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Image Loader

Dragonfly's Image Loader works like a wizard, in which a succession of screens — Load Data and Image Settings — are presented to help you navigate the process of importing image files. In addition, two optional dialogs — Preview and Crop the Image — are available to preview datasets and to select the cropping settings. You should note that supported file formats can be imported from local and network drives or from storage devices such as CDs, DVDs, and USB keys (see Supported File Formats).

See Miscellaneous Preferences for information about selecting a default loader for application start.

Load Data

The first step of importing image files is to choose the files you want to import. This task can be accomplished on the Load Data screen, shown below.

Load Data screen

*Options for loading datasets*
	Description
Add	Opens a standard Add File(s) dialog. All standard image files must all be of the same size and type so that multiple 2D image files can be combined into a single 3D volume. For this reason you cannot add multiple TIFF stacks, raw data, or other 3D volumetric image files. To facilitate the file selection process, the following pre-defined file types are available — TIFF, TXM, JPEG, PNG, Bitmaps (BMP, DIB), RAW, DAT, Analyze 7.5 or NIfTI, REK, MRC, and ORSObject (see Supported File Formats).
Open Folder	Opens a standard Current Folder dialog that allows you to choose a folder. All files in the selected folder, and its subfolders, will be added to the list of files to be imported.
Remove	Removes selected files from the list.
Recent Files	Click this button to select from a list of recently imported files.
Reverse sort	Changes the sort order of image files added to the Image Loader. If checked, the last image in the image sequence will become the first image in the stack and the first image in the sequence will become the last.
See Preview	Click this button to view the selected file in a Preview window (see Previewing Images).
Use Another Loader	Lets you choose a different loader — the DICOM Loader, Mesh Loader, or Session Loader — to import data. DICOM Loader… Opens the Manage DICOM Images dialog, in which you search for and open DICOM image files (see Using the DICOM Loader). Mesh Loader… Lets you choose a mesh to load (see Importing Meshes). Session Loader… Opens the Load Session File dialog, in which you can load a saved session file (see Loading Sessions).

Previewing Images

Before importing a dataset, you can preview any TIFF file in an image stack as well as scroll through a preview of raw data.

Image Settings

You can select settings for image sampling, data offset and slope, axis transformations, as well as crop an image during the import process. You can also choose to continue importing additional image files. These options are available on the Image Settings screen, shown below.

Image Settings screen

You can select the following in the image settings when you import datasets.

*Image settings*
	Description
Image group	You can enter a new name for the imported dataset here, if required. Implementing a naming convention is recommended if you typically work with multiple datasets at the same time.
Image sampling	By default, the image sampling values are always set to “1”. If you choose to resample your image, you can do so by modifying the X-Y-Z values. Increasing the X-Y-Z values will reduce the number of data units used to represent your visual. For example, if X = 5, then only one layer out of every five will be imported into the image. This can be useful if you need to manipulate very large datasets. The same principle applies to the time parameter (T). X, Y, Z… Determines the sampling rate for the X, Y, and Z axes. T… Determines the sampling rate for time volumes.
Time steps	By default, the number of time steps is set to “1”. If you are importing a dataset with a time dimension, you may need to manually enter the number of time steps in this edit box. If that information is present in the file being imported, the correct value will appear automatically in this field. You should note that the number of time steps must be a factor of the number of images in the dataset.
Image spacing	This number represents the absolute distance between slices of data. Some file formats, such as DAT files exported from Dragonfly, contain this information, in which case the fields will automatically show the correct values. For other file formats, you may have to set these values accordingly.
Physical conversion	Some file formats contain this information, in which case the fields will show the correct values. If not, you can select values for these fields as follows: *Offset… Changes the default Offset value. Offset is a basic transfer function that controls the brightness of an image. The nominal value is 0. Slope…* Changes the default Slope value. Slope is a basic transfer function that controls the contrast of an image. The nominal value is 1. Unit… Determines the type of units associated with the dataset, such as intensity or density. * See Image Properties for more information about these parameters.
Transform	Determines the sequence in which the dataset will be parsed. Data is typically structured inside a Cartesian coordinate system following the right-hand rule. Invert X axis… If selected, all data along the X axis will be read from maximum to minimum values. Invert Y axis… If selected, all data along the Y axis will be read from maximum to minimum values. Invert Z axis… If selected, all data along the Z axis will be read from maximum to minimum values. Invert intensity… If selected, all data values will be inverted. Axis transformation… Lets you choose which axis alignment will be displayed by default — X-Y-Z, X-Z-Y, Y-X-Z, Y-Z-X, Z-X-Y, Z-Y-X. Crop Image… Opens the Crop the Image dialog, in which you can select the portion of the image data that you want to load (see Cropping Image Data). Reset Crop… Discards the selected image cropping settings.
Information	Displays a summary of the file that will be imported, including its size, dimensions, bit depth, and mode. Total size… Indicates the total byte count, calculated as XYZT. Width (X)…* Indicates the number of pixels along the X-axis. Height (Y)… Indicates the number of pixels along the Y-axis. Depth (Z)… Indicates the number of pixels along the Z-axis. Time steps (T)… Indicates the number of time steps. Bits… Indicates the bit depth. Mode… Indicates the mode — either Grayscale or Color.
TXM axis transformation*	Provides additional options for importing TXM files. Scout and Zoom mode (XYZ)… If selected, imports TXM files with an XYZ matrix encoding consistent with ZEISS Xradia stage coordinates. This is the recommended option for importing TXM files. Legacy Mode (XYZ)… If selected, imports TXM files with standard XYZ matrix decoding. This was the default behavior for all releases of Dragonfly Pro prior to version 3.6. Other transformation… If selected, then a ZYX axis transformation will be applied. You should note that you can also make your adjustments in the Axis transformation drop-down menu in the Transform box that is available for all file formats. Note This option is available for Dragonfly Pro only. Contact Object Research Systems for information about the availability of Dragonfly Pro.
RGB output	Provides additional options for importing RGB images* when the selected data contains color information. As three separate channels… If selected, all three channels — Red, Green, and Blue — will be loaded and each separate channel will be identified as to its originating channel in the Data Properties and Settings panel. For example, Blue Imported Data. As one luminance channel… If selected, the RGB image will be converted into a single-channel luminance representation. In Dragonfly, the conversion of an RGB image to a luminance channel is computed as follows: Luminance = 0.2126R + 0.7152B + 0.0722G (refer to https://en.wikipedia.org/wiki/Grayscale for more information about luminance conversions). As one grayscale channel (RBG channels are identical)…* If selected, one channel will be loaded. You should note that if the Image Loader determines that all three channels are not identical after the loading, a message box will appear. * The above options are not available for RGBA images. For these images, all four channels — Alpha, Red, Green, and Blue — will be imported and added automatically to the Data Properties and Settings panel. Note You can export RGB channels in the BMP, JPEG, PNG, and TIFF file formats. Select the three separate channels on the Data Properties and Settings panel — Red, Green, and Blue — right-click, and then choose Export as RGB in the pop-up menu. You can drag channels up and down to match them to a specific output in the Export as RGB dialog, as well as replace channels.
Continue importing	Provides options for importing additional datasets. Import another dataset… Check this option if you plan to import an additional dataset. Keep same geometry… Check this option if want the dimensions of the next dataset that is imported to be consistent with the current dataset. If required, datasets will be clipped to the dimensions of the current dataset or to the cropping that was applied to the original dataset.

* This option is available for Dragonfly Pro only. Contact Object Research Systems for information about the availability of Dragonfly Pro.