Export/Import

Directory

Selects the folder with txm images that should be converted to czi. After the conversion, the images will again be stored in this folder.

Recursive

Converts also files in subfolders of the selected folder.

Overwrite

Overwrites already converted files.

Preview Only

Displays a preview of the images in the folder, but does not convert them.

Multichannel

Activated: Activates the settings to import multichannel images.

Adjust the settings for the multichannel image to be imported in the list below.

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Use Channel Name as Identifier

Activated: Uses the name specified in the Name column to identify the channel. The channel name will appear in the Preview display field in the Specify the Identifiers section.
Deactivated: Activates the Identifier, Start Index and Interval columns in the Specify the Identifiers section.

Z-Stack

Activated: Activates the settings to import Z-Stack images.

Adjust the settings for the Z-stack image to be imported in the list below.

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Interval

Here you enter the value in µm for the distance between the individual slices. The total height of the Z-stack is calculated automatically from this value and the number of slices.

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Slices

Here you enter the number of slices of the Z-Stack image.

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Range

Here you enter the total height (range) of the Z-stack in µm.

The distance between the individual Z-stacks is calculated automatically from this value and the number of slices and displayed in the Interval display field.

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Extended Microscope Parameters

Activates additional parameters that are necessary for further processing of the imported image (e.g. for deconvolution), like:

• Magnification:
• Select the objective magnification that was used for acquisition here.
• Aperture:
• Here you can enter the value of the numerical aperture of the objective that was used for acquisition.
• Immersion:
• Select the immersion medium that was used for acquisition here.

Time Series

Activated: Activates the settings to import time series images.

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Interval

Here you enter the value for the interval between the individual time points. Select the unit of time from the dropdown list to the right of the input field.

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Cycles

Here you enter the cycles of the time series. The entered value will affect the duration/the interval depending on which value you have selected.

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Duration

Here you can enter the value for the duration of the entire time series. Select the unit of time from the dropdown list to the right of the input field. Enter the number of time points in the Time Points input field.

Tiles

Activated: Activates the settings to import tile images.

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Columns

Here you can enter the number of columns of the tile image.

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Overlap

Here you can enter the percentage by which the tiles do overlap.

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Rows

Here you can enter the number of rows of the tile image.

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Meander

Select this option, if the images to be imported were acquired in the Meander acquisition/travel mode.

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Comb

Select this option if the images to be imported were acquired in the Comb acquisition/travel mode.

Positions

Activated: Activates the settings to import images of individual positions.

Scalings

To show the section in full, click on the arrow button.

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Use Current Scaling

Uses the geometric scaling currently selected and displays the values for Scale (X) and Scale (Y) with the corresponding unit in the relevant display field.

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Define scaling

Enter the desired values in the Scale (X) input field and in the Scale (Y) spin box/input field. Select the unit for the scaling value from the dropdown list to the right of each input field.

Automatic

If selected, all images that are available in an import folder are imported automatically.

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Import From

Here you can select the import folder.

To select a folder, click on the folder button to the right of the display field. The names of the images are displayed in the File Name list below the display field.

Sequential

If selected, an image sequence in a certain order (e.g. image dimensions that are encoded by means of numbers in the image name) can be imported.

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Import From

Here you can import images according to a File List or a Multi page image.

Click on the folder button to the right of the display field. The names of the images are displayed in the File Name list below the display field.

Specify the Identifiers

Here you can enter and check all the settings you need to identify your images.

Select Files

Opens a file browser to select the images for import.

Z-Spacing

Sets the slice distance in z. Per default, Auto is activated, and the distance is calculated automatically with information from the image metadata of the first and last selected image.
Deactivate Auto to enter a value manually.

XY-Scaling

Sets the scaling in x and y. Per default, Auto is activated, and the scaling is automatically taken from the image metadata of the first selected image.
Deactivate Auto to enter a value manually, e.g. if you import images without scaling information in the metadata.

Sample Angle

Sets the angle of the sample. Per default, Auto is activated, and the sample angle is automatically calculated from the image metadata or set to the default of 54 degree and the image is rendered with a 90 degree tilt (if no information is available in the metadata). In this case the SmartFIB stack will be displayed perpendicular to the images acquired on a light microscope.
Deactivate Auto to enter a value manually, e.g. if you know the original sample angle as set in the SmartFIB software and import images without using the information in the metadata.

Read XY Offsets

Activated: Reads the xy offset of the individual slices from the metadata. Note that this can lead to a slanted z-stack depending on the sample orientation during imaging and the metadata.

Input

Selects a txm file for import.