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.
3. 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.
4. You can enter a name for the FIB stack. This step is optional.
5. 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!
6. 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.
7. 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).
8. 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!
9. 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.