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First Steps

Starting Software

Using pre-recorded Images

For using pre-recorded images when starting the software, in the menu Tools > Options > Startup, the Reload Last Used Documents checkbox must be activated.

  1. Microscope and hardware components are switched on and are ready for operation.
  2. ZEN software is installed on your computer.
  1. Double-click on the program icon on your desktop.
    Desktop shortcut showing round blue ZEN logo and label ZEN
  2. Alternatively click Start > Carl Zeiss Microscopy > ZEN.
  3. The software starts and displays a loading screen. After a while you see the smart profile selection screen. The application automatically detects your microscope based on your hardware, MTB configuration and licenses.
  4. Click on the ZEN profile you want to work with. Alternatively, click Go to Manual Profile Selection to manually select a specific software profile.
  5. The software starts. During the program start, the hardware settings are initialized.
  6. The Welcome Screen opens, see Welcome Screen.
    ZEN software screen titled Recently Opened with ZEN logo left and buttons Open File, Acquire New Image, Create Project
  7. To open a recently opened file, click on the respective entry.
  8. The Welcome Screen closes, and the file is opened in ZEN.
  9. To create a new ZEN Connect project, click Create Project.
  10. The New ZEN Connect Project dialog opens to create a new project.
  11. To acquire a completely new image, click Acquire New Image.
  12. The Welcome Screen closes and allows you to set up a new image acquisition experiment.
  13. To open an existing file, click Open File.
  14. A file browser opens.
  15. Select the file and click Open.
  16. The Welcome Screen and file browser close and the file is opened in ZEN.

Setting User Language

If the Select Automatically checkbox is activated, the software uses the language which is set in the system settings of your computer. This is the default setting.

  1. You have started the application.
  1. Go to Tools > Options.
  2. The Options dialog opens.
  3. Deactivate the Select Automatically checkbox to select the language manually.
  4. Select the user language from the Fixed Language drop-down list.
  5. A message appears to restart the application.
  6. Note that the availability of additional languages can differ between software versions.
  7. Click OK.
  8. The Options dialog closes.
  9. Exit and restart software.

Activating Show All Mode

  1. With the Show All mode deactivated (default setting), only the basic functions of tool windows or view options are shown.
  2. To show the advanced settings or expert functions of tool windows or view options, click Show All.

Configuring Microscope Components

This chapter refers to the manual configuration of the microscope components in ZEN lite. All microscope components definitions will be stored in the meta data of the acquired image.

  1. You have selected the Camera tab.
    ZEN 2 lite Camera tab UI showing Active Camera Axiocam 506 and panels: Microscope Components, Camera, Movie Recorder
  1. Click Microscope Components.
  2. The tool will open. Consider that the button Show all is activated.
    Microscope Components expanded showing Axio Imager, Objective 10x, Zoom 1.0x, Reflector BF, Camera Adapter 1.0x, Total 10x
  3. For Objective select that objective you will use for your acquisitions.
  4. Select all other microscope components you will use (i.e. Optovar, Reflector, etc.).
  1. You have successfully configured your microscope components.

If you have activated the Select automatically button in the status bar under Scaling (standard settings), the scaling will be calculated on the basis of your definitions. If you want to perform a manual scaling, read the chapter Creating Manual Scaling.

Acquiring Camera Image

This topic guides you through acquiring your first camera image with the software.

  1. You have connected and configured a microscope camera (i.e. Axiocam 305 color/mono) to your system.
  2. You have started the software.
  3. You have configured the microscope components (e.g. objective, camera adapter) and you are using the automatic or manual scaling.
  4. You are on the Camera (ZEN lite only) or Locate tab.
  5. You see your microscope camera available in the Active Camera section. If not, select the camera from the list.
    Locate tab panel with Find Focus, Set Exposure, Live, Snap buttons; Active Camera Test Camera #2 and blue control sections
  1. Position your sample on the microscope and adjust the microscope to see a focused image through the eyepieces.
  2. Adjust the tube slider of the microscope to divert the image to the camera (e.g. 50% camera and 50% eyepieces).
  3. Click Live.
  4. The Live Mode will be activated. In the Center Screen Area you will see the camera live image. By default, the live image shows a crosshair helping to navigate on the specimen. In the chapter Adjusting Live Image Settings you will learn how to optimize live image display.
    Workspace with Locate panel at left and live camera view showing blue crosshair and concentric bright rings at lower left
  5. Click Set Exposure.
  6. The exposure time will be automatically determined and set.
  7. Click Snap.
  1. You successfully acquired your first image. Save the image in the file system via the File menu > Save as.

If you do not see a focused image, please refocus the specimen on the microscope. You may activate the focus bar as an additional aid. Right-click in the Center Screen Area to open the context menu. Select the entry Focus Bar. The focus bar will be shown.

Adding Annotations

Annotations are the generic term for all the graphics (e.g. rectangle, arrow, scale), measurements, texts or other metadata (e.g. recording time) that you can add to your image.

  1. You have loaded an image.
  1. Select Graphics.
    Graphics panel showing Annotations/Measurements list with 'Scale Bar' ID 1 and 'Arrow' ID 2, plus X Y W H dimension fields.
  2. Click Short horizontal black scale bar with white vertical tick marks Scale Bar.
  3. The scale bar will appear directly in the image.
  4. To edit an annotation (e.g. color, line width) you can right-click on the annotation in the image and select Format Graphical Elements from the context menu.
  5. Click Black rectangle containing a white diagonal arrow pointing up and to the right Draw Arrow.
  6. You can now draw an arrow into the image.

Adjusting Live Image Settings

  1. You have started the Live mode via the Live button and see the camera’s live image in the Center Screen Area.
  2. Under the image area you see the general view options on Dimensions tab, Graphics tab and Display tab.
  1. In the Dimensions tab activate the Range Indicator checkbox. This will mark overexposed (too bright) areas in the live image in red and underexposed (too dark) areas in blue.
  2. On the Display tab click 0.45. The display curve will be adapted to a gamma value of 0.45. This will set the optimum color presentation. If you do not see this button, activate the Show all mode.
  3. Move the controls under the display curve left and right in order to directly adjust the values for Contrast (Black) , Gamma , and Brightness (White) in the live image.

With the settings above the display of the live image will be adapted. These settings will also be transferred to your acquired image. This will not change the camera settings.

Creating Manual Scaling

NOTICE

Blue circular sign with a centered white exclamation mark

Risk of camera mismatch on dual-camera systems

Changing the scaling on a dual-camera system can cause a mismatch between the two cameras, which results in a shift between the images of the individual cameras.

  1. Scaling should not be changed for dual-camera systems of the Lattice SIM family (Lattice SIM 3, Lattice SIM 5, ELYRA 7 with Lattice SIM) as this will affect camera synchronization. Contact your local Service Support if the scaling was changed.

Availability of created scaling

If you create a manual scaling, this data is by default user specific, i.e. the scaling is not globally available for all users of the PC. The scaling is saved in C:\Users\Username\Documents\Carl Zeiss\ZEN\Documents\Scalings.

  1. If you create a scaling that should be available to all users on the PC, you have to place the file into C:\Program Files\Carl Zeiss\ZEN 2\ZEN 2 (blue edition)\ZEN\en\Documents\Scalings.
  1. You have an object micrometer oriented horizontally on the microscope stage.
  2. You have defined all your microscope settings correctly with the Microscope Control tool, or the Microscope Components tool (ZEN lite only). In our example we use an objective with a 10x magnification.
  1. Acquire an image of the scale in your object micrometer using the objective to be scaled manually, see also Acquiring Camera Image.
  2. The image is displayed in ZEN.
  3. In the bottom status bar click the small arrow in the Scaling section.
  4. The Scaling dialog opens.
  5. In the dialog, deactivate Select Automatically.
  6. In the Create new scaling section, click Interactive Calibration....
  7. The calibration window opens in the image area.
  8. Click Single Reference Line (selected by default) and activate Automatic Line Detection.
  9. Draw in the reference line along the scale.
  10. Enter the true distance between both scale lines in the calibration window. In our example this is 500 micrometers.
  11. Enter a name for the scaling (i.e. Obj 10x) and click Save Scaling.
  1. You performed a manual scaling for your objective. Repeat this sequence for all objectives you need a manual scaling for. Always ensure that you select the correct objective in the Microscope Control tool (or the Microscope Components tool in ZEN lite), as well as the matching performed scaling in the status bar.

  1. The function Automatic Line Detection calculates the theoretical maximum of the reference line‘s both end points to the closest scale lines in the image. Thus, the distance will be calculated with sub-pixel accuracy.
  2. If you have defined a manual scaling for an objective and activate the checkbox Select Automatically, the software will use the measured scaling instead of the theoretic one. You will recognize this via the label Measured instead of Theoretic beside the pixel size.

Closing Software

  1. Click File > Exit. Alternatively, you can use the shortcut Alt+F4 or click Close in the program bar.

If you have not saved your files, the Save Documents dialog opens before the software closes. Select the files you want to save or the files you want to discard. If you are connected to ZEN Data Storage, you can also select to save and upload the files to the server.

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