Image Export

This method allows you to export single images into various file types so that you can continue to use them in other programs. Multidimensional images (e.g. multichannel, z-stack, tile images) are exported as individual images.

File Type Section

Name		Function
File Type		Select the desired file type from the dropdown list: JPEG File Interchange Format (JPEG) Windows Bitmap (BMP) Tagged Image File Format (TIFF) Tiff Format (64 bit) (Big TIFF) Portable Network Graphics (PNG) JPEG XR (WDP) DigitalSurf SUR (SUR) Note that different options are available depending on the file type you have selected. It is recommended to work with the Carl Zeiss Image format (.czi). CZI has lossless compression and best compatibility within the ZEISS ecosystem. The format also includes metadata that allow the reuse of imaging parameters.
Quality		Only available for the file types JPEG and JPEG XR. Enter the image quality using the slider or input field to influence the size of the file. Although low values result in very small files, image quality may be considerably reduced.
Resize		Adjust the image size in percent using the slider or input field. The resizing uses an algorithm for point-sampling from the nearest pyramid tile (the nearest pyramid tile which has higher resolution, so there is only sub-sampling and no up-sampling). Online pyramid is sub-sampling by a factor of 2, using a 5x5 Gaussian kernel, and offline pyramid is sub-sampling by a factor of 3, using a binomial kernel.
Convert to 8 Bit		Only available for the file types TIFF, BigTIFF, PNG and JPEG XR. Activated: Converts a 16 bit gray level image into an 8 bit gray level image, or a 48 bit color image into a 24 bit color image.
Compression		Only available for the file type TIFF and BigTIFF. Selects the compression method for reducing the data size.
-	None	Retains the data size of the original image. No compression is performed.
-	LZW	Only available for the file type TIFF. Performs lossless compression in accordance with the Lempel-Ziv-Welch algorithm (LZW).
-	ZIP	Only available for the file type TIFF. Performs lossless compression in accordance with the ZIP method.
-	Lossless	Only available for the file type BigTIFF. Performs lossless compression in accordance with the Lempel-Ziv-Welch algorithm (LZW).
-	Lossy	Only available for the file type BigTIFF. Performs lossy compression in accordance with the JPEG XR (extended range) method.
BigTIFF		Only available for the file type BigTIFF. Activated: Generates a BigTIFF image. The maximum image size is larger than 4GByte. Deactivated: Generates a TIFF image with maximum size of 4GByte.
TIFF Tiles		Only available for the file type BigTIFF. Activated: Generates new rectangle tiles for internal data handling. Deactivated: Combines tiles as stripes for internal data handling.
Pyramid		Only available for the file type BigTIFF. Activated: Calculates an image pyramid.
Merge All Scenes		Only available for the file type BigTIFF. Activated: Generates one image including all scenes. Deactivated: Generates single scene images.

Image Data Section

Parameter		Description
Original Data		Activated: Exports the image with the original channel colors and the original display characteristic curve.
–	Shift Pixel	Activated: The pixel are shifted to 16 bit before converting to 8 bit. For example, a 14 bit image is first transformed to a 16 bit image, which is then converted to an 8 bit image. The 14 bit range is mapped to the whole 8 bit range. Deactivated: No shift takes place. A 14 bit image is treated as a 16 bit image and therefore the transformation to 8 bit covers only a reduced range.
Apply Display Curve and Channel Color		Activated: Exports the image with the changed channel color and display characteristic curve settings. These settings are applied to the pixel values of the exported images. They are particularly important if you want to use dark images with a dynamic range of more than 8 bits in other programs.
–	Burn-in Annotations	Activated: Burns the graphical elements into the image. The pixels under the graphical element (e.g. scale bars) are overwritten. The burnt-in graphical elements cannot be modified.
–	Burn-in Analysis Results	Only available if Burn-in Annotations is activated. Activated: If the image contains analysis results, the masks of the results are burned into the image.
–	Zoom	Only available if Burn-in Annotations is activated. Sets the zoom of graphic elements for export. Note that this is only applied to regions for which Zoom with Image is deactivated in the Format Graphical Elements dialog, see Format Graphical Elements Dialog. The default is 100%, which means that the graphical elements are rendered as they would if the viewer zoom was 100%. When the zoom increases, the graphical elements are rendered larger (e.g. with zoom 200, graphical elements are rendered twice as large, but it corresponds to the size they would have if the viewer zoom was 50%).
–	Get Zoom from Viewer	Only available if Burn-in Annotations is activated. Gets the current zoom factor of the graphical elements in the 2D view.
–	Merged Channels Image	Only visible for multichannel images. Activated: Exports the pseudo color image of all selected channels.
–	Individual Channels Image	Only visible for multichannel images. Activated: Exports the individual colored image of all selected channels.
Short Format		Selects which type of naming convention is used for the exported image, see Naming Convention for Image Export. Activated: Uses the short format naming convention. This is the default setting. Deactivated: Uses the long format naming convention.
–	Use Channel Names	Only visible for multichannel images. Activated: Integrates the channel name in the name of the exported image.

Dimensions Section

Parameter	Description
Use Full Set of Dimensions	Select this option if you want to export all dimensions without changing them.
Define Subset	Select this option if you only want to export individual dimensions or subsets of individual dimensions.

Each of the sections described below is only visible if the corresponding dimension is present in the input image.

Parameter		Description
Channels		Here you can select which channels of the input image you want to be used. All channels are selected by default. To deselect a channel, click on the relevant channel button.
Z-Position, Time, Block, Scene		Here you can select which parts of the input image you want to use for the resulting image.
-	Extract All	If selected, all parts of the corresponding image are extracted.
-	Extract Single	If selected, you can select a single image to be extracted.
-	Extract Range	If selected, you can select a certain range of images to be extracted.
-	Extract Multiple	If selected, you can select several continuous ranges and individual sections. Enter one or more sections that you want to select in the input field. To do this, enter the first section, followed by a minus sign, and then the last section. If you want to define an interval, after the last section enter a colon and then the interval. The entry "2-10:2" means that every second section is selected from section 2 to section 10. Enter a comma after the first section if you want to define another section. You can also select individual sections separated by commas. By entering "2-10:2,14-18,20,23", you select every second section from section 2 to section 10, followed by sections 14 to 18, as well as sections 20 and 23.
-	Get current position	Adopts the position from the current display in the image area.
-	Interval	Activated: Interval mode is active. The Interval spin box/input field appears. Enter the desired interval here. E.g. if you enter the value 2 only every 2nd value from the range is considered.
Region		Here you can select if you want to use the entire image or just a region (ROI) of the input image. Note that in combination with image dimensions, the rectangle is only drawn into one and only this is considered for export. For example, in an image with multiple scenes, the image export only considers the ROI that is always drawn into the currently displayed scene defined by the Dimensions view options tab.
-	Full	If selected this option, the full image is used for the new image.
-	Rectangle Region (ROI)	If selected this option, you can draw in a rectangle region of interest which is used for creating a new image. If a rectangle region is drawn in, you can see and change its coordinates by editing the input fields for X, Y, W, and/or H.
Tiles		Not available for the OME TIFF Export.
-	Export Selected Tiles	Exports the tiles according to the selected original image.
-	Crop to Selection and Generate New Tiles	Creates new tiles according to your entries in the fields Columns/Rows and Overlap.
-	Columns/Rows	Only available if Crop to Selection and Generate New Tiles is activated. Defines, with how many rows and columns the re-tiling is performed.
-	Overlap	Only available if Crop to Selection and Generate New Tiles is activated. Defines the overlap of the re-tiled tiles in %.

Export To Section

Parameter		Description
Export To		Sets path to the folder where images are exported to.
Create Folder		Creates a folder for your exported data.
Generate xml File		Creates xml files, containing general information and metadata information for the exported image(s).
–	Long Format	Activated: Selects the long format naming for the xml files, which includes the file type suffix in the xml titles as well as metadata for the metadata xml, see Naming of xml Files for Exported Images.
–	Short Format	Activated: Selects the short format naming for the xml files, which excludes the file type suffix from the xml titles as well as shortens metadata to meta for the metadata xml, see Naming of xml Files for Exported Images.
Generate zip File		Exports the image as a .zip file.
Prefix		Adds the specified name as a prefix to the exported data. By default, this is the name of the original image data. For information on naming conventions, see Naming Convention for Image Export.
Defaults		Sets the settings back to default.

Image Export

File Type Section

Image Data Section

Dimensions Section

Export To Section

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