is duplicated, and the second entry is added to the list.
  3. To replace a step, select it in the list and click Dark blue square icon with white circular refresh arrows. Alternatively, right-click the entry and select Replace.
  4. The Workflow container on the right displays a view to select a step.
  5. Select the category for your step. Alternatively, use the search field to search for a step.
  6. The respective steps are displayed.
  7. Select the step and click Add. Alternatively, double click the entry.
  8. The step is replaced with the new one.
  9. Next to the Workflow dropdown list, click Dark blue rounded square icon with a white gear and a small white sparkle to its right and select Save.
  10. You have saved the workflow with the changes.

Moving or Deleting a Workflow Step

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  1. To move a step, select the step in the list and click White upward-pointing chevron icon on dark square background to move it one position up, or click White downward-pointing chevron icon on dark square background to move it one position down in the list. Note that some groups have a locked order of steps, for example the Image Analysis, and you cannot move the individual steps but only the entire group. You also cannot move steps into or out of a locked group.
  2. The step is moved based on your selection.
  3. To delete a step, select it in the list and click White trash bin on dark blue rounded-square icon. Alternatively, right-click the step and select Delete. Note that some groups have a locked order of steps, for example the Image Analysis, and you cannot delete the individual steps but only the entire group.
  4. The step is deleted from your workflow.
  5. Next to the Workflow dropdown list, click Dark blue rounded square icon with a white gear and a small white sparkle to its right and select Save.
  6. You have saved the workflow with the changes.

Customizing Steps and Tools

You can customize many steps and tools of workflows, including setting the accessibility of individual tool parameters. Note that the customization described here is not available for all steps or tools.

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  1. Select a step in the workflow list and click Blue rounded square icon with a white diagonal pencil.
  2. The corresponding step and added tools are displayed in the column to the right and switched to an edit mode.
  3. Each tool parameter where accessibility can be adapted has an icon on its right. The icon indicates the accessibility state and provides a tooltip which explains the state.
  4. To add instructions, expand the Instructions section.
  5. The section is expanded.
  6. Use the text field to write useful information or instructions for this step of the workflow.
  7. You have added written instructions.
  8. To add an image to the instruction, click Add image.
  9. A dialog opens.
  10. Click Dark rounded square button with three white horizontal dots, navigate to the desired image, select it, and click Open.
  11. The image and the image path are displayed in the dialog.
  12. In the Link Text field, enter a corresponding text, and click OK.
  13. The image is displayed in the step and the link text is displayed as the header of the image.
  14. To change the accessibility of a tool parameter, click the icon for the parameter.
  15. The icon changes and the tooltip explains the new state. The following states are indicated:
    - The parameter is displayed and can be edited.
    - The parameter is only displayed but cannot be edited.
    - The parameter is completely hidden.
  16. Click the icon for each parameter until all desired states are set.
  17. You have defined the availability of individual tool parameters.
  18. To change the permitted value range or value for a tool parameter, for example for a slider, go to the tool header and click Blue square icon with white gear symbol.
  19. The Workflow container displays the setup of the tool, including the individual parameters.
  20. Adapt the value ranges or values and click X.
  21. The permitted value range or value for the parameters are changed.
  22. Click Apply on the bottom.
  23. The customization of the step and tool parameters is applied.
  24. Next to the Workflow dropdown list, click Dark blue rounded square icon with a white gear and a small white sparkle to its right and select Save.
  25. You have customized and saved the workflow with the changes.

Exporting and Importing Workflows

  1. To export a workflow, you have opened it, see Opening a Workflow.
  2. To import a workflow, you need to have a workflow available for import.
  1. Next to the Workflow dropdown list, click Dark blue rounded square icon with a white gear and a small white sparkle to its right and select Export.
  2. A file browser opens.
  3. Navigate to the folder where you want to export the workflow to and click Select folder.
  4. The currently opened workflow is exported and saved at the selected location.
  5. To import a workflow, go to the Workflow dropdown list, click Dark blue rounded square icon with a white gear and a small white sparkle to its right, and select Import.
  6. A dialog for importing workflow templates opens.
  7. For Source Directory, click Dark rounded square button with three white horizontal dots.
  8. A file browser opens.
  9. Navigate to the folder with the workflow(s) you want to import and click Select folder.
  10. The file browser closes and all workflows available in the selected folder are displayed in the import dialog.
  11. Activate the checkbox for every workflow you want to import and click Import.
  12. The selected workflows are imported and can be opened and used in ZEN.

Running a Workflow Stepwise

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  2. The first workflow step loads input data or acquires an image.
  3. The workflow does not contain pause markers.
  1. Click Run First Step.
  2. The workflow starts and the first step is run.
  3. Your loaded data or acquisition is displayed in the Workflow container.
  4. Set the parameters in the tool to the desired values.
  5. The changes are applied to your data, and the view is updated. If they are not automatically applied, you can click Run in the header.
  6. Click Continue to Next Step.
  7. The workflow continues and runs to the next step.
  8. Repeat the previous steps to go through the entire workflow.
  9. Your workflow runs until it is finished.
  10. The last step with the saving options is displayed.
  11. Click Save Results to save your results at the location defined on the Workflow tab. Click Discard Results to discard the results.
  12. You have finished the workflow, and the result data is saved or discarded based on your selection.

Running a Workflow Automatically

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  2. Your first workflow step loads input data or acquires an image.
  1. If your workflow does not contain pause markers, activate Auto-Run All Steps and then click Auto-Run All Steps. If your workflow contains pause markers, click Run to First Pause Marker.
  2. The workflow starts and the all steps are run.
  3. If the workflow has pause markers, all steps until the first pause marker are run.
  4. Your data is displayed in the Workflow container.
  5. Set the parameters in the tool to the desired values.
  6. The changes are applied to your data, and the view is updated. If they are not automatically applied, you can click Run in the header.
  7. Click Auto-Run Remaining Steps if no more pause markers are in the workflow, otherwise click Continue to Next Pause Marker.
  8. The workflow continues and runs to the next step with a pause marker.
  9. Repeat the previous steps to go through the entire workflow.
  10. Your workflow runs until it is finished.
  11. The last step with the saving options is displayed. If you have not set a pause marker for the Save Results step, it is not displayed and all results are saved and opened in ZEN automatically.
  12. Click Save Results to save your results at the location defined on the Workflow tab. Click Discard Results to discard the results.
  13. You have finished the workflow, and the result data is saved or discarded based on your selection.

Running Parts of a Workflow or Individual Steps

You can run parts of your workflow, or even just individual steps. This can, for example, be helpful if you want to check the parameter settings of a tool during the setup of a workflow.

  1. You are on the Workflow tab and have opened a workflow, see Opening a Workflow.
  1. To run the workflow only until a certain step, select the entry in the list and click Dark blue right-pointing triangle next to a dark blue vertical bar on white backgroundRun to here. Note that there needs to be input data available.
  2. The partial workflow execution starts and runs to the selected step.
  3. To execute a single step, for example during setup, select it in the list and click Run in the step header. Note that there needs to be input data available.
  4. The selected workflow step is executed and the parameters set in the respective tool are applied.

Example Workflow Acquisition and Processing

This example workflow shows a generic combination of image acquisition, the application of a processing operation (e.g. enhance contrast), and a measurement, like a distance between two objects. This workflow is meant to be a template and a starting point for you to build your own workflows and tailor them to your needs.

Multi-Dimensional Acquisition

This step allows you to set up a flexible acquisition with different acquisition dimensions, see Multi-Dimensional Acquisition Step.

  1. Use the Channels tool to define the settings for your channels.
  2. Channels are defined.
  3. If necessary, add more tools to further define your acquisition, including stage, focus, tiles, and z-stack specifications.
  4. The acquisition is defined.
  5. Click Start.
  6. The acquisitions starts.
  7. After the acquisition is finished, the image is displayed in the Workflow container of the Center Screen Area.

Image Processing: Enhance Contours

This step enables you to directly process the image, see Image Processing Step.

  1. In the Enhance Contour tool, adapt the parameters to enhance the contours of your image, see Enhance Contour.
  2. The image is processed accordingly.

Interactive Measurements

this step enables you to measure distances, angles, area, and intensities of pixels in your image, see Interactive Measurements Step.

  1. Add a tool and use it to conduct your measurement.
  2. You have measured a feature of your image.

Save Results

After running through the workflow, you can save your results, see Save Results Step. When you run your workflow automatically and have not set a pause marker for this step, the results are saved and opened in ZEN. You have the following options:

  • Save Results & Open in ZEN
  • Save Results & Open File Explorer
  • Save Results
  • Discard Results

 

Example Workflow Image Analysis

This example workflow is a generic example of how an automatic image analysis can be set up. In this case the images are deconvolved before the analysis is started. This template serves as a starting point to either add more steps and functions, or to adjust parameters based on the images you want to analyze or objects you want to segment, for example by using conventional thresholding or machine learning models. Keep in mind that an image analysis can be combined with acquisition or processing depending on the level of automation you would like to achieve.

Load File

This step enables you to load files, see Load File Step.

  1. In the Load Image tool, click Dark rounded square button with three white horizontal dots.
  2. A file browser opens.
  3. Select the image you want to deconvolve and analyze, and click Open.
  4. The image is loaded and displayed.

Image Processing: Default Deconvolution

This step enables you to directly process the image, see Image Processing Step.

  1. In the Default Deconvolution tool, select a deconvolution algorithm, see Deconvolution (defaults).
  2. The image is processed accordingly.

Image Analysis

This step enables you to perform your image analysis and select an image analysis setting with the Load Setting tool. The Image Analysis is added to the workflow list as a locked group with predefined steps that correspond to the steps of the image analysis wizard, see Image Analysis Wizard. This step and the possibility to select an analysis setting is only available when setting up the workflow and not during a run. You cannot set a pause marker for this step, only for the subsequent ones.

Class Setup

This step enables you to define the classes for measured objects, see Class Setup.

  1. Define the classes for your objects.
  2. Classes are defined.

Frame Setup

This step enables you to define one or more measurement frames, see Frame Setup.

  1. If necessary, define frames for your measurements. Only the area within the measurement frames gets analyzed. You can also define how the analysis treats objects that are cut by the border of the image or the frame.
  2. Measurement frames are defined.

Image Segmentation

This step enables you to select the segmentation method that is applied and set parameters for the segmentation of the objects that you want to measure, see Image Segmentation.

  1. Select your segmentation method and set the parameters.
  2. The image is segmented.

Region Filter

This step enables you to define the region filter conditions under which you want an object to be measured, see Region Filter.

  1. Define the region filters for the objects in the image.
  2. Filters are defined.

Interactive Image Segmentation

This step enables you to post-process the segmented objects, see Interactive Image Segmentation.

  1. If necessary, set the parameters for post-processing.
  2. Parameters are set.

Features Setup

This step enables you to select the measurement features, see Features Setup.

  1. Select all features you want to measure in your image.
  2. Measurement features are defined.

Statistic Features

This step enables you to define custom statistical features for your regions or objects, see Statistic Features.

  1. if necessary, define your custom statistical features, see Creating Custom Statistical Features.
  2. Statistical features are defined.

Measurement Data

This step enables you to see a preview of the result, see Measurement Data.

Save Results

After running through the workflow, you can save your results, see Save Results Step. When you run your workflow automatically and have not set a pause marker for this step, the results are saved and opened in ZEN. You have the following options:

  • Save Results & Open in ZEN
  • Save Results & Open File Explorer
  • Save Results
  • Discard Results

 

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