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Basic Functionality

The following functionalities are included in the base software:

Interactive Measurements

Interactive measurements enable you to measure the properties of a sample, for example, angles, area, and intensities of pixels. The tools can be classified as follows (the available tools depend on your hardware setup and licenses):

  • Annotations
  • Enable you to add text labels to an image, mark objects of interest, or determine the coordinates of a point in the standard or relative coordinate system.
  • Areas/Contours
  • The majority of these tools enable you to calculate the area (in pixels) enclosed by various shapes. Furthermore, the mean intensity of the enclosed pixels is also calculated. Some Area Tools are used to calculate the length of curves, such as the Spline Curve tool.
  • Distances
  • Enable you to measure angles and distances between lines, curves and points.

The software offers the possibility to use a magnetic cursor in your image. This cursor detects edges/contrast changes and automatically moves to them, which can help you to add measurements or annotations. Note that this cursor only works reliably on one channel, so for multi-channel images only activate one channel in the view options. The magnetic cursor can be activated and deactivated via the right-click context menu of your image, or with the shortcut Alt + C.

For more information on an individual tool, see the tool reference.

Adjusting Interactive Measurements

You can adjust various properties of interactive measurements, for example:

  • Line color, strength, and style
  • Text font, color, and size
  • Opacity
  • Measurement results displayed in the in the Center Screen Area next to the interactive measurement and in the corresponding tool
  1. An interactive measurement workbench is selected.
  2. You have performed at least one interactive measurement.
  1. Select the desired interactive measurement tool.
  2. Click the gear wheel icon.
  4. Adjust the parameters as desired.
  5. The measurements are updated immediately.

Using Interactive Measurement Tools

Interactive measurement tools enable you to measure distances, angles, areas, and intensities of pixels. In the Favorites section you can arrange your favorite tools by simply dragging them from the tools selection to the favorites bar.

  1. An image is displayed.
  2. The Interactive Measurement workbench is selected.
  1. Select the desired measurement tool from the tool selection. Note that by default the Keep Measurement Tool checkbox at the bottom of the tool selection is activated. This will keep the selected tool active after you have drawn in a measurement.
  2. Alternatively, select a tool from the Favorites bar.
  3. If it is not visible, click + Add Tool and double-click on the desired tool.
    Note that only parameters of the active tool are displayed in the workbench area.
  4. Click to place the measurement tool in the image.
  5. For more information about how to use each tool, see Interactive Measurements Workbench.
  6. To add more measurements, repeat the above steps.
  7. The selected tool remains active until you press Esc or close the window Apply selected tool (Esc to abort).

If desired, you can modify the measurement as follows:

  • Sorting interactive measurements
  • Editing interactive measurements
  • Adding an annotation to interactive measurements
  • Repeating or correcting an interactive measurement

Layering Interactive Measurements

Each measurement is stored in an imaginary layer. By default, the first measurement is the bottom layer and the most recent measurement is the top layer. You can change the order of the layers, for example if two measurements overlap and one is obscuring the other.

To move a measurement up or down a layer:

  1. Right-click the measurement.
  2. Select how you want to move the measurement:
  3. Bring Forwards: up one layer
  4. Send Backwards: down one layer
  5. Bring to Front: to top
  6. Send to Back: to bottom

Editing Interactive Measurements

You can change the following properties of an interactive measurement:

  • Size and position of the entire measurement (measurement result and individual nodes)
  • Position of measurement result
  • Number and position of individual nodes

For some tools you can change their orientation (rotation or placement of the measurement arcs).

For more information, refer to the help topic for the corresponding tool.

Entire measurement

To change the properties of the entire measurement:

  1. At least one measurement is visible in the Center Screen Area.
  1. Click the desired measurement and perform one of the following actions:

Graphic

Aim

Action

Move measurement

Click within the bounding box and drag

Resize freely

Drag the sides of the bounding box

Resize (proportional)

Press Ctrl and drag the corners of the bounding box

Measurement result

To change the properties of the measurement result:

  1. At least one measurement is visible in the Center Screen Area.
  1. Click the desired measurement and perform the following action:

Graphic

Aim

Action

Move measurement result

Drag the node of the measurement result

Annotation position

To alter the position of an annotation:

  1. At least one measurement is visible in the Center Screen Area.
  1. Click the desired measurement.
  2. Place the cursor over the annotation node. The cursor changes to a hand icon.
  3. Drag the node to the new location.

Individual nodes

To change the properties of individual measurement nodes:

  1. At least one measurement is visible in the Center Screen Area.
  2. The measurement was created by defining multiple nodes.
  1. Right-click the desired measurement.
  2. Click Edit Points.
  3. Perform one of the following actions:

Graphic

Aim

Action

Move node

Drag node

Add node

Click between two nodes

Remove node

Press Ctrl and click node

Hiding an Interactive Measurement

Normally, when a job is run, interactive measurements are automatically placed on the image at the location specified in Create a new template and edit it within Job Mode. However, it is also possible to create an interactive measurement task where the image has no measurements pre-placed. In this case, ensure that the operator knows where to perform the measurement (e.g. using a suitable workbench description).

  1. Click the desired measurement.
  2. Delete the measurement using the DEL key on your keyboard.

The tool remains in the Workbench Area but the measurement is no longer displayed in the image. The operator running the job later can create the measurement freely instead of modifying a pre-placed measurement.

You can also use this feature to correct a faulty measurement while working in Create a new template and edit it within Job Mode:

  1. Delete the measurement from the image and click the Redraw button in the tool to repeat the measurement correctly.

Changing Units of Measurements

  1. You have drawn in a measurement to an image, e.g. a Distance measurement.
  1. Select the measurement by clicking on it.
  2. Click on the Properties icon in the measurement box.
  3. The Properties dialog opens.
  4. Select the desired unit from the Unit drop-down list, e.g. mm instead of µm.
  1. The changed unit will be displayed in the image and in the measurement box.

Adding Measurements to a Live Image

  1. The 2D Acquisition or 2D Acquisition (automatic) Workbench is selected.
  2. You see the Live image of the microscope camera.
  1. Click on + Add Tool.
  2. The list of tools is displayed.
  3. Double-click on the desired measurement tool under Areas/Contours or Distances, e.g. Distance.
  4. The measurement tool is active.
  5. Draw in the measurement to the live image.
  6. If you click on Snap, the image will be acquired including the drawn in measurement. Do not forget to save the image to your file system.

Panorama

This module enables you to acquire an overview image (or panorama image) exceeding the image size of a single image. This is the case when the field of view of your microscope is too small for the sample area you wish to acquire. Acquire a set of connected, overlapping images (tiles) manually to stitch the tiles together to a single large image.

Acquiring a Panorama Image (automatic)

Using the Panorama (automatic) workbench you can automatically acquire panorama images from a sample area which is larger than the camera sensor can cover by a single snap. By moving the stage the software automatically acquires and stitches the individual images and creates a panorama image. Note that automatic panorama works also for coded and manual stages.

  1. You have set-up and configured your microscope system correctly.
  2. You have started the software and activated the module.
  3. You are in Free Mode.
  1. In the Panorama (automatic) workbench, click Live to get a live image from the microscope camera. Adjust the camera and microscope settings to see a well illuminated and sharp live image.
  2. Navigate to a specific area on your sample you want to image and click Start.
  3. After a short moment, the camera rectangle changes to green and you can move the stage. Note that when the software loses the stitching algorithm, the color of the rectangle changes to orange or red. Then you have to manually go back to the last "good" position.
  4. The panorama acquisition starts. You see the live image of the sensor area.
  5. Move the stage slowly by using the hardware or software joystick, e.g. in right direction.
  6. During the stage movement the software automatically acquires the panorama image.
  7. In our example we now move the stage a bit up and back to the starting point.
  8. To finish the acquisition, click Stop.
  1. The panorama image will be added to the Documents Area. Save the final image on your file system.

Panorama (automatic) Workbench

This workbench enables you to acquire panorama images from a sample area which is larger than the camera`s sensor can cover by a single snap. By moving the stage the software automatically acquires and stitches the individual images and creates a panorama image. Note that automatic panorama works also for coded and manual stages.

To learn how to acquire panorama images automatically, see Acquiring a Panorama Image (automatic).

Panorama (interactive) Workbench

This workbench enables you to acquire a panorama image with a manual stage, for example if the total sample area to be acquired exceeds the area that can be acquired with a single acquisition. You can manually acquire multiple images (tiles) of neighboring areas on the sample, which then are stitched to a panorama image.

You can save the oversize image as tiles or you can stitch the tiles together into a single oversize image.

Panorama Acquisition Options Tool

This tool can only be added to the Panorama (automatic) workbench. Note that the options should only be activated, if you have problems with the camera/live image during acquisition. It is only available for troubleshooting up and normally not needed.

The default state of the checkboxes is set to "undefined" (checkboxes are marked with a rectangle) which means the software tries to use an determined value for the current camera automatically. Meaning if you are unsure, if your camera supports the functionality, we recommend to leave the state to "undefined".

Parameter

Description

Use Camera Streaming (if possible)

If activated, the software uses the free running/streaming mode of the camera. This option is intended for slower cameras.

Stop and Go

If activated, during acquisition you have to move the stage, e.g. about one camera frame, and the stop the movement. Then you have to move the stage for the next frame and stop again. Compared to the "default" mode, the images to be stitched are acquired only when the stage movement stops.

This option is intended for cameras that produce motion artefacts (e.g. rolling shutter effect) and for exposure times greater than about 50 ms.

Third Party Import

This module enables you to import the BIO-Formats by OME (Open Microscopy Environment). More details on the supported BIO-Formats, see https://www.openmicroscopy.org/.

ZEN Application Programming Interface

ZEN API is an interface to connect to a running ZEN application (with all its processes). Once connected, interaction is possible from an external process possibly running on another machine. The interaction includes, for example, the following:

  • Monitoring, push-based where appropriate.
  • Controlling
  • Data streaming, for example, image data.
  • Multi-client support

 

ZEN API is available in two modes:

  • Supervised API Mode
  • When in Supervised API Mode, the system prevents concurrent actions initiated from UI and API. The user has two possibilities:
    • To enter API Mode: This mode allows the usage of any API calls, but mostly locks the UI.
    • To use UI: In this case the UI is enabled, while only uncritical monitoring APIs are allowed to be called. Such API calls do not change the state of the system and thus do not create conflicts when executed at any time.
  • Unsupervised API Mode
  • This mode disables control synchronization and allows concurrent usage of UI and API (monitoring and controlling APIs), that is, it allows critical actions that may cause conflicts or errors when executed randomly, for example, moving the stage. This mode is meant for expert users.

 

Unsupervised API mode can be enabled under Home Screen >Maintenance > General Options > ZEN API.

To call ZEN API as a client, the following prerequisites must be fulfilled:

  • The API client must always connect to the gateway.
  • The API client must send API tokens.
  • The API client must connect via TLS to the gateway.
  • The API client must trust or know the certificate of the gateway.

ZEN API User Interface

Supervised API Mode

In the Supervised Mode, you can open the API Server console for providing remote jobs and hardware control. This is done in the Home Screen:

Unsupervised API Mode

In the Unsupervised API Mode, the following information is displayed to indicate that ZEN core is in unsupervised mode and that the API server is running:

When the Unsupervised API Mode is enabled, the API Mode button in the Home Screen is hidden.

Enabling Unsupervised API Mode

You can switch between the Unsupervised and the Supervised API mode.

  1. You are logged in as an administrator.
  1. Click Home Screen > Maintenance > General Options > ZEN API.
  2. Under Unsupervised API Mode, activate the checkbox Enable Unsupervised API Mode.
  1. The Unsupervised API Mode is enabled after the application is restarted.

 

Additional ZEN API Information and Reference

For detailed information about ZEN API, see the ZEN API GitHub page: https://github.com/zeiss-microscopy/OAD/tree/master/ZEN-API. This page includes instructions for installing and configuring ZEN API, several Python client examples, and a complete API reference.

ZEN Data Storage Client

Time Deviation

In the very unlikely event that there is a time deviation greater than five minutes between the client and the server, the authentication of the client fails for security reasons. In this case an error message is displayed and working with ZEN Data Storage is not possible. You have to fix the system time of the client and/or server before a retry.

In ZEN core, you can store your data on your computer's file system in your local archive, or you have the option to save your data in a database called ZEN Data Storage.

ZEN Data Storage is an additional product which has to be installed. For more information, refer to the installation guide of ZEN Data Storage. You also need configure ZEN Data Storage as your archive, see Configuring a ZEN Data Storage Archive.

Creating a Collection for Data

You can create collections to structure your data and share it with others.

  1. You have set up ZEN Data Storage as your archive, see Configuring a ZEN Data Storage Archive.
  2. You have started the application with active user management to be able to add users or groups to a collection.
  1. Click Home Screen > Maintenance > Archive Options.
  2. Click Manage Collections.
  3. The Manage Collections dialog opens.
  4. Click .
  5. The Add Collection dialog opens.
  6. Enter a name for the new collection.
  7. Click .
  8. The Add Collection Access dialog opens.
  9. On the Groups and/or Users tab, select the group or user you want to grant access to the collection. Selection of multiple users and groups is possible by pressing Ctrl.
  10. Select the Access Level for the currently selected users/groups.
  11. Click OK.
  12. The dialog closes and the selected users and/or groups are granted access based on the selection.
  13. You can now adapt the Access Level of individual users and groups of this collection, if necessary.
  14. Click OK.
  15. The Add Collection dialog closes.
  1. You have created a collection for your data. You can now structure your data and share job results with the people having access to this collection, see Adding Job Results to Collections in Browse Results.

Editing or Deleting a Data Collection

  1. You have created a collection for your data. For more information, see Creating a Collection for Data.
  2. You have started the application with active user management to be able to add users or groups to a collection or edit them.
  1. Click Home Screen > Maintenance > Archive Options.
  2. Click Manage Collections.
  3. The Manage Collections dialog opens.
  4. To delete a collection, select it and click .
  5. To edit a collection, select it and click .
  6. The Edit Collection dialog opens.
  7. If you want to change the name, adapt it under Collection Name.
  8. If you want to change the access of a particular user, change the Access Level with the respective dropdown.
  9. To add a new user or group, click .
  10. The Add Collection Access dialog opens.
  11. On the Groups and/or Users tab, select the group or user you want to grant access to the collection. Selection of multiple users and groups is possible by pressing Ctrl.
  12. Click OK.
  13. The dialog closes and the selected users and/or groups are granted access based on the selection.
  14. Click OK.
  15. The Edit Collection dialog closes.
  16. Click Close.
  17. The Manage Collections dialog closes.

Sharing Job Results in Job Mode

  1. ZEN Data Storage is configured as your archive, see Configuring a ZEN Data Storage Archive.
  2. You are in Job Mode and have finished your Job.
  1. Click Save and Close. Alternatively, click Save and Repeat if you want to repeat the job afterwards.
  2. The Save Results dialog opens.
  3. Click Select Collections to which saved Results should be added to.
  4. The section with all available collections is displayed. Every collection that is shared with other users/groups is marked with in the Shared column.
  5. If you want to search for a particular collection, input your search term in the Search for Collections field.
  6. The collections displayed in the table are updated accordingly.
  7. In the table, activate the checkbox for each collection the result should be shared with.
  8. Click Archive.

Creating Custom Metadata

With ZEN Data Storage, you can create and use custom metadata in ZEN core.

  1. You have ZEN Data Storage configured as your archive, see Configuring a ZEN Data Storage Archive.
  2. You are on the Home Screen.
  1. Click Maintenance > Archive Options.
  2. The Archive Options dialog opens.
  3. Under Settings, click Custom Metadata.
  4. The Custom Metadata tab opens and all custom metadata entries are displayed.
  5. Click .
  6. A new empty field is created.
  7. Enter the name for your custom metadata and press Enter.
  8. Click OK.
  9. The Archive Options dialog closes and the new metadata entry is saved.
  1. You have created custom metadata that are displayed in the Custom Metadata tab of the Archive Options dialog. Note that custom metadata are created case insensitive.
  2. The custom metadata can be used for your jobs by adding them as a Data Link field property in the Form Designer when creating or editing a form template, see Form Designer.
  3. When running a job which includes the form with custom metadata, you can enter a value for the metadata. Additionally, all previously entered values for the respective metadata are available as a dropdown list and sorted alphabetically.
  4. The custom metadata can be displayed as a column in Browse Results and can be used as additional filter criteria for searching the job results, see Filtering Results and Documents using Metadata and Filter Criteria.

Adding an Active Directory User

Domain Administrator

It is not possible to use the initial Active Directory domain administrator as a user for ZEN Data Storage. The administrator account for the Active Directory domain should only be used for the administration of the Active Directory itself.

When you are using ZEN core with ZEN Data Storage, you can add individual Active Directory users to your user management.

  1. ZEN core is open with active user management and you are signed in as administrator.
  2. You have ZEN Data Storage configured as your archive and have configured an Active Directory group, see Configuring a ZEN Data Storage Archive and Setting up the Login with Windows Credentials (Active Directory) respectively.
  3. During the installation of ZEN Data Storage, you have set the parameter Enable Active Directory to True on the Settings tab of the installer. For more information also refer to the installation guide for ZEN Data Storage.
  4. The ZEN Data Storage server must be part of the same Windows domain from where the software tries to login with its Windows credentials.
  1. Click Maintenance > User Management.
  2. The User and Group Management dialog opens.
  3. Click Users.
  4. The tab displays all currently configured users.
  5. Click .
  6. The New User dialog opens.
  7. For Type, select Active Directory.
  8. For Name, click .
  9. The Select User dialog opens.
  10. The fields for object type and location are filled with a default. To change them, click Object Types or Locations to open another dialog to select the respective Object Types or Locations.
  11. In the text field below, enter the name of the user you want to select. If you are not sure if your name is correct, click Check Names to open a dialog and select the suitable entry.
  12. Click OK.
  13. The name is displayed in the New User dialog.
  14. Click OK to close the New User dialog.
  15. The respective Active Directory is added to the list of users.
  16. Click OK to close the User and Group Management dialog.
  1. You have configured an Active Directory user. You can now assign this user to a group to grant him certain rights and privileges.

Browse Results with ZEN Data Storage

If you use ZEN Data Storage as your archive, you have the following additional functionalities in Browse Results:

Searching and Filtering in Browse Results

  1. You have ZEN Data Storage configured as your archive, see Configuring a ZEN Data Storage Archive.
  2. You are in Browse Results.
  1. In the drop down bellow the Search field, select which data should be displayed and filtered or searched.
  2. All: Displays all accessible data.
  3. My Data: Displays only my data.
  4. Shared With Me: Displays all files that are shared with me, including public documents.
  5. My Collections: Enables you to select one of your collections and displays only those documents that are part of the this collection.
  6. Collections Shared With Me: Enables you to select one of the collections that is shared with you and displays only those documents that are part of the this collection.
  7. The displayed documents are updated accordingly.
  8. To search results and documents with metadata, follow the general instruction Searching for Results and Documents with Metadata.
  9. To filter results and documents with Quick Filters, follow the general instruction Filtering Results and Documents using Quick Filters.
  10. To filter results and documents based on metadata and filter criteria, follow the general instruction Filtering Results and Documents using Metadata and Filter Criteria.

Adding Job Results to Collections in Browse Results

  1. ZEN Data Storage is configured as your archive, see Configuring a ZEN Data Storage Archive.
  2. You have created or access to at least one collection, see Creating a Collection for Data.
  3. You are in Browse Results.
  1. Select the job result you want to share and click . Alternatively, right click the job result and select Add to Collection.
  2. The Add to Collection dialog opens.
  3. In the table, activate the checkbox for every collection you want to share the data with.
  4. Click Save.
  1. You have shared your job result with other users/groups that are part of the collection. They can now see the results as well. The job result is also marked with in the Shared column of Browse Results.

Moving a Single Image from ZEN Data Storage to a Job Result

Note that this procedure is NOT possible when you have licenced and activated the GxP module.

  1. ZEN Data Storage is configured as your archive, see Configuring a ZEN Data Storage Archive.
  2. You are in Browse Results.
  1. Under Results, click External Images.
  2. The single images stored in the ZEN Data Storage archive are displayed under Result Documents.
  3. Under Result Documents, right-click the image you want to add to a job result and select Cut.
  4. Under Results, right-click the respective job result and select Paste.
  1. You have added a single image from the ZEN Data Storage archive to a particular job result.

Browse ZEN Data Storage Dialog

With this dialog you can open images saved in the ZEN Data Storage archive.

1

Stored Data
Displays the data available in ZEN Data Storage. For more information, see Stored Data Section.

2

Image Preview
Displays a preview of the currently selected image. For image documents that contain attachments like thumbnails, label or preview scans, a special control in the Image Control Section allows you to switch the view to those attachments.

3

Image Control Section
Controls for the image preview as well as the general controls to open the selected data or close the dialog. For more information, see Image Control Section.

Image Control Section

Parameter

Description

Z

Only available for z-stack images.
Selects which z-slice is displayed in the preview.

T

Only available for time series images.
Selects which time point is displayed in the preview.


Preview Image Control

Only visible, if the selected image document contains attachments (e.g. a thumbnail, label or preview scans) like for Axioscan images.

Selects which image is displayed in the preview area by using the arrows or clicking on the small circles. The small circles also display a tooltip indicating what kind of image it is (e.g. Label).

Metadata

Displays a section with metadata for the currently selected image. The metadata is synchronized with the displayed columns in the stored data section on the left.

OK

Opens the image and closes the dialog.

Cancel

Closes the dialog without opening a file.

Add to Collection Dialog

Parameter

Description

Search for Collections

Searches the collections according to the input.

Table

Displays all available collections.

–

Name

Displays the name of the collection.

Activated: The image is shared with the respective collection.

–

Shared

Shared collections are marked with .

Manage Collections

Opens the Manage Collections dialog to manage the collection.

Save

Saves the changes and closes the dialog.

Cancel

Closes the dialog without saving.

Manage Collections Dialog

Here you can manage collections for your data and specify their access.

Parameter

Description

Collection table

Displays the existing collections.

–

Collection Name

Displays the name of the collection.

–

Collection Owner

Displays the owner of the collection.

–

Access Granted To

Displays the groups/users that have access to this collection.

–


Add

Opens the Add Collection dialog to add a collection.

–


Delete

Deletes the selected collection.

–


Edit

Opens the Edit Collection dialog to edit the selected collection.

Add/Edit Collection Dialog

With this dialog you can add or edit a collection.

Parameter

Description

Collection Name

Sets the name for the collection.

Table

–

Name

Displays the group or user with access to this collection.

–

Access Level

Displays and sets the access level of the user/group with the dropdown. For a description of the available access levels, see Add Collection Access Dialog.

–


Add Access

Only available if you have started the application with active user management.
Opens the Add Collection Access dialog to add access for a user/group.

–


Remove Access

Only available if you have started the application with active user management.
Removes the access for the selected user/group from the collection and deletes it from the list.

OK

Adds the defined collection and closes the dialog.

Cancel

Closes the dialog without adding a collection.

Add Collection Access Dialog

With this dialog you can select a group/user who should have access to the collection. It is only available if you have started the application with active user management.

Parameter

Description

Groups

Displays all currently configured groups.

Users

Displays all currently configured users.

Access Level

Sets the access level for the currently selected group/user with the dropdown.

–

Read

Grants the group/user access to see, open or download a document.

–

Write

Grants the group/user access to modify a document.

–

Manage

Grants the group/user access to modify the access control list.

OK

Adds the selected group/user with the set access level to the collection and closes the dialog.

Cancel

Closes the dialog without adding any group/user to the collection.

Share and Manage Access Dialog

Parameter

Description

Enter Name

Searches all available users and groups according to the input and selects a user or group from a dropdown.

Access Rights dropdown

–

Read

Grants the group/user access to see, open and download a document.

–

Write

Grants the group/user access to modify a document.

–

Manage

Grants the group/user access to modify the access control list.

Add

Adds the selected user or group with the selected access right to the table.

User and Group table

Displays all users and groups added for sharing the file.

–

User or Group

Displays the name of the user or group.

–

Access Right

Displays the access right for the respective user or group and allows you to change the access.

–

Remove

Removes the entry by clicking the button.

Save

Shares the file with the users and groups defined here and closes the dialog.

Cancel

Closes the dialog without sharing the file.

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