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 ([MIPAV_QuickStart.html#1074295 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 ([MIPAV_QuickStart.html#1074295 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

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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 [MIPAV_QuickStart.html#2693625 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

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