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Import and Export

Importing Data

You can import simple images, such as camera images or more complex images, such as a light microscope image with overlays, to your ZEN Connect project. For more information, see Adding an Image to the ZEN Connect Project.

Alternatively, you have the option to import BioFormats into your ZEN Connect project. For more information, see Importing Third-party Images.

Note: If you import an Airyscan image, ZEN Connect displays only the raw data and not the calculated Airyscan. Such images should be processed before you add them to ZEN Connect. If you want to add an unprocessed Airyscan image, a warning will appear asking if you want to continue.

Importing Third-party Images

ZEN uses BioFormats as an integrated library for reading and writing life sciences 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 into an intermediate format, e.g., CZI or OME-TIFF. For example, it is possible to load simple images you can import simple images, such as camera images or more complex images, such as a light microscope image with overlays, to your ZEN Connect project.

  1. You have licensed the Third Party Import.
  1. Select File > Export/Import > BioFormats Import.
  2. Navigate to the image with the proprietary image format you want to import, select it, and click Open.
  1. The image is converted and added to ZEN (not to the ZEN Connect project itself).

Alternatively, you have the following options to import data in your ZEN Connect project:

For more information on BioFormats, see http://www.openmicroscopy.org/bio-formats/

Importing a SmartFIB Stack into ZEN Connect

With ZEN Connect you can import SmartFIB stacks of crossbeam microscopes and align them with data from light microscopes. The orientation of these stacks slightly differs from standard z-stack acquisition, as the acquired images are tilted by a certain angle compared to a usual z-stack. The import calculates this tilt from the metadata of the image. If the import finds no metadata concerning the tilt angle and the user does not enter a value, it uses a default of 90 degrees. Alternatively, you can enter the angle of your sample during import, if you know it, and the import then calculates the tilt angle based on this sample angle.
During import, the XY offset metadata of the individual slices is ignored by default and only the offset of the first tiff file is considered. This default avoids the creation of a slanted z-stack in case some slices contain incorrect metadata. Activate the checkbox consider individual slice offsets on the import dialog to change the behavior.

  1. You have opened/created a ZEN Connect project.
  1. In the Project view, select the session where you want to import the FIB stack.
  2. Right click on the session and select Import SmartFIB z-stack.
    Alternatively, select Import SmartFIB z-stack for the Import button.
  3. A file browser opens.
  4. Select the images you want to import as FIB stack.
    Note: Select only images which belong to one dataset!
    Note: To make sure the stack is composed/ ordered correctly, watch out how the images are sorted in the explorer and in which order you choose them.
  5. You can enter a name for the FIB stack. This step is optional.
  6. If you import images without scaling information, you can manually enter them as optional Z-stack XY scaling.
    Note: ZEN currently cannot determine automatically if scaling information are present!
  7. You can set the slice distance. This step is optional and should only be done if you have reason to believe the information calculated with the metadata is incorrect. Leave the input field empty and the slice distance is automatically calculated with information saved in the metadata of the images.
    Note: When you set the slice distance manually, the information in the metadata is ignored.
  8. If you know the angle of your sample, enter it under optional sample angle. Otherwise the tilt for the image is calculated with the metadata or set to the default of 90 degree (if no information is available in the metadata).
  9. If you want to consider the XY offset metadata of the individual slices for the import, activate the checkbox consider individual slice offsets. Note that this can lead to a slanted z-stack if the metadata contain incorrect offset information!
  10. Click on Open.
  1. The FIB stack is now imported into the selected session.
    Note: When importing larger image files it may take a while until the entire stack is visible in the viewer. This also applies when you open a project that contains such larger stacks.

Note: To improve the alignment of the z-stack, the TrakEM2 format is supported. Before importing the SmartFIB z-stack, use a specific fiji script (for information, see https://imagej.net/Register_Virtual_Stack_Slices#API_documentation) that creates xml-files with TrakEM2 format within the transferred input folder. Those xml-files are then considered during the import and replace the stage-position information with the computed pixel delta x/y shifts. Only the stage-position of the first image is used for absolute positioning, all other images of the stack are positioned according to this first slice and the computed shifts.

Importing Non Image Data

  1. You have opened/created a ZEN Connect project.
  1. In the ZEN Connect tool, select Import non-image data for the Import button.
  2. A file browser opens.
  3. In the file browser, select your file. If the file should be copied into the data folder of the project, make sure the checkbox Copy Files is activated (it is activated by default). If the file should only be linked into the project, deactivate the checkbox.
  4. Click on Open.
  1. You have successfully imported the non-image data into your ZEN Connect project. The file is listed under Non-Image Data in the tree of the ZEN Connect tool.

Exporting Single Image Data

You can export data of ZEN Connect projects as a single image for distribution to collaborators, or for the use in publications. The content can be a single image, tiles, a collection of images, or a view of the entire ZEN Connect project. You can drag or resize the region to control the area that you want to export, or activate if image names and frames are shown on the exported image or not. You can pan and zoom using the mouse in the Image View to get fine control of the export area.

  1. You have loaded a ZEN Connect project.
  2. In the loaded ZEN Connect project, you have activated and deactivated the respective areas of interest.
  1. In the ZEN Connect tool, open the Project View or the Layers View. Right-click an image and select Single Image Export.
    Alternatively, select an image and select Single Image Export for the Export button.
  2. A wizard opens.
  3. Make your settings and click Export Data.
  4. Navigate to the folder where you want to store the exported image. The default file name is the ZEN Connect project name. Click Save.
  1. You have exported one image in a standard image format. The exported image is based on the export area you set up in the Image View.

Exporting a ZEN Connect Project as a Video

You can export data of ZEN Connect projects as a video.

  1. You have loaded a ZEN Connect project.
  2. In the loaded ZEN Connect project, you have activated and deactivated the respective areas of interest.
  1. In the ZEN Connect tool, open the Project View or the Layers View. Right-click an image and select Video Export.
    Alternatively, select an image and select Video Export for the Export button.
  2. The wizard for video export opens.
  3. Choose your key frames by positioning the export area in the Image View and add them to the list of key frames by clicking Add current view as key frame.
  4. Make your settings, and click Start Export.
  5. Navigate to the folder where you want to store the exported video. The default file name is the ZEN Connect project name. Click Save.
  1. You have exported a video in a standard video format.

Exporting Data for SerialEM

ZEN offers the functionality to export image data as an MRC file which makes it compatible to the software application SerialEM and available for TEM users. This export is available for z-stacks and multi-channel images with all the common pixel types (8/16 Bit, 32 Bit Float, RGB 24/32/48). Tiles, time series, multi-scene images, and images with unprocessed data or special dimensions are not supported. For images with more dimensions, you can use the image processing function Create Image Subset to extract a single image or stack and then export it with this function.
The export creates a MRC file as well as a NAV file, which contains regions of interests (e.g. points, rectangles, polygons,...). The NAV file can be loaded in the SerialEM software and it then loads the MRC file, so that the image with the respective regions is shown.

  1. You have opened an image in ZEN.
  1. Click on File > Export/Import > MRC Export.
  2. A file explorer opens.
  3. In the file explorer, select a folder to save the file.
  4. Name the file and click on Save.
  1. You have exported the image data as an MRC (and NAV) file.

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