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
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Image View |
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ZEN Connect Tool |
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Button bar below Image View |
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Regions Tool |
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View Options |
Opening the Correlative Workspace
- Start the software. For more information, see Starting Software.
- 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.
- You have opened a ZEN Connect project with at least two z-stacks.
- In the ZEN Connect tool or the Image View, select one or a maximum of two z-stacks while pressing Ctrl.
- Right click one of the selected images in the ZEN Connect tool and select Show in 3D. Alternatively, click
and select Show in 3D. - 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.
- 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.
See also
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.
See also
Raman Images
If you have licensed ZEN Connect, the software supports the display of images with the specific Horiba LabSpec HDF5 Raman image format. These supported images basically represent a map (score map) of intensities of the different channels. This means the higher the concentration of a detected material, the higher the displayed color saturation. To display the data the image codec HDF5 is used.
HDF5 is only used as a standard image codec to display this specific type of image (Horiba LabSpec HDF5 Raman image format) and is not a HDF5 import!
Display of Raman Images
- The image can be opened just as any other image. In the file explorer, make sure that the file type is set either to HDF5 (*h5) or to Image files. Then the file(s) with the Horiba LabSpec HDF5 Raman image format can be selected.
- The files of this format can only be displayed, but changes to the image cannot be saved. To save the file after changing parameters (e.g. the image display curve), you have to save the image in another format like *.czi.
- To display the image(s) the FLOAT values of the original file are converted or mapped to 16 bit format. Exception: If the values in the file contain constant, NAN or INF values, no conversion to 16 bit is done.
Select Template Dialog
In the Select Template Dialog, you select carriers and holders.
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Parameter |
Description |
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Celldiscoverer |
Only available for celldiscoverer application. Shows a list of celldiscoverer sample holders. |
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Tiles |
Shows a list of all generic sample holders. |
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Correlative |
Shows a list with all relevant correlative sample holders. |
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See also
Alignment Tab
The alignment tab is visible as soon as you enter the alignment mode. For more information, see Activating the Alignment Process.
You can perform Three-Point Alignment:
- Line-up an imported image with reference marks, such as the precision fiducials on a CorrMic Holder.
- Line-up features in an imported image with LM, EM and SEM images of the same features.
- Line-up a session of LM, EM and SEM imagery with previously acquired LM, EM and SEM imagery session.
With the three-point alignment process you can set the position, rotation, and scale of an image or tile. This is used to line the image or tile up with reference marks or other images. Once an image is lined up, it can be used as a reference (road map) to move the stage to control further image acquisition.
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Parameter |
Description |
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Alignment Mode |
Sets which data properties you can change during the alignment. |
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Translate Only |
Moves the item you are aligning in x and y only without changing its size or orientation. |
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Translate and Rotate Only |
Moves the item in x and y direction and changes its orientation. It does not change the scale of the item you are aligning. |
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Translate, Rotate and Scale Only |
Moves, reorients, and resizes the item you are aligning. It does not shear it. |
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Translate, Rotate, Scale and Shear |
Supports full three-point alignment. |
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Alignment Handles |
Displays alignment handles to rotate and resize the image. |
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3D Alignment |
Displays options to align an image in z direction and for three dimensional rotation. |
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Mirrors the image horizontally. |
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Mirrors the image vertically. |
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Mirrors the image stack in z direction around the middle z-height. |
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Relative Z Offset |
Only visible if 3D Alignment is selected. |
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Step Size |
Only visible if 3D Alignment is selected. |
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Set to current Global-Z |
Only visible, if 3D Alignment is selected and only active if the Global-Z slider is activated on the Dimensions tab. |
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Apply 3D Rotation |
Only visible, if 3D Alignment is selected. |
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Rotation X-Axis |
Sets the rotation along the x-axis with the slider or input field. Click on the |
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Rotation Y-Axis |
Sets the rotation along the y-axis with the slider or input field. Click on the |
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Rotation Z-Axis |
Sets the rotation along the z-axis with the slider or input field. Click on the |
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Angle Step Size |
Sets the angle step size for the slider/input fields above. |
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View Cube Control |
With this cube control, you can rotate the stack interactively. It has a visual representation of the current stack (white box) and the cutting plane which is displayed in the 2D view above. |
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Presets |
Sets the View Cube Control to a predefined position. You can set it to the Default, or you can select an orientation from the dropdown of the button to show the Default, Viewer Perspective, Left, or Right orientation. |
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Manual Control |
Controls the orientation of the View Cube Control. |
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Reset |
Resets the alignment as it was when you started this alignment operation. |
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Clear |
Resets the alignment to where it was when the data was first acquired or imported. |
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Finish |
Exits from the alignment operation, keeping the alignment you have established. |
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Cancel |
Returns to the alignment as it was when you started, and exits from the alignment operation. |
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button to reset the angle.See also
Measurement Tab
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Parameter |
Description |
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Measurement Tools |
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Allows the user to add two points to measure a distance. |
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Allows the user to add three points to measure an angle. |
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Allows the user to draw a polygon contour to measure an area. |
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Allows the user to draw a circle to measure a diameter. |
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Measurement table |
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Value |
Displays the measured value. |
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Type |
Displays the icon of the measurement type. |
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Toggles the visibility of each measurement. |
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Name |
Displays the name of each measurement. |
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Line |
Displays the color of the measurement. A click on the color field opens a selection window to change the color. |
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Text |
Displays the color of the measurement text. A click on the color field opens a selection window to change the color. |
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Deletes the currently selected measurement. |
See also
Button Bar below Image View
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Parameter |
Description |
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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. For more information, see Zooming to Extent. |
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Activates the mouse for panning around and zooming in and out in the Image View. For more information, see Panning & Zooming. |
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Selects an image/ a region in the Image View. For more information, see Selecting Region. |
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Activates a mode to interact with measurements added to the project. For more information, see Editing Measurements in a ZEN Connect Project. |
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Creates a Region of Interest in the Image View. For more information, see Using Regions of Interest in Zen Connect. |
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A |
Hides or displays image names and frames of images in the Image View. For more information, see Toggling the Display of Region Caption and Frame. |
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Select Carrier/Holder |
Opens a dialog to select a carrier or sample holder that matches. For more information, see Selecting and Clearing Carrier/Holder. |
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Activates a 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. For more information, see Toggling View Modes. |
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Activates the carrier/holder view mode where the coordinate system of the correlative workspace is aligned with the screen and images of the current session might be rotated. For more information, see Toggling View Modes. |
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Grab Image |
Creates an image of the ZEN Connect project. For more information, see Grabbing an Image. |
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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.
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Parameter |
Description |
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Color Style |
Controls the color format of the export. Select RGB (color) or Intensity (black and white). |
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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. |
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Intensity |
Images are saved in 8-bit format. |
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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. |
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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. |
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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. |
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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. |
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Tif Image |
Exports the image as a standard TIFF file. TIFF files are limited in size. |
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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. |
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Bitmap Image |
Exports the image as a standard Windows Bitmap. Bitmap files are limited in size. |
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Jpg Image |
Exports the image as a standard JPEG file. JPEG files are limited in size. |
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Burn-in Data Bar |
Activated: Burns the currently configured data bar into the exported image. |
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Show Region Caption |
Controls if image names and frames are shown in the exported image. |
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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. |
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Rotation |
Rotates the view to the desired orientation. Drag the slider, or in the text field, type in the value. |
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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. |
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Smallest |
Sets pixel size of the coarsest image, i.e. the smallest pixel size. |
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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)). |
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Largest |
Sets pixel size of the finest image, i.e. the largest pixel size. |
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Custom |
Sets a custom pixel size which can be entered in the input field. |
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Width (px) |
Sets the width to directly alter the export pixel count and export area (the pixel size is unchanged). |
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Height (px) |
Sets the height to directly alter the export pixel count and export area (the pixel size is unchanged). |
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Width (µm) |
Displays the full width of the export area in µm. |
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Height (µm) |
Displays the full height of the export area in µm. |
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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. |
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Export Data |
Opens a file browser to export the image with your settings. |
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Finish |
Saves the changes and closes the wizard. |
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Cancel |
Closes the wizard without saving the changes. |
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For more information on exporting single images, see Exporting Single Image Data.
Field of View Width Dialog
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Parameter |
Description |
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FOV Width |
Displays the current width of the field of view and allows you to enter a value. |
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OK |
Sets the width to the entered value. |
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Cancel |
Closes the dialog box without setting the field of view. |
Pixel Size Dialog
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Parameter |
Description |
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Pixel Size |
Displays the current pixel size and allows you to enter a value. |
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OK |
Sets the pixel size to the entered value. |
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Cancel |
Closes the dialog box without setting the pixel size. |
Video Export Wizard
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Parameter |
Description |
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Burn in Data Bar |
Burns the currently configured data bar into the exported video. |
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Show Region Caption |
Controls if the image names are shown in the exported video. |
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Show Region Outline |
Controls if the image frames are shown in the exported video. |
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Export Resolution |
Sets the resolution and format for the video export. Resolutions available in the drop down list:
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Zoom to Extent |
Places the image to the center of the preview area. |
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Rotation |
You can use the slider or the input field to rotate the view. |
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Start Delay |
Sets the delay at the start of the video. The default setting is 1,0 seconds. |
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Key Frames |
Lists the key frames, including the data of the position and FOV. |
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Moves the selected key frame up in the list. |
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Moves the selected key frame down in the list. |
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Deletes the selected key frame. |
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Displays the selected key frame. |
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Sets the values of the selected key frame to the current view. |
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Load Export Key Frames |
Loads stored key frames. |
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Save Export Key Frames |
Saves the key frames in XML format. |
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Transit To |
Sets the transition time for zooming to a selected key frame. The default setting is 3,5 seconds. |
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Pause At |
Sets the time to stay at the selected key frame. Default setting is 0,5 seconds. |
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Return to first at end |
Returns to the first key frame at the end of the video. |
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Add current view as key frame |
Adds the current view as a key frame. |
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Preview export |
Displays a real-time preview of the video. |
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Start Export |
Exports and saves the video. |
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Finish |
Saves the changes and closes the wizard. |
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Cancel |
Cancels the video export. |
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See also
Regions Tool
This tool displays a list of regions of interest (ROI) which are drawn into a ZEN Connect project.
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Parameter |
Description |
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ROI List |
Here you see a list of all ROI in your ZEN Connect project. |
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Deletes the currently selected region of interest. |
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Allows you to rename the currently selected region of interest. |
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Moves the stage to the center of the currently selected region. |
See also
ON THIS PAGE
- ZEN Connect
- Licensing and Functionalities of ZEN Connect
- User Interface
- Opening the Correlative Workspace
- Opening Images in the ZEN Connect 3D View
- Non Image Data
- Raman Images
- Select Template Dialog
- Alignment Tab
- Measurement Tab
- Button Bar below Image View
- ZEN Connect Single Image Export Wizard
- Field of View Width Dialog
- Pixel Size Dialog
- Video Export Wizard
- Regions Tool