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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. The Correlative Workspace (CWS) is the efficient way to analyze and correlate images from multiple sources. You can manage, correct, and align these images in 2D as well as in 3D. 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.

The module 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 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.

Licensing and Functionalities of ZEN Connect

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

  • ZEN Connect correlative workspace, including the display of images with their relations.
  • 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 for 2D and 3D work is available.

Additional 2D functionality:

  • Export of merged project view as image.
  • Movie export as fly-through videos.
  • Import of third-party microscopy images powered by Bio-Formats.
  • SerialEM export.
  • Adding of measurements to the ZEN Connect project.
  • Two dedicated wizards to support manual alignment and 2D point alignment.
  • S&F calibration, see also Shuttle & Find.
  • Definition of regions of interest in the correlative workspace.
  • Retrieval of defined regions of interest.

Additional 3D functionality:

  • Control of the displayed z-position in ZEN Connect.
  • Alignment of images in z-dimension.
  • Viewing of two 3D stacks (provided you have the necessary licenses).
  • Alignment of two 3D stacks in x, y and z (provided you have the necessary licenses).
  • Import FIB stacks.
  • Alignment wizard for 3D Point alignment.

User Interface

1

Image View
Area where you interact with images. Here, for example, you can select images and align them.
ZEN Connect provides its own 3D viewer. For more information on the user interface of this 3D viewer, see ZEN Connect 3D View. You can use the view tabs on the left side of the Image View to switch between the two viewers.

2

ZEN Connect Tool
Area where you manage your projects and contained images. For more information, see ZEN Connect Tool.

3

Button bar below Image View
Functionalities to pan, zoom, select a region, toggle region captions or view modes, and select a carrier/holder. For more information, see Button Bar below Image View.

4

Regions Tool
Displays a list of Regions of Interest which are drawn into a ZEN Connect project. For more information, see Regions Tool.

5

View Options
Area for general view options of the Dimensions Tab and specific view options on the Measurement Tab and Alignment Tab. The Alignment tab is only visible when you have entered the mode to align images (see also Activating the Alignment Process).

ZEN Connect 3D View

The 3D view for ZEN Connect allows you to see and align two 3D volumes from your project. The viewer and functionality is based on the Tomo3D view, see Tomo3D View. For this functionality, you also need the license for the 3D Toolkit.

1

Image Views
Area where you interact with the image views, set the cut lines with the mouse and align the adjustable image in the 2D views. You can display up to four different views, including a 3D and different 2D views. The number of image views can be set in the Ortho Display tab, the type can be set by the dropdown in the top left corner of each view. For further information on the functionality, see Tomo3D View.

2

ZEN Connect Tool
The standard ZEN Connect tool where you manage your projects and contained images, see ZEN Connect Tool.

3

View Options
Area for general and the Tomo3D specific view options as well as the dedicated Alignment and Connect 3D tabs, see Alignment Tab ZEN Connect 3D and Connect 3D Tab.

Alignment Tab ZEN Connect 3D

Parameter

Description

Mirror

-


Flip Horizontally

Mirrors the image horizontally.

-


Flip Vertically

Mirrors the image vertically.

Pre-Align

In case the two volumes are some distance apart, Pre-Align helps to bring the volumes in close proximity to each other by centering the adjustable volume on the fixed reference volume.

Recalculate

Recalculates the bounding box around the two volumes. A bounding box is displayed surrounding both images. After an alignment of the images, the bounding box can be too large (enclosing empty space) or too small (not surrounding both images anymore) and can be recalculated.

Reset

Resets the alignment as it was when you started this alignment operation.

Apply

Applies the alignment to the ZEN Connect project.

Opening the Correlative Workspace

  1. Start the software. For more information, see Starting Software.
  1. The software opens and ZEN Connect is available.

Note that before working with ZEN Connect, you need to create a ZEN Connect project. For more information, see Creating a ZEN Connect Project.

Opening Images in the ZEN Connect 3D View

In the ZEN Connect 3D view you can display two z-stacks as 3D volumes and interact with them. Note that more than two volumes cannot be displayed in this 3D view.

  1. You have opened a ZEN Connect project with at least two z-stacks.
  1. In the ZEN Connect tool or the Image View, select one or a maximum of two z-stacks while pressing Ctrl.
  2. Right click one of the selected images in the ZEN Connect tool and select Show in 3D. Alternatively, click and select Show in 3D.
  3. If you want to open the volumes directly in 3D alignment mode, go to the ZEN Connect tool and select Align Two images in 3D for the Alignment button. Note: For the alignment mode two volumes need to be selected. The image you selected second is then automatically preset for alignment.
  1. The ZEN Connect 3D view opens and displays the selected z-stacks as 3D volumes. The images displayed in the 3D view are marked with an icon in the tree view of the ZEN Connect tool.

Non Image Data

In Zen Connect, it is also possible to import 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 the marker in the image area. Per default, the marker for this non image data is toggled invisible. To toggle data visible and invisible, see also Moving or Hiding Images.

Project and Image Management

Creating a ZEN Connect Project

Within a ZEN Connect project, in the ZEN Connect tree view, you manage your data in a project structure tree combined with the viewer. Before acquiring or importing any images, you need to create the ZEN Connect project. Only within a ZEN Connect project, you can use all ZEN Connect functionality.

You can open only one ZEN Connect project at a time.

  1. You have set up the sample on the microscope.
  1. In the ZEN Connect tool, click Create.
  2. The New Document Dialog dialog opens.
  3. In the New ZEN Connect Project Setup area, select the Project Path where you want to store the ZEN Connect project file.
  4. Select the relevant data to configure the ZEN Connect project. If you select the holder/carrier now, you can change it later. Note: If you change the holder/carrier after a S&F calibration, the S&F calibration needs to be redone.
  5. Click on OK.
  6. The ZEN Connect project is created with the project file name <Projectname>.a5proj. Note that all new images are saved in the subordinated folder <Projectname_data>. You can always check the path on the Acquisition tab in the Auto Save tool. Alternatively, right- click on the project container in the Center Screen Area and select Open Containing Folder.
  7. In the Image View, the sample holder is displayed.
  8. In the ZEN Connect tool, the empty ZEN Connect project is displayed. Here, the structure of the ZEN Connect project will be displayed as soon as you acquire or import images. In the folder on your computer, the ZEN Connect project file <CWS project name>.a5proj is generated. A <ZEN Connect project name>.a5lock is generated to prevent more than one user to work on the project at the same time. It is generated any time you load a ZEN Connect project.
  9. At the bottom of the Image View, a scale bar with size, the width of the field of view (FOV), and scaling is displayed.
  10. You have created a ZEN Connect project.
  11. Acquire an image.
  12. In the Project View, a new session node is created, and each acquisition is displayed.
  13. In the Image View, all images are displayed. They are signed with a colored frame (blue: normal image, red: selected image).
  14. When you close the project or the software, you are prompted to save the project file.

For information on setting up holders and carriers, see Selecting and Clearing Carrier/Holder.
For information on the ZEN Connect tool, see ZEN Connect Tool.

Zooming Images

You can zoom images in and out of a field of view (FOV).

Zooming to

  1. A ZEN Connect project is loaded.
  1. In the Project tree View, right-click an image and select Zoom to. Alternatively, click on the Context menu button and select Zoom to.
  1. The image is centered in the view space of the Image View.

Zooming to 100%

  1. A ZEN Connect project is loaded.
  1. In the Project tree View, right-click an image and select Zoom to 100%. Alternatively, click on the Context menu button and select Zoom to 100%.
  1. The image is zoomed in the view space of the Image View to 100%.

Renaming Images in a ZEN Connect Project

  1. You have loaded a ZEN Connect project.
  1. In the Project view or in the Layer view, select an image to rename.
  2. Right-click, select Rename data and rename the image, or press the F2 key. Alternatively, you can double click the image name to rename it, or click on the Context menu button , and select Rename data.
  1. You have renamed the image. It is updated either in the Layer or the Projectview respectively.
  2. The image name is not changed on the disk.

Opening Images in ZEN

  1. You have loaded a ZEN Connect project.
  1. In the Project View or in the Layers View, select one or more images you want to open, and right-click Open image(s) in ZEN. Alternatively, click on the Context menu button and select Open image(s) in ZEN. Additionally, you can also simply double click on an image in the Project View or in the Layers View.
  1. The image is opened in ZEN and displayed on a separate tab.

ZEN Data Storage

If you have opened a project from ZEN Data Storage, you can also open an individual image this way. The image is then downloaded and each change is not updated in the viewer and the project until you upload the image again. For information on uploading an image to the data storage, see Saving an Image to ZEN Data Storage.

Showing an Image in the Explorer

You can locate an image on your computer.

  1. You have loaded a ZEN Connect project.
  1. In the Project View or in the Layers View, right-click an image and select Show in Explorer. Alternatively, click on the Context menu button and select Show in Explorer.
  1. The explorer opens and the folder with the selected image is displayed.

Moving or Hiding Images

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

  1. You have loaded a ZEN 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 ZEN 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 or click on the Context menu button and select Show/Hide.
  1. The results of your changes are displayed immediately in the Image View.

Starting a New Session

To organize your work, you can start a new session within your ZEN Connect project any time.

  1. You have loaded a ZEN Connect project.
  1. In the ZEN Connect tool, click on the Context menu button and select New session.
    Alternatively, click on the New Session button.
  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.

Toggling View Modes

In ZEN Connect you can switch between two different view modes for your projects. The default is the carrier/ holder view mode, where the coordinate system of the correlative workspace is aligned with the screen and images of the current system/ session might be rotated. The second is the stage centric view mode, where the coordinate system of the current session is aligned with the screen and the carrier/ sample holder as well as other sessions might be rotated.

  1. You have opened a ZEN Connect project.
  1. In the button bar below the Image View of the correlative workspace, click on the button for the carrier/ holder or the stage centric view mode.
  1. The view is changed according to the selected view mode.

Closing a ZEN Connect Project

You have the following options to close a ZEN Connect project:

  1. Click on File > Close
  2. In the Image View, click on the cross next to the ZEN Connect project name.

Alignment

In a ZEN Connect project, you can manually align images in your workspace to correct their position or size with respect to the samples. To do so, you activate the alignment process and start aligning image data. Within a ZEN Connect project, you can also calibrate your system using a sample holder with fiducial markers by moving between the markers and confirming their positions.

Activating the Alignment Process

The alignment process lets you align your current session with fiducial marks or previous images. You can align image data manually.

You should create a new session any time the alignment of the sample in the microscope has been disturbed.

  1. A ZEN Connect project is loaded.
  1. In the Layer View, or in the Project View, select the image you want to align. Alternatively, you can select a region to select a couple of images.
  2. The image is marked with a square in each frame corner.
  3. As long as the alignment process is not activated, this is indicated with a little lock next to the cursor.
  4. Right-click the selected image and select Align Data.
    Alternatively, right-click the image(s) in the ZEN Connect tool and select Align Data. You can also select Align for the Alignment button and click it.
  1. You have activated the alignment process for one or more images. The Alignment Tab below the Image View is displayed.
  2. You can start aligning image data. If you start an alignment on a session node, the set alignment is used for all current and future images of the session. You can use this if you change your sample between different systems and want to align their coordinate systems to each other.

Rotating a Z-Stack

In the alignment mode you can also perform a three dimensional rotation of a z-stack.

  1. You have opened a ZEN Connect project.
  1. Select the z-stack you want to rotate.
  2. In the ZEN Connect tool, click on Align. Alternatively, right-click the image and select Align Data.
  3. The Alignment Tab below the Image View is displayed.
  4. For Alignment Mode, select 3D Alignment.
  5. Activate the checkbox Apply 3D Rotation.
  6. The Manipulation Controls for rotation are activated.
  7. Use the respective sliders or input fields to rotate the z-stack around the x, y, or z axis. Alternatively, you can use the View Cube Control to rotate the stack interactively.
  8. Click on Finish.
  1. You have now rotated the selected z-stack around the respective axis.

Aligning Images in the ZEN Connect 3D View

With the ZEN Connect 3D view you can display and align two z-stacks as 3D volumes. This alignment mode allows a translation of the volumes in x, y and z.

  1. You have opened two z-stack images in the ZEN Connect 3D view or directly in 3D alignment mode, see Opening Images in the ZEN Connect 3D View.
  1. In the Connect 3D tab, click the button for the volume you want to align, e.g. Align Volume 1. If you opened the 3D view directly in alignment mode, one volume is already selected for alignment.
  2. You are in alignment mode and the Alignment tab is displayed.
  3. To mirror the selected image, go to the Alignment tab and click to mirror the image horizontally, or click to mirror it vertically.
  4. In one of the 2D image views, shift the volume via drag and drop and align it with the second volume as reference.
  5. The changes are automatically updated in all views, including the 3D view.
  6. If you are satisfied with your alignment, go to the Alignment tab and click Apply.
  7. Your alignment changes are saved in the ZEN Connect project.

Aligning Images in the Point Alignment Wizard

  1. You have opened a ZEN Connect project.
  1. In the correlative workspace or in the ZEN Connect tool, select the image(s) you want to align.
  2. In the ZEN Connect tool, for the Alignment button, select Point Alignment Wizard and click on it.
  3. The ZEN Connect Point Alignment Wizard opens.
  4. In the list on the left, use the button to add as many points as necessary for your point alignment.
    With one point only a translation operation is possible, with two translation and rotation, and three or more points enable all transformations.
  5. In the Algorithm dropdown list, select the alignment operations you want to perform.
  6. Click on Draw for the first point.
  7. You enter the drawing mode for the first point.
  8. In the Image Window on the left, click to set the point in your image(s) (Subject point).
  9. In the Project Window on the right, click to set the corresponding location for this point in the project (Reference point).
  10. Both color makers in the table are green and the first point for the alignment is set successfully.
  11. Repeat these three steps for every point you add/need.
  12. If you want to redraw a point pair, click on Redraw and click to set the new positions in both windows.
  13. Click on Next.
  14. The second step of the wizard opens. It displays a preview of the final alignment result and values for the parameter changes.
  15. If you want to change the alignment, click on Back to get back to the previous step. Otherwise, click on Finish to save the alignment and close the wizard.
  1. You have aligned the selected image(s) in the ZEN Connect project.

Aligning Images in the 3D Point Alignment Wizard

  1. You have opened a ZEN Connect project.
  1. In the correlative workspace or in the ZEN Connect tool, select the image(s) you want to align.
  2. In the ZEN Connect tool, for the Alignment button, select Point Alignment 3D Wizard and click on it.
  3. The ZEN Connect 3D Point Alignment Wizard opens.
  4. In the left image window (Tomo3D view), select the 2D image view you want to use from the dropdown as points for alignment can only be set in the 2D views.
  5. In the list on the left, click to add as many points as necessary for your point alignment.
    With one point only a translation operation is possible, with two translation and rotation, and four or more points enable all transformations.
  6. In the Algorithm dropdown list, select the alignment operations you want to perform.
  7. Click Draw for the first point.
  8. You enter the drawing mode for the first point.
  9. In the Image Window on the left, click to set the point in your image(s) (Subject point).
  10. In the Project Window on the right, click to set the corresponding location for this point in the project (Reference point).
  11. Both color makers in the table are green and the first point for the alignment is set successfully.
  12. Repeat these steps for every point you add/need.
  13. If necessary, use the controls in the Dimensions tabs, e.g. to switch to a different z-slice to set the points on specific z-levels.
  14. If necessary, change the left image view via the dropdown to add or check points in other 2D image dimensions.
  15. The view changes to the selected 2D image dimensions.
  16. If you want to redraw a point pair, click Redraw and click to set the new positions in both windows.
  17. Click Next.
  18. The second step of the wizard opens. It displays a preview of the final alignment result and values for the parameter changes.
  19. If you want to change the alignment, click Back to get back to the previous step. Otherwise, click Finish to save the alignment and close the wizard.
  1. You have aligned the selected image(s) in the ZEN Connect project.

Handling of Images and Data

Zooming to Extent

  1. You have loaded a ZEN Connect project.
  1. In the button bar below the Image View, click the Zoom to Extent icon.
    Alternatively, click on the Context menu button and select Zoom to extent.
  1. In the Image View, the sample holder is centered. All images in the ZEN Connect project are displayed.

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 below the Image View, click the A button.
  1. The region caption of the images is displayed or hidden.

Selecting and Clearing Carrier/Holder

The sample is usually mounted on a carrier or directly on a sample holder. Select the appropriate sample holder for your configuration when you configure your project.

We offer specific sample holders and carriers with certain markers, e.g., "L"-markers or others. These CorrMic sample holders are necessary for a Shuttle & Find workflow. Note: If you change the holder/carrier after a S&F calibration, the S&F calibration needs to be redone.

  1. You have loaded a ZEN Connect project.
  1. In the button bar below the Image View, click the Select Carrier/Holder button.
  2. Select a template you want to add to your ZEN Connect project, and click OK.
  3. The frame of the selected template is displayed in the Image View of your ZEN Connect project.
  4. To deselect the carrier/holder, click the Select Carrier/Holder drop down list and select Clear/Carrier Holder.

For information on correlative sample holders, see Correlative Sample Holders.

Adding Measurements to a ZEN Connect Project

  1. You have opened a ZEN Connect project.
  1. In the Measurement Tab, click on the button for the respective measurement tool.
  2. In the image view, click to set the points for the measurement. For a distance measurement, set two points, for an angle three and for an area measurement create a polygon that covers the desired area.
  3. In case of area measurements, the last click has to be at the first point to "close" the polygon. Alternatively, click with the right mouse button to finish the polygonal area.
  4. The respective measurement is displayed in the view as well as the table of the Measurement tab.
  1. You have added a measurement to your ZEN Connect project.

ZEN Connect Tool

The ZEN Connect tool provides a layer's view and a project 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 is listed in the views.

The ZEN Connect tool offers different options to open a ZEN Connect project or to create a new ZEN Connect project.

Alternatively, you can create a new ZEN Connect project via File > New Document. For more information, see New Document Dialog.

The ZEN Connect tool displays the following:

  • Images that have been acquired for the ZEN Connect project.
  • Images that have been imported to the ZEN Connect project.
  • Position of the image in the project or the layers.
  • Non image data added to the ZEN Connect project.

ZEN Connect Project Layer view

Images in your ZEN Connect project are displayed in the Image View according to its position in the Layers View. With drag & drop, you can move images over and under other images. You can also hide them completely . For more information, see Moving or Hiding Images. Additionally, you can see the objective magnification with which the image was acquired and if an image is a z-stack .

Button Bar

Parameter

Description

Opacity

Changes the opacity of layers. The overall opacity determines to what degree it obscures or reveals the layer beneath it. A layer with 1% opacity appears nearly transparent, whereas one with 100% opacity appears completely opaque.

Alignment

Only available if you have selected one or more images or a session.
Starts the selected alignment operation for the currently selected image(s) or session. Click on the arrow button to select an alignment.

–

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.

–

Manual Alignment Wizard

Opens the wizard for manual alignment, see Aligning Images in the Manual Alignment Wizard.

–

Point Alignment Wizard

Opens the wizard for point alignment, see Aligning Images in the Point Alignment Wizard.

–

Point Alignment 3D Wizard

Opens the wizard for 3D point alignment, see Aligning Images in the 3D Point Alignment Wizard.

–

Align Two Images in 3D

Opens the selected images directly in alignment mode in the ZEN Connect 3D view, see also Aligning Images in the ZEN Connect 3D View.

Import

Starts the currently selected operation to add and/or import an image. Click on the arrow button to select an import operation, see also Importing Data.

–

Add image

Opens the file browser to add an image, see Adding an Image to the ZEN Connect Project.

–

Add image from storage

Opens the Stored Documents dialog to add an image from the ZEN Data Storage, see Adding an Image to the ZEN Connect Project.

–

Import non-image data

Opens the file browser to select non-image data for an import, see Importing Non Image Data.

–

Import SmartFIB z-stack

Opens the file browser to import a SmartFIB z-stack, see Importing a SmartFIB Stack into ZEN Connect.

–

Add dataset

Opens the file browser to add a dataset, see Adding Datasets when Adding Images.

Export

Starts the currently selected operation to export an image. Click on the arrow button to select an export operation.

–

Single Image Export

Opens the wizard to export the selected data in one single image, see Exporting Single Image Data.

–

Video Export

Opens the wizard to export the selected data as a video, see Exporting a ZEN Connect Project as a Video.

–

Export Project

Opens a file browser to export your current ZEN Connect project, see Exporting a ZEN Connect Project from ZEN Data Storage.

New Session

Creates a new session, see Starting a New Session.

Context menu

–

Zoom to

Zooms one or more selected images into the center of the Image View, see Zooming Images.

–

Zoom to 100%

Zooms to the selected image in the Image View and displays it at 100% scale, see Zooming Images.

–

Show/Hide

Toggles the visibility of an image or a session, see Moving or Hiding Images.

–

Open image(s) in ZEN

Opens the selected image(s) in ZEN, see Opening Images in ZEN.

–

Open Attachment

Only available for non-image data.
Opens the attached file in the respective application.

–

Show in Explorer

Locates an image or file on your computer, see Showing an Image in the Explorer.

–

Remove Data

Removes the selected image from the ZEN Connect project, but does not delete it from the computer, see Removing Images from the ZEN Connect Project.

–

Delete

Only visible for non-image data.
Deletes the file from the project and from the project folder. If the file was added as a link, only the link in the project is deleted.

–

Rename Data

Renames an image, see Renaming Images in a ZEN Connect Project.

–

Align Data

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

–

Single Image Export

Opens the wizard to export the selected data in one single image, see Exporting Single Image Data.

–

Video Export

Opens the wizard to export the selected data as a video, see Exporting a ZEN Connect Project as a Video.

–

Add image

Opens the file browser to add an image, see Adding an Image to the ZEN Connect Project.

–

Add image from storage

Opens the Stored Documents dialog to add an image from ZEN Data Storage, see Adding an Image to the ZEN Connect Project.

–

Import SmartFIB z-stack

Opens the file browser to import a SmartFIB z-stack, see Importing a SmartFIB Stack into ZEN Connect.

–

Show in 3D

Only available if one or two z-stack images are selected in the tree view.
Opens the images in the ZEN Connect 3D view, see Opening Images in the ZEN Connect 3D View.

–

New Session

Starts a new session. The images acquired next will be subordinated below a new session node, see Starting a New Session.

–

Clear alignment

Resets the alignment and places the selected image at its initial position.

–

Zoom to extent

Resets the view space of the Image View to be centered on the holder with a field of view (FOV) that includes all visible images in the project, see Zooming to Extent.

–

Export Project

Opens a file browser to export your current ZEN Connect project, see Exporting a ZEN Connect Project from ZEN Data Storage.

–

Import non-image data

Opens the file browser to select non-image data for an import, see Importing Non Image Data.

Select Template Dialog

In the Select Template Dialog, you select carriers and holders.

Parameter

Description

Celldiscoverer

Only available for celldiscoverer application.

Shows a list of celldiscoverer sample holders.

Tiles

Shows a list of all generic sample holders.

Correlative

Shows a list with all relevant correlative sample holders.

Measurement Tab

Parameter

Description

Measurement Tools

–


Distance

Allows the user to add two points to measure a distance.

–


Angle

Allows the user to add three points to measure an angle.

–


Area

Allows the user to draw a polygon contour to measure an area.

–


Circle

Allows the user to draw a circle to measure a diameter.

Measurement table

–

Value

Displays the measured value.

–

Type

Displays the icon of the measurement type.

–


Visibility

Toggles the visibility of each measurement.

–

Name

Displays the name of each measurement.

–

Line

Displays the color of the measurement. A click on the color field opens a selection window to change the color.

–

Text

Displays the color of the measurement text. A click on the color field opens a selection window to change the color.

–


Delete

Deletes the currently selected measurement.

ZEN Connect Single Image Export Wizard

With the ZEN Connect Single Image Export wizard, you configure the parameters of the image you want to export.

Parameter

Description

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. Only the file formats that support the number of pixels you are exporting will be shown. If your export is too large, formats like BMP, JPG and TIFF are not displayed. If you wish to export to one of these formats, you must pick a larger pixel size, or smaller export area for your export.

-

Raw Image

Exports the image as a raw binary dump of the pixel values. An XML file is also written detailing the image width and height in pixels, the pixel size in microns, the bits per sample and samples per pixel. Raw files are not limited in size.

-

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.

-

Tif Image

Exports the image as a standard TIFF file. TIFF files are limited in size.

-

Tif Tiles

With this option, the export is in TIFF format, but broken into 2K x 2K tiles saved as individual TIFFs. An XML file is written listing the file names of the tiles and their positions. This export option is unlimited in size, but designed for someone who is writing scripts to import the data into image processing applications or similar.

-

Bitmap Image

Exports the image as a standard Windows Bitmap. Bitmap files are limited in size.

-

Jpg Image

Exports the image as a standard JPEG file. JPEG files are limited in size.

Burn-in Data Bar

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

Show Region Caption

Controls if image names and frames are shown in the exported image.

JpgXr Compression Quality

Activated: Uses the (lossy) JpgXr compression of the image during export and sets the quality for the compressed image with the input field.

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 coarsest 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 finest 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.

Export Data

Opens a file browser to export the image with your settings.

Finish

Saves the changes and closes the wizard.

Cancel

Closes the wizard without saving the changes.

For more information on exporting single images, see Exporting Single Image Data.

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.

Pixel Size Dialog

Parameter

Description

Pixel Size

Displays the current pixel size and allows you to enter a value.

OK

Sets the pixel size to the entered value.

Cancel

Closes the dialog box without setting the pixel size.

ZEN Connect Manual Alignment Wizard

1

Alignment Parameter
Control parameters to align the respective image in the project. For more information, see Alignment Parameter Section.

2

Image View
Displays the images of the project and allows alignment of images.

3

View Options
Here you have the general options of the Dimensions tab. The options are always those of the image selected in the Select Node For Dimensions tab.

Alignment Parameter Section

Parameter

Description

Translate

 

–

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

–

X-Direction

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

–

Y-Direction

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

Rotate

 

–

Rotation Center

Defines the rotation center around which the image is rotated. It is indicated in the Image View with a pin.

–

Angle

Sets the rotation angle. The reset button resets the value to the default.

–

Custom

You can set the pin in the image to your custom rotation center.

Flip/Mirror

–


Horizontally

Mirrors the image in horizontal direction.

–


Vertically

Mirrors the image in the vertical direction.

Shear

–

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.

Reset All Parameters

Resets all alignment parameters in the wizard to the default values.

Parameter

Description

Finish

Saves the changes and closes the wizard.

Cancel

Closes the wizard without saving.

ZEN Connect 3D Point Alignment Wizard

This wizard guides you through a 3D point alignment of the image in your ZEN Connect project.

Step 1: Setup Points

1

Point Alignment Options
Options to configure your point alignment. For more information, see 3D Point Alignment Options.

2

Image Window (Tomo3D)
Displays the image(s) you are aligning with a special implementation of the Tomo3D View. With the dropdown in the upper left corner, you can switch to a different 2D view pane as well as display a 3D view. You set the subject points in this view. Note that setting points is only possible in the 2D views.

3

Project Window
Displays all the images of the project except the one you are aligning. Area where you set the reference points.

4

View Options
Displays some general view options of the Dimensions Tab for the respective windows.

3D Point Alignment Options

Parameter

Description

Point list

–

Name

Displays the name of the point.

–

Subject

Displays the status of the subject point with a color.

  • Yellow: You are in drawing mode and have not yet set the subject point in the Image Window.
  • Green: You have set the subject point.

–

Reference

Displays the status of the reference point with a color.

  • Red: You have not yet set the subject point and cannot set the reference point.
  • Yellow: You are in drawing mode and have not yet set the reference point in the Project Window.
  • Green: You have set the reference point.

–

Draw

Only visible if no points have been drawn for the current point entry.
Enters the drawing mode for the respective point.

–

Cancel

Only visible if you are in drawing mode.
Cancels the drawing of points for the current point.

–

Redraw

Only visible if you have already drawn the reference and subject point for this entry.
Reenters the drawing mode to redraw the points for this entry.

–


Add

Adds another point entry in the list.

–


Delete

Deletes the currently selected list entry and removes all drawn points of the entry.

Algorithm

Selects the algorithm for alignment. The algorithm is preselected based on the number of positioned points.

–

Autoselect

Automatically selects the algorithm suitable for the drawn points.

–

Translation

Moves the item you are aligning in x and y only, without changing its size or orientation.

–

Translation and 2D Rotation

Moves the item in x and y direction and changes its 2D orientation. It does not change the scale of the item you are aligning.

–

Translation and 2D Scaling

Moves and resizes the item you are aligning.

–

3D Rotation and Translation

Moves and rotates the item in three dimensions. It does not change the scale of the item you are aligning.

–

Allow all transformations

Supports all possible transformations.

Step 2: Preview

This step displays a preview of the finished alignment and the parameter values of each alignment.

Parameter

Description

Algorithm Result

Displays the resulting alignment changes.

Translation

Displays the resulting translation in X-Direction, Y-Direction and Z-Direction.

Rotation

Displays the resulting rotation angle around the x-, y- and z-axis.

Scaling

Displays the resulting scaling factor for the X-Dimension, Y-Dimension and Z-Dimension.

Back

Moves to the previous step of the wizard.

Finish

Saves the changes and closes the wizard.

Cancel

Closes the wizard without saving.

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