Difference between revisions of "Creating new images"
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− | + | '''To create a new image file'''<br /> | |
− | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Do one of the following: <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If an image file is not already open, select File > Open Image(A) > Create Blank Image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If an image file is already open, select File > Load Image (B)> Create Blank Image. The Raw dialog box (Figure 29) appears.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 In the dialog box, select the image type. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 Select the units of measure for each dimension. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Enter the header offset and byte ordering information.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 5 Click OK. A blank image (Figure 29) appears in an image window.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 6 Use the paint and VOI tools to create an image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 7 Click File > Save image as. The Save dialog box opens.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 8 Type the name of the file in File Name, and select the file type in Files of type.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 9 Click OK. MIPAV saves the image under the file type you selected.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | |
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<div class="CellBody">Displays online help for this dialog box.TBD.</div> | <div class="CellBody">Displays online help for this dialog box.TBD.</div> | ||
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== Delineating volumes of interest (VOIs) == | == Delineating volumes of interest (VOIs) == | ||
− | + | '''MIPAV''' provides tools that allow you to automatically, semiautomatically, and manually identify and modify volumes of interest (VOIs). <br />< | |
− | + | '''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.<br /> | |
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. | 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. | ||
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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: | 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 === | === Generating contour VOIs using predefined shapes === |
Revision as of 19:19, 16 February 2012
To create a new image file
Image type
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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
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Dimensions and resolutions
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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.
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Units of measure
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Indicates the unit of measurement for each of the applicable dimensions.
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Header offset
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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.
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Big endian
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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.
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OK
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Applies the parameters that you specified and creates a blank image.
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Cancel
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Disregards any changes you made in this dialog box, closes the dialog box, and does not create a blank image.
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Help
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Displays online help for this dialog box.TBD.
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Contents
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
Adding and moving boundary points on VOIs
Automatically adjusting contour boundaries
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
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Enter values for X,Y, and Z directions which will be used to correct blurring. The default value is 2.0
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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
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. |
To restore the text to the image, select Edit > Undo VOI. The text reappears on the image.
Calculating VOI statistics
Using VOI properties
The Include for Processing option is very helpful if you have a set of VOIs delineated on your image and want to use some of them for masking. In that case, select the VOI(s) of interest, then activate the Include for Processing option, and after that, call one of the mask tools, e.g. the Quick AND VOI mask operation. The tool will apply on the selected VOI(s). In case when the Include for Processing option has not been activated, then the Quick AND VOI mask operation will apply on the whole image and darken it. See [MIPAV_QuickStart.html#2829292 Figure 34] (a) and (b).
Figure 34. Using the Include for processing option for the Quick AND VOI mask operation. (a) The Include for Processing option is activated and (b) the Include for Processing option is disabled.
Using the Statistics Generator
Using the Statistics Generator involves three tasks: