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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.
  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.
  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.

User Interface

The software user interface is divided into three main areas.

User interface

1

Left Tool Area
With the tabs you can access all the main tools for microscope control (Locate tab), acquisition (Acquisition tab), image processing (Processing tab), image analysis (Analysis tab), and applications (Applications tab).

2

Center Screen Area
This area is used to display your images with several image views available.

3

Right Tool Area
Here you find the Images and Documents tool and hardware controls e.g. for stage and focus. Additionally, system specific tools are available here (e.g. Definite Focus and ZEN Connect controls).

Title Bar

Parameter

Description

Help icon

Activates the "drag & drop“ help function. A question mark appears beside the mouse pointer. Move the mouse pointer to a place in the software where you need help. Left-click on the desired location. The online help opens.

Minimize

Minimizes the program window.

Maximize Over 2 Screens

Maximizes the program window across 2 screens if available. This option is only possible if you are working with 2 screens with the same resolution.

Maximize

Maximizes the program window to the main screen.

Restore Down

Reduces the program window to any selected size.

Close

Closes the program window.

Workspace Configuration

Workspace Configuration
Workspace Configuration

Here you find settings to adjust your workspace. Select Light/Dark Design of the user interface or enlarge the screen with Workspace Zoom slider. You can also save and reload all personal settings in a workspace configuration, the name must have at least one character. With the Dock all tool windows button in the top right corner you can easily dock all undocked tools with one click.

Tool Bar

Tool Bar
Tool Bar

Here you gain quick access to important functions, e.g. saving or opening files. Further right you find more workspace settings, e.g. Design and Workspace selection. Read how to customize the Tool bar in chapter Customizing Toolbar.

Left Tool Area

This area contains the main tabs for microscope and camera settings (Locate tab), image acquisition (Acquisition tab), image processing (Processing tab), and image analysis (Analysis tab). The main tabs are organized in an order which follows the typical workflow of experiments in bioscience or material science.

Left Tool Area
Left Tool Area

Right Tool Area

This area contains mainly the tools for image and file handling (e.g. Image Gallery) and hardware control (e.g. Stage/Focus tool). Depending on your system configuration, other tools can be available. The tools are described in the corresponding chapters of the online help.

Document Bar

Here you see tabs of all open documents. Click on a tab to view the image/document. On the right end of document bar, you find buttons to switch view mode from Exposé to Splitter mode and further view options (View menu).

An asterisk (*) next to an image/document title indicates that changes have been made to this document which are not yet saved. Save your pictures/documents from time to time in order to avoid data loss.

Parameter

Description


Exposé Mode

Opens the exposé view mode.


Splitter Mode

Opens the splitter view mode.


Options

Displays the options of the view menu.

Status Bar

The status bar shows important information on the system status:

Parameter

Description

Scaling

Displays which lateral scaling is currently being used. If you click on the arrow, the Scaling dialog will be opened. There you have access to advanced scaling settings and the scaling wizard.

System Information

Always shows the latest, currently active process that the system is performing.

Progress bar

Displays the progress of the currently active process. Each new process added supersedes older still active processes. If you click on the arrow button, a window opens with a list of all processes in chronological order. You can stop a process that is running using the Stop button.

Performance indicators

In this group you will see an overview of the performance of individual computer components:

  • Free RAM indicates how much physical memory is still available.
  • Free HD indicates how much space is still available on the hard drive onto which the next image is to be acquired (see Tools > Options > Saving).
  • CPU indicates the usage of the Central Processing Unit.
  • The small status bar provides an overall assessment of the system usage.
  • GPU indicates the usage of the Graphics Processing Unit by ZEN and ZEN related services. It is also visualized by a small status bar on its right.
    Note: This GPU indicator is only visible if you your computer has Microsoft Windows 10 version 1709 or higher.

Info: Double-clicking in the Performance Indicators area opens the Windows Task Manager. In case you do not have sufficient Windows access rights to open the Task Manager from here, a message is displayed.

Frame Rate

Indicates the current frame rate in frames per second (fps) used by the active camera for producing new images. Please note in most cases that at speeds greater than 100 frames per second, this value cannot always be accurately determined.

Pixel Value

Displays the gray value to the image at the current position of the mouse pointer. In the case of multichannel images, the gray value/channel is displayed for up to 4 channels.

Position

Displays the X/Y position (in pixel coordinates) of the mouse pointer in the image.

Information (i)

If you click on the icon, a window opens with System Messages.

Storage Folder

Displays the location where new images are automatically saved. This path can be changed in the menu Tools > Options > Saving.

Optional
Status: Airyscan Detector Alignment

If you click on the arrow the Alignment Tool window opens.

User

Shows the Windows user name of the logged in user.

Time

Shows the current Windows system time.

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.
  1. Click Microscope Components.
  2. The tool will open. Consider that the button Show all is activated.
  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.
  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.
  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.
  2. Click 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 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

notice

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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