Next: 5. Looking At Images Up: 1 A. Overview Previous: 3. Starting and Running Contents
Subsections
4. Application Structure
4.1 Application Structure Overview
All BioImage Suite applications (e.g. the Brainsegment tool shown above) consist of typically three parts (a) a menu bar at the top, (b) a viewer in the middle and (c) a status bar on the bottom. The exception to this rule are the registration tools which have a main registration application consisting of a menu bar and a status bar and a pair of viewers (Reference Viewer and Transform Viewer) each containing the two images.
There are two basic viewers in BioImage Suite: the Orthogonal Viewer and the Mosaic Viewer. The Orthogonal Viewer also has two extended versions: the 4D Orthogonal Viewer which adds Movie/Cine mode for Cardiac applications and the objectmap viewer (used in Brain Segment, shown above) which allows for the transparent overlay of a presegmented image map (an objectmap) on the original image.
The menu for each application consists of a subset of common options and additional options specific to the application. The following common submenus are available in most applications:
- File Menu - this provides options for Loading/Saving Images as well as looking at Image Properties - described below.
- Display Menu - options for displaying different images - described below
- Image Processing Menu - options for image histogram display/manipulation and image processing tools. Described in more detail here.
- Segmentation Menu - Options for image segmentation, including thresholding/mathematical morphology, histogram clustering, and Markov Random Field (MRF) smoothing. In addition, facilities are included for Levelset segmentation and Bias Field Correction, as well as integration to the FSL software package for use of its Brain Extractor and Gray/White Segmentation Tools. Described in more detail here
- Features Menu - Facilities for clicking and manipulating landmarks, surfaces and surface objectmaps. Additional options may be available here depending on the application
- Talairach Menu - Options for setting the custom transformation for mapping image coordinates to stereotactic space.
- Additional application specific menus may also be present here.
- Help Menu - provides access to the ``Preferences Dialog''
4.2 The File Menu
Loading an Image:
To load an image into the viewer's display, simply choose (File | Load) and select an image header file from the dialog box.
Saving an Image:
Similarly, to save the image currently in the ``Image'' display, choose (File | Save), choose a directory with the dialog box, and input a file name. Images are saved in the NIFTI file type. A header is written based on the image dimensions, as well as any information you specified upon import, if the image was imported from another file type, as described in the next section. This command saves the currently displayed image regardless of whether this is the ``Image'' or ``Results'' as described in the Display Menu below.Byte swapping Depending on what platform the data will be used, you may wish to check the ``Swap Bytes on Save'' option when saving your images. A 16-bit integer requires two bytes to save; one that contains the value for the lower portion (0-255) and one for the higher portion (256-65535). Intel-based machines store the least significant (little) byte first, followed by the more significant byte. This is referred to as ``little-endian'' storage. Other computers, based on the Motorola 68000 family of processors, however, store integers in the opposite order (``big-endian'' storage). The situation is the same when dealing with floating-point and double-precision numbers, which require 4 or more bytes to save. BioImage Suite deals with all these data types, and when reading files, checks to ensure that the byte order is correct (by ensuring that data is within a reasonable numerical range when read for the first time). However, if you are planning on using data processed with BioImage Suite in Windows in other software running on an older SGI machine, for example, you may need to swap bytes on saving. In most cases, you should not enable byte-swapping on save.
Switch Directory:
This is a very simple convenience feature. It simply switches the base directory currently used by the viewers. Thus, when you go to open a file, the file selection dialog box will begin in this directory. This way, you do not have to navigate back to the same directory repeatedly. Select (File | Switch Directory) and choose a directory. That's it. Now any other file open dialog box will begin at this directory. It is the equivalent of the Unix ``cd'' command!
Standard Images
The (File | Standard Images) flyout contains links to a number of standard images and masks in Analyze format that may be useful for comparisons, as well as experimentation with various program features.
Custom Images and Directories
A user can add links to their frequently used images or directories using the (File | Custom Images) or (File | Custom Directories) menu item. This allows for faster access and eliminates lengthy navigations to a certain data directory. The files can be added by going to the (File | Custom Images | Add) option. The left image in Figure 4.2 shows the location of the ``Custom Images'' menu item and the right image shows the result of adding two images.
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The list of images can be edit by clicking on (File | Custom Images | Edit) which brings up a window that lets you select/deselect images. Figure 4.3 shows an example where the two added images can be seen. By clicking on any image in the list, it gets deselected and is shown with a white background. All the selected images are shown with a blue background.
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The list of these images is read from a file called .pximagelist in each users' home directory. Clicking on (File | Custom Images | Info) brings up a box that informs the user of the location of the file, as shown in Figure 4.4. The format is simply a set of lines (all lines beginning with # are treated as comments and are ignored) as shown below for the two files:
#BioImage Suite File # Format # Image Files : Full Filename # e.g # MyFile : myfile .hdr .hdr.gz .nii .nii.gz mouse_hessian : C:/yale/testing/images/vessel/mouse_hessian.hdr absStd : C:/yale/bioimagesuite26/images/absStd.hdr
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Similarly, Custom Directories can be added by clicking (File | Custom Directories | Add). The Add, Info, Edit operations are the same as ``Custom Images,'' except that the name of the file containing the list of directories is called ``.biodirlist'' instead of ``.pximagelist''.
Image Header Editor:
The (File | Image Header Editor) menu choice brings up a tool that allows you to explicitly view and/or edit the header file for an NIFTI/Analyze format image loaded into the viewer. Any changes to the values put into these fields will not take effect until the image is saved and reloaded.
Importing and Exporting:
The (File | Export) Command allows you to save the image in the viewers ``Image'' display as a set of JPEG images, corresponding to each of the native image slices Invoking the (File | Import) command brings up the Import dialog box, which lets you open images of various file types. The ``Filename'' tab contains a file selection box with possible file types for import. Currently supported file types are: NIFTI, Analyze, Signa LX, Prism (SPECT), Binary, Raw MR, Signa SPR, Nmr47, TIFF, PNM, BMP, and JPEG. The ``Properties'' tab lets you edit the information contained in the Image Header of the file you are importing. This will be saved with the image when you save it as an NIFTI/Analyze file. If the image for import is not in the Analyze format, the header info will be mostly empty, but will contain information about the dimensions of the image selected. You can also fill in values, which will be written into the header when you save your Analyze file. A more detailed description of this complex control will be made available soon.
4.3 The Display Menu
4.3.0.0.1 ``Images'' and ``Results'':
Most applications incorporating a viewer in BioImage Suite, maintain two images simultaneously in memory. One image is stored as the ``Image'' display, and the other is stored as the ``Results'' display. When you perform an operation on an image, the output is sent to the ``Results'' display, which then becomes active (and visible). In order to do more calculations on the result, it must be copied into the ``Image'' display. To check which display is active, click the Display menu; the radio button associated with the active image will be highlighted.Under the Display menu, you will find two options: ``Image'' and ``Results'' When an operation is performed on an image, the results are saved in the ``Results'' display of the viewer. This allows you to revert back to the original image, which still resides in the ``Image'' display. In order to perform further operations on a result image, you must choose (In order to perform further operations on a result image, you must choose (Display | Copy Results to Image). This will overwrite the Image display with the Results display. This process can be undone, uncommitting any changes that have been made and reverting back to the image in memory before copying results, by using the (Display | Undo Copy Results) command. The top two commands in the ``Display'' menu, ``Image'' and ``Results'' simply select which display image is shown. Choosing one does not delete the other - the opposite display image is simply hidden. It can be accessed by switching back. It is important to note that most of the operations provided by the Image Processing toolbox and other analysis tools take the Image Display as input and send their output to the Results display. In order to work with them further, the results must be copied to the Image display.
4.3.0.0.2 Mask Image:
When the application makes use of the ObjectmapOrthogonal Viewer (which can be identified by the presence of a ``Mask'' Slider above the ``X-Coord'' slider) there is an additional image in memory - the mask which can be transparently overlaid on the underlying image. In addition, in such cases, two additional options appear under the Display Menu, namely ``Copy Mask to Image'' and ``Copy Mask to Results'' which allow for better access to the mask image.
Next: 5. Looking At Images Up: 1 A. Overview Previous: 3. Starting and Running Contents