Creating new images

To create a new image file

1 Do one of the following:

If an image file is not already open, select File > Open Image(A) > Create Blank Image.

If an image file is already open, select File > Load Image (B)> Create Blank Image. The Raw dialog box (Figure 29) appears.

2 In the dialog box, select the image type.

3 Select the units of measure for each dimension.

4 Enter the header offset and byte ordering information.

5 Click OK. A blank image (Figure 29) appears in an image window.

6 Use the paint and VOI tools to create an image.

7 Click File > Save image as. The Save dialog box opens.

8 Type the name of the file in File Name, and select the file type in Files of type.

9 Click OK. MIPAV saves the image under the file type you selected.

Figure 29. Raw dialog box

Image type	Synonymous with data type. The image type determines the number of intensities that can be represented in an image. For example, a Boolean image can display two intensities: 1 and 0. Boolean-1 bit per pixel (1 on, 0 off) Unsigned byte-1 byte per pixel (0, 255) Unsigned short-2 bytes per pixel (0, 65535) Unsigned integer-4 bytes per pixel (0, 232 -1) Float-4 bytes per pixel (-3.4E38, 3.4E38) ARGB-3 bytes per pixel, plus 1 byte; 8 bits per color channel (alpha, red, green, and blue) Byte-1 byte per pixel (-128, 127) Short-2 bytes per pixel (-32768, 32767) Integer-4 bytes per pixel (-231, 231-1) Long-8 bytes per pixel (-9.22E18, 9.22E18) Double-8 bytes per pixel (-1.8E308, 1.8E308) ARGB U short-2 bytes per color channel and 2 bytes for alpha channel
Dimensions and resolutions	Degree of manifolding of a quantity such as space or time. Two-dimensional datasets are composed of one image (the two dimensions are length and width). Generally, three-dimensional datasets are composed of more than one image. The third dimension is generally space. The fourth dimension is generally time. (Either time or space can be the third or fourth dimensions.) Zeros in the text boxes indicate that the dimension is not represented in the image. For example, if the text boxes for the first and second dimensions are filled, and the rest of the text boxes are filled with a zero, the image only has two dimensions. Dimensions 1st-Width (along x axis) 2nd-Length (along y axis) 3rd-Depth (along z axis) 4th-Time (along t axis) 5th-Fifth dimension Resolutions Size of pixel or voxel per dimensions 1 through 5.
Units of measure	Indicates the unit of measurement for each of the applicable dimensions.
Header offset	Indicates the size of the space reserved at the beginning of the file where specific types of information is kept. This space, which is called the header, precedes the image data. If you know the length of the header, type it in this box. When MIPAV accesses the file, it skips the header offset and begins to read the image data. Note that not all image file formats have a header.
Big endian	Indicates whether image data is stored in the big endian format. If not, the image data is stored in the little endian format. Endianess refers to the byte ordering of the data. Some computers order the data with the least significant byte (LSB) first followed by the most significant byte (MSB). This byte order is referred as little endian or Intel byte ordering. Machines that use little-endian byte ordering are VAXes, Intel x86, and Pentium. The reverse is MSB and then LSB, which is referred as big endian or Motorola byte ordering. Machines that use big-endian byte ordering are IBM System 3D, RISC, and a Motorola 680x0. MIPAV is biendian; it supports both big- and little-endian byte-ordering formats.
OK	Applies the parameters that you specified and creates a blank image.
Cancel	Disregards any changes you made in this dialog box, closes the dialog box, and does not create a blank image.
Help	Displays online help for this dialog box.TBD.

Delineating volumes of interest (VOIs)

MIPAV provides tools that allow you to automatically, semiautomatically, and manually identify and modify volumes of interest (VOIs).
< volume of interest-the portion of the image in the dataset on which you want to focus. It may be either one slice or multiple slices throughout the dataset.

Each VOI can be formed from multiple contours in a single slice or multiple slices. Once an object is segmented and defined by a VOI, statistics of the volume can be calculated.

MIPAV supports over 32,000 unique VOIs on a single dataset. Additionally, you can move or delete nodes on the VOI and add new points. VOI types include:

• Point, which is created by using
• 2D line
• Rectangular
• 3D rectangular
• 2D elliptical
• Polygonal
• 3D polygonal
• Interactive level-set

Generating contour VOIs using predefined shapes

MIPAV includes icons of predefined shapes, such as points, lines, ellipses, or rectangles, that you can use to create VOIs. These icons are on the VOI toolbar.
To generate contour VOIs using the predefined shapes

1 Select one of the contour icons from the VOI toolbar in the expanded MIPAV window. See also Figure 12.

2 Move the pointer to the image window. The pointer changes to a cross-hair shape. Do one of the following:

Points, levelset: Position the cursor on the area where the point or levelset should be drawn. Click the mouse button.

Straight lines, rectangles (2D and 3D), ellipsoids: Position the cursor on the area where the contour should begin.

Click the mouse button.

While holding down the mouse button, drag the cursor until the contour is the desired size.

Polylines, polygons: Position the cursor over the area where the contour should begin.

Click the mouse button. A point appears. Alternate between moving the mouse and selecting the mouse button to outline the VOI.

To complete a polyline, double-click the mouse button. To complete a polygon, connect the first and last nodes.

Tip: To draw the same shape several times in succession, hold down the Shift key while you select the applicable icon from the VOI toolbar and draw.

Adding and moving boundary points on VOIs

No matter which method chosen to delineate a VOI, you can add points and change the boundaries of the VOI. For example, suppose you created a VOI on an image with the Rectangle VOI icon. If you notice that a part of the image that should be included in the VOI is not included, the boundary of the rectangle needs to be adjusted to include the missing portion of the image.
To add a point and change the boundary of the VOI

1 Select the VOI. Notice that white points appear at the corners of the VOI and a small cross appears in the middle of the VOI.
2 Place the cursor on the portion of the VOI you want to adjust. The cursor changes from a cross to.
3 Click once. A white point appears on the line.
4 Select the point and drag it to include the missing part of the image.

Tip:Circular VOIs are composed of a continuous series of points around the diameter of the circle. You only need to select one of those points and drag it to enlarge the circle.

Figure 30. Adding a point and adjusting the boundary of a rectangular VOI

Automatically adjusting contour boundaries

After a contour is drawn, it might be necessary to adjust the boundaries so it more closely matches the VOI region.
To adjust contours
1 Click a contour. The nodes become visible.
2 Select VOI > Evolve boundary 2D >Active Contour. The Evolve Boundary dialog box opens.
3 Modify the information in the window if necessary.
4 Click OK.
A new contour, that more closely outlines the VOI, appears on the image. The old contour also remains.

To delete an old contour, select the contour, and then select Cut Selected Contour, or press the Del key on the keyboard.

Figure 31. Evolve Boundary dialog box

Scale of the Gaussian	Enter values for X,Y, and Z directions which will be used to correct blurring. The default value is 2.0
Resolution options	If this box is checked, the algorithm uses the image resolution to normalize the Z scale.
Evolve Boundary	Replace Original Contour - the original VOI will be replaced with the new one.
Algorithm parameters	Move Boundary - depending on the selected option, the VOI will be moved in 1) any direction, 2) only inward, 3) only outward. Boundary Iterations- specify the number of iterations needed to calculate the new boundary. Smoothness- enter the number from 0.5 to 2.4 to specify smoothness.
OK	Applies the algorithm according to the specifications in this dialog box.
Cancel	Disregards any changes that you made in this dialog box and closes it.
Help	TBD.

Annotating images with text

Another icon on the VOI toolbar is the Annotation tool icon, which you can use to place text directly on an image at any position on the image. You can use any font family, or typeface, that is installed on your computer to display the text.

To annotate images with text

1 Open an image.

2 Click the Annotation tool icon. The Annotation dialog box (Figure 32) opens.

3 Click the image on which you want the text to appear. The image becomes the active image.

4 Select the font family and style (bold or italic). To select a regular font style, simply specify the font family.

5 Type the font size of type in the pt. box.

6 Press Enter. The Annotation dialog box either enlarges or reduces in size depending on the type size you chose (see "Previewing Font Selection" below).

7 Click Color to select the color of the text. The color of the type in the Text box changes to the color you have chosen.

8 Select "Enter text here" and type the text that you want to display on the image in the Text box.

9 Click OK. The text appears near the top of the image.

10 Click the text and drag it to any position on the image.

Figure 32. Annotation dialog box

Font options	Font-Specifies the font family, or typeface, for the text. When you select another typeface, "Enter text here" appears in that typeface.
	Bold-Specifies that the type style should be bold.
	Italic-Specifies that the type style should be italic.
	Pt. (point) size-Specifies the point size of the typeface.
	Color-Specifies the color of the text. When you click this box, the Pick VOI Color dialog box opens.
Text	Displays the text that should appear on the image.
Marker options	The arrow marker appears if you check the Use Arrow Marker box.
OK	Applies the parameters that you specified and places the text on the image, which you can move to any position on the image.
Cancel	Disregards any changes you made in this dialog box, closes the dialog box, and does not place text on the image.
Help	Displays online help for this dialog box.

Previewing Font Selection The Annotation dialog box allows you to preview the font family, style, size, and color of the text before you click OK and add the text to the image.