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ZEN Connect

This module enables you to work with images from multiple sources: zoom in from the full macroscopic view of your sample down to nanoscale details. ZEN Connect is the efficient way to analyze and correlate images from multiple sources. It works with images from SEM, FIB-SEM, X-ray, light microscopes and any optical images, e.g. from your digital camera. Its sample-centric workspace lets you build a seamless multimodal, multiscale picture of your sample. Use it to guide further investigations and target additional acquisitions.

Understand your sample fully. ZEN Connect employs a novel graphical user interface concept that makes it easy to investigate all your samples. Design a workflow tailored precisely to the complexity of your experiment, no matter whether it’s a simple one-step task or a compound experiment. A sophisticated workflow environment guides you all the way from the setup for automated acquisition to post processing and customized exports, and right on through to analysis.

ZEN Connect lets you manage, align, and export images in correlation with images from other sources.

Licensing and Functionalities of ZEN Connect

For working with ZEN Connect projects or images, you might need a separate license file. The basic ZEN Connect functionality is available for all versions. This functionality includes:

  • ZEN Connect correlative workspace, including the display of images with their context.
  • Manual alignment of captured images.
  • Auto-registration of images using stage coordinates.
  • Image acquisition into the project.
  • Import of images into the correlative workspace.
  • Interactive control of stage movement from the correlative workspace.

Licensed Functionality

If you have the necessary license, additional functionality is available.

  • Import of Third-party images (Bio-Formats).
  • Export of a ZEN Connect view as a single image.
  • Movie export as fly-through video.
  • S&F calibration.
  • Definition of regions of interest in the correlative workspace.
  • Retrieval of defined regions of interest.

Loading an Image and Adding it to the ZEN Connect Project

You can add simple images, such as camera images or more complex images, such as a light microscope image with overlays, into your ZEN Connect project.

You can use an imported image as a backdrop to navigate the region. You can correlate imported images with sample holder marks, e.g. fiducials or other images through the alignment process. The imported image is displayed according to its position in the Graphical view along with any other image in the project. ZEN Connect saves the results to the archive. You can restore results from the archive.

Any time you open an image with the Load Image or the Load image from ZEN Data Storage tool, it is added to the ZEN Connect project.

Open the ZEN Connect workbench before performing a S&F calibration.

  1. You have opened a ZEN Connect project.
  1. On the Load File workbench, add the Load Image tool or the Load image from ZEN Data Storage tool if you want to add an image from the Data Storage.
  2. Click on the browse button to select an image in the respective tool.
  3. In case of the Load Image tool, the usual Windows explorer opens to select the image. For the Load image from ZEN Data Storage tool, the Browse ZEN Data Storage dialog opens. It displays all images in the data storage and you can search the images and also sort the list of images, e.g. by name, size, etc.
  4. Click on Open or OK to confirm your selected image.
  5. Click on Apply.
  6. The image is loaded and displayed in the Image view. It is also displayed in the Documents Area on the right.
  7. In the Project view, the image is displayed in the tree, subordinated to Imported Data unless it contains session information.
  8. If Shuttle & Find-calibration is available for the image, the image is placed in the Image view according to the Shuttle & Find stage position. Take care that you select the correct sample holder when importing an S&F-calibrated image. The correct sample holder is the same sample holder that was used during acquisition. If no Shuttle & Find data is available, the image is displayed in the Image view according to its stage coordinates.

Non Image Data

In Zen Connect, it is also possible to import (via drag & drop) non image data into your project, have a visual representation (marker) of it in your image area, and align the position of the data marker with respect to the images in the project. The data is listed under Non-Image Data in the tree of the ZEN Connect tool and represented by this marker in the image area:

Per default, the marker for this non image data is toggled invisible. To toggle data visible and invisible, see Toggling the Visibility of Data.

EDS spectral images

EDS spectral images contain specific metadata that determine their handling in a ZEN Connect project. If you add EDS spectral images to a ZEN Connect project, they are added as non image data because they have the special document subtype metadata ChartImageDocument. In this case the marker is visible by default. EDS spectral images are also placed at a certain position in the ZEN Connect project, determined by the SpatialRelations and Scaling metadata information.

Import and Export

Importing a ZEN Connect Project

You can load any of your ZEN Connect projects to continue with your work. There are limitations when you work with ZEISS Atlas 5 projects.

You can import a ZEN Connect project, even if an existing ZEN Connect project is loaded.

  1. You have added the Load File workbench.
  1. Add the Import ZEN Connect Project tool.
  2. In the Filename field, navigate to the .a5proj project file and click Open.
  3. A confirmation message is displayed. The currently opened ZEN Connect project will be replaced by the one to be opened. Note that all existing alignments and modifications will be lost, because your ZEN Connect project will be overwritten.
  4. To continue, click Yes. To cancel the import, click No.
  1. The project is imported and is loaded to the ZEN Connect tool. All images which are contained in the project are also loaded into ZEN core.
  2. If a ZEN Connect project was added at the import time of a second project, the first project is discarded. Any images contained in this project will be integrated into the loaded project and will be present in the ZEN Connect tree view.
  3. The newly imported second ZEN Connect project is displayed in the Image view.

Importing an Image into a Session

  1. You have opened a ZEN Connect project.
  2. You have added the Import Images into Session tool to the Load File workbench.
  1. On the Load File workbench, in the Import Images into Session tool, click on the browse button for File Names.
  2. A file browser opens.
  3. In the file browser, select the image(s) you want to import and click on Open.
  4. For Correlative Session, select the session of the ZEN Connect project where you want to import the image.
  5. If you want the image(s) to serve as background image, activate the checkbox Background Image.
  6. Click on Apply.
  1. The images are imported into the selected session of the ZEN Connect project.

Exporting a ZEN Connect Project as a Video

You can export your ZEN Connect project, an individual session, or an image from the project as a video.

  1. You have opened the ZEN Connect Video Renderer Workbench with the Video Export Renderer Tool.
  2. You have loaded a ZEN Connect project.
  3. In the loaded ZEN Connect project, you have activated and deactivated the respective areas of interest.
  1. In the Video Export tool, select the image or the session you want to export in the Project View.
  2. Choose your key frames by positioning the export area in the Image View and add them to the list of key frames by clicking on Add current view as key frame.
  3. Make your settings and click on Start Export.
  4. A file browser opens.
  5. In the file browser, name your video file and select a folder where your video should be exported to.
  6. Click on Save.
  1. Your video is now exported to the selected location. A progress bar indicates the status of the export.

Toggling the Display of Region Caption and Frame

For a better overview, you can toggle the display of the image name and of the frame of images in the Image view of your ZEN Connect project.

  1. You have loaded a ZEN Connect project.
  1. To toggle the region caption, in the button bar above the Image view, click Toggle Region Captions
    .
  1. The region caption of the images are displayed or hidden.

Panning & Zooming

  1. You have loaded a ZEN Connect project and activated the alignment process.
  1. In the button bar above the Image view, click .
  1. With your mouse, or alternatively, with the pressed Ctrl key, you can pan and zoom in and out in the Image view.

Using Regions of Interest in ZEN Connect

ZEN Connect offers the functionality to draw and delete regions of interest (ROI) in a project. The regions are shown in the project and they are saved and loaded together with the project.

Deleting a Region of Interest in ZEN Connect

  1. You have loaded a ZEN Connect project with Regions of Interest.
  2. You have added the ROI List tool to the ZEN Connect workbench.
  1. In the Image View or the ROI List tool, right-click the Region of Interest and select Delete. Alternatively, select the region in the ROI List tool and click .
  1. The selected region is deleted.

Renaming a Region of Interest in ZEN Connect

  1. You have loaded a ZEN Connect project with Regions of Interest.
  2. You have added the ROI List tool to the ZEN Connect workbench.
  1. In the ROI List tool, right-click the region in the ROI List tool and select Rename. Alternatively, select the region in the ROI List tool and click .
  2. Type the new name and press Enter.
  1. You have successfully renamed the Region of Interest.

Zooming to a Region of Interest in ZEN Connect

  1. You have loaded a ZEN Connect project with Regions of Interest.
  2. You have added the ROI List tool to the ZEN Connect workbench.
  1. In the Image View or the ROI List tool, right-click the Region of Interest and select Zoom To.
  1. The view zooms to the selected region.

Moving the Stage to a Region of Interest in ZEN Connect

  1. You have loaded a ZEN Connect project with regions of interest.
  2. You have added the ROI List tool to the ZEN Connect workbench.
  1. In the Image View or the ROI List tool, double click on an entry of a region. Alternatively, select an entry and click , or right click the entry and select Move to.
  1. The stage moves to the center of the respective region.

Editing Measurements in a ZEN Connect Project

  1. You have opened a ZEN Connect project and added a measurement, see Adding Measurements to a ZEN Connect Project.
  1. In the button bar above the Image view, click .
  2. You are now in edit mode.
  3. To resize measurements, click on the end points of a measurement to drag and drop them. In case of an area measurement, you cannot rescale the contour.
  4. The measurement values are updated instantly.
  5. To move a measurement, drag and drop the respective measurement in the Image view.
  6. To change the Name of a measurement, in the Measurement tool, double click the current name in the table.
  7. The name in the field gets editable.
  8. Enter the desired name and press Enter.
  9. The measurement is renamed.
  10. To toggle the visibility of a measurement, click for the respective entry in the list.
  11. The measurement is toggled (in-)visible.
  12. To delete a measurement, select the measurement in the list and click . Alternatively, select the measurement and press Del.
  13. The measurement is deleted.

Using the Global-Z slider

In ZEN Connect you can use a mode called Global-Z if you have a project with at least one z-stack. In this mode, you can change the displayed z plane of all z-stacks in the project with only one slider, the Global-Z slider. The range of the slider is comprised of the z values of all stacks in the project. The displayed slice for each stack is always the one closest to the value set by the Global-Z slider, as long as the value is within the boundaries of the entire stack. When you use the Global-Z slider and are beyond the range of a certain z-stack, only a frame is displayed to show where the stack is positioned.
Note: If you have selected a particular z-stack, the Global-Z and Z-Position sliders are interdependent. Changing the value with one slider updates the other slider as well.

  1. You have one or several z-stacks in the ZEN Connect project.
  1. Activate the Global-Z checkbox on the Dimensions tab.
  2. Use the slider or the input field to set a global value for z.
  1. All the slices closest to the set value are displayed for all z-stacks. Z-stacks which are out of range are illustrated by an empty frame.

Creating a Snapshot of the Workspace

  1. You have opened a ZEN Connect project.
  1. Prepare the view according to your needs, e.g. zoom to a desired area, or hide images that should not be visible in the snapshot.
  2. In the button bar above the Image View, click .
  1. A snapshot of the current view in the workspace is created. In Free Mode, the snapshot image is added to the gallery on the right. In Job Mode, the snapshot image is added to the job result.

Workbenches/Tasks

ZEN Connect Workbench

This workbench enables you to manage your data in a project structure tree combined with the viewer. Additionally, you can draw regions of interest into your project and add measurements to the project. Before loading any images, you need to open the ZEN Connect project to display images correlatively. Only within a ZEN Connect project, you can use all ZEN Connect functionalities. You can open only one ZEN Connect project at a time.

Open first the ZEN Connect workbench before performing a S&F calibration.

ZEN Connect Renderer Workbench

This workbench enables you to configure the parameters of the image you want to export to the Documents Area, see also ZEN Connect Renderer Tool and Exporting Images from a ZEN Connect Project.

ZEN Connect Video Renderer Workbench

This workbench enables you to configure the parameter to export your ZEN Connect project or an individual session or image as a video, see Video Export Renderer Tool and Exporting a ZEN Connect Project as a Video.

ZEN Connect Alignment Workbench

This workbench enables you to align the images of your ZEN Connect project with various operations, see Aligning Images with ZEN Connect Alignment Workbench.

Tools

Import Bioformats Image Tool

This tool enables you to use Bioformats as an integrated library for reading and writing image file formats. It is capable of parsing both pixels and metadata for a large number of formats. It achieves this by converting proprietary microscopy data into an open standard called the OME data model. With Bioformats, you can read proprietary formats and convert them. For example, it is possible to load simple images you can import, such as camera images or more complex images, such as a light microscope image with overlays, to ZEN core.

Parameter

Description

File Name

The path and filename of the table to be loaded

Click on to open the file browser and select the desired file.

For more information, see ZEN Connect.

Import ZEN Connect Project Tool

Parameter

Description

Filename

The path and filename of the project to be loaded.

Click on to open the file browser and select the desired project.

For more information, see Importing a ZEN Connect Project.

For more information, see ZEN Connect Module.

ZEN Connect Tool

Within a ZEN Connect project, you manage your data in a project structure tree combined with the viewer.

Parameter

Description

Project / Layers

The ZEN Connect tool provides a Layers view and a Tree view of image data that you have acquired for the ZEN Connect project. Every image that you have acquired for the ZEN Connect project is listed. As you acquire or import more image data, the new image data will be listed in the views.

Change Opacity

Adjusts the opacity of detected objects.

Align

Activates the alignment process for the selected data, see Activating the Alignment Process.

Align System

Activates the alignment process for the current microscope session, see Activating the Alignment Process.

New Session

Creates a new session.


Context Menu

Displays the context menu for ZEN Connect, see Context Menu.

For more information, see ZEN Connect.

ZEN Connect Renderer Tool

Parameter

Description

Tree View tool

For more information, see ZEN Connect Tool.

Color Style

Controls the color format of the export. Select RGB (color) or Intensity (black and white).

–

RGB Color

Based on the RGB (Red-Green-Blue) color model. Be aware that color files may be up to three times as large as intensity files.

–

Intensity

Images are saved in 8-bit format.

Export Format

Selects the format for the exported file.

–

CZI image (Single Channel)

Exports the image as a Carl Zeiss Image file. CZI files are not limited in size. The images are exported in a single channel CZI.

–

CZI image (Multi-Channel)

Exports the image as a Carl Zeiss Image file. CZI files are not limited in size. The images are exported as a multi-channel CZI.

Note that the resulting image might look different when reopened in ZEN than it does in ZEN Connect.

Burn in Data Bar

Activated: Burns the currently configured data bar into the exported image.

Rotation

Rotates the view to the desired orientation. Drag the slider, or in the text field, type in the value.

Pixel Size

Sets the pixel size of the export. The smaller the pixel size, the more disk space your export will take. The options Low, Medium and High only have an effect, if several images are exported as a single image.

–

Smallest

Sets pixel size of the finest image, i.e. the smallest pixel size.

–

Medium

Calculates and sets the pixel size to the log average of finest and coarsest image (i.e. 10^(0.5*(log(fine)+log(coarse)).

–

Largest

Sets pixel size of the coarsest image, i.e. the largest pixel size.

–

Custom

Sets a custom pixel size which can be entered in the input field.

Width (px)

Sets the width to directly alter the export pixel count and export area (the pixel size is unchanged).

Height (px)

Sets the height to directly alter the export pixel count and export area (the pixel size is unchanged).

Width (µm)

Displays the full width of the export area in µm.

Height (µm)

Displays the full height of the export area in µm.

Approx. Data Size

Displays an approximation for the data size of the exported image. The actual file size after export may be less, depending on compression of some file formats.

For more information, see Exporting Images from a ZEN Connect Project.

Export ZEN Connect Project (for ZEN) Tool

This tool enables you to export a ZEN Connect project file to be used in ZEN.

Parameter

Description

Destination Folder

Displays the location on the disk where you want the project file to be saved.

Click on to open the file browser and select the desired folder.

Project Name

Enter the project file name with the format <name>.aproj

For more information, see

ROI List Tool

In this tool, you can see a list of your regions of interest (ROI) and edit or rename them.

Parameter

Description


Add ROI

Adds a region into the Image View.

List of ROI

Here you see a list of all ROI in your ZEN Connect project.
A double click on an entry moves the stage to the center of the respective ROI.


Delete

Deletes the currently selected region of interest.


Rename

Allows you to rename the currently selected region of interest.


Move to

Moves the stage to the center of the currently selected region.

Import Images into Session Tool

This tool enables you to import an image directly into a ZEN Connect session (e.g. as a background image).

Parameter

Description

File Names

Selects and displays the files which are imported.

Correlative Session

Selects the session where the image(s) should be imported.

Background Image

Activated: Imports the image(s) as background image.

ZEN Connect - Alignment Tool

Parameter

Description

Apply

Applies the changes for alignment.

Discard

Discards all changes for alignment.

Project/Layers

The tool provides a Layers view and a Project tree view of image data that you have in your ZEN Connect project.

Undo

Reverses the last alignment action(s).

Redo

Restores the last undone action(s).

Translate Tool

Parameter

Description

Step Size

Sets the step size for the translation in x and y.

X-Direction

Sets the translation in x direction. The reset button resets the value to the default.

Y-Direction

Sets the translation in y direction. The reset button resets the value to the default.

Scale Tool

Parameter

Description

X-Dimension

Sets the scaling factor in x direction. The reset button resets the value to the default.

Y-Dimension

Sets the scaling factor in y direction. The reset button resets the value to the default.

Flip/Mirror Tool

Parameter

Description


Horizontally

Mirrors the image in horizontal direction.


Vertically

Mirrors the image in the vertical direction.

Shear Tool

Parameter

Description

Enable

Activated: Activates the shearing mode and displays the three shearing pins in the image.

Reset Shearing Pins

Resets the pins to the default location.

Field of View Width Dialog

Parameter

Description

FOV Width

Displays the current width of the field of view and allows you to enter a value.

OK

Sets the width to the entered value.

Cancel

Closes the dialog box without setting the field of view.

Context Menu

In a ZEN Connect project, from the context menu of the image, in the Tree view or with the Context menu button, you can perform several functionalities.

Image

Tree view

Context Menu
button

Zoom to
For more information, see Zooming

X

X

X

Zoom to 100%
For more information, see Zooming

X

X

X

Show/Hide
For more information, see Moving or Hiding Images

X

X

X

Remove Data
For more information, see Removing Data

X

X

X

Rename Data
For more information, see Renaming Data

X

X

X

Align Data
For more information, see Activating the Alignment Process

X

X

X

New Session
For more information, see Starting a New Session

−

−

X

Clear Alignment
For more information, see Clear Alignment

−

−

X

Zoom to Extent
For more information, see Zooming

−

−

X

Zooming

You have different options to zoom images in ZEN Connect. You can zoom images in and out of a field of view (FOV). As a prerequisite, a ZEN Connect project is loaded.

Zooming to

  1. In the Project tree view, select an image, right-click > Zoom to. Alternatively, click Context menu

    and select Zoom to. The function is also available from the context menu of the image in the Image view.
  1. The image is centered in the view space of the Image view.

Zooming to 100%

  1. In the Project tree view, select an image, right-click > Zoom to 100%. Alternatively, click Context menu

    and select Zoom to 100%. The function is also available from the context menu of the image in the Image view.
  1. The image is zoomed in the view space of the Image view to 100%.

Zooming to extent

  1. In the button bar above the Image view, click Zoom to Extent
    .
    Alternatively, click Context menu

    and click Zoom to Extent.
  1. In the Image view, the sample holder is centered. All images in the ZEN Connect project are displayed.

Moving or Hiding Images

In the Layers view, you can move images over and under other images, or hide them completely.

  1. You have loaded a Connect project with at least two images.
  1. To change the image order, in the Layers view, move the image by dragging it up or down.
  2. In the Image view, the changed order is immediately visible.
  3. To hide the image from the Connect project, in the Layers view, activate or deactivate the image by clicking the Eye icon on the right of the image name. Alternatively, in the Project view, right-click Show/Hide.
  1. The results of your changes are displayed immediately in the Image view.

Removing Data

You can remove images from your ZEN Connect project. The data files will not be deleted from your disk.

  1. In the Project tree view, select an image, right-click Remove Data. Alternatively, click Context menu

    and select Remove Data. The function is also available from the context menu of the image in the Image view.
  1. The selected image is removed from the ZEN Connect project.

Renaming Data

  1. You have loaded a ZEN Connect project.
  1. In the Project view, in the Layer view, or in the Image view, select an image to rename, and choose Rename Data. Alternatively, click the Context Menu

    and choose Rename Data or press the F2.
  2. The corresponding image name is activated in the Project or Layer view.
  3. Rename the image.
  1. You have renamed the image. It is updated either in the Layer view or in the Project view respectively, as well as in the Image view.

Starting a New Session

To organize your work or if you have moved your sample, you can start a new session within your ZEN Connect project any time.

  1. You have loaded a ZEN Connectproject.
  1. In ZEN Connect in the Project or Layers view, click the Context menu
    ,
    and click New Session.
  1. A new session is activated. As soon as you acquire a new image, a new session node is created, and the new image will be subordinated. Note that you have to perform again an alignment of the newly created session to the old data.

Clear Alignment

  1. You have activated the alignment process and have aligned images.
  1. Click Context menu > Clear Alignment.
  2. The session is restored to its un-aligned state.

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