Difference between revisions of "Understanding Image Basics"
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== Supported graphic formats overview == | == Supported graphic formats overview == | ||
− | + | MIPAV supports three categories of graphic file formats: vector (i.e., volume of interest, or VOI), bitmap (i.e., 2D to 5D grayscale or RGB images), and 3D images.<br />'''Vector file formats ''' are usually used to store line-based elements. These elements can be geometric shapes, such as polygons, curves, or splines. MIPAV can read and generate several vector-formatted file types including the MIPAV lookup table (LUT), MIPAV MTX, MIPAV Graphics Plot (PLT), and MIPAV VOI. See also [[Supported Formats|Appendix C: "Supported formats" ]].<br />'''Bitmap file formats''' are usually used to store real-world graphics data e.g., photographs or medical images such as CT scans. The data portion of bitmap files contains numerical data that indicates the color of each pixel or voxel in the image. MIPAV can read and generate a number of bitmap formatted file types, such as Adobe Photoshop (PSD), Graphics Interchange File (GIF), Sun Raster (RS), Tagged Image File Format (TIFF), and Truevision Graphics Adapter (TGA).<br /></font>'''MIPAV uses 3D graphic formatted files''' to store descriptions of the color and shape of 3D models of real-world and imaginary objects.<br /> | |
− | + | To support the wide range of image-processing needs of the NIH intramural research community, MIPAV reads and writes the image file types indicated in Table 1, refer to [[Supported Formats |Appendix C: "Supported formats"]]. <br /> | |
== Understanding the MIPAV dimensionality and coordinate system == | == Understanding the MIPAV dimensionality and coordinate system == |
Revision as of 15:26, 17 February 2012
Contents
Understanding Image Basics
In this chapter. . .
- Supported graphic formats overview
- Understanding the MIPAV dimensionality and coordinate system
- Data types
- Headers
- Endianness
- Viewing and editing image attributes
This chapter also explains the dimensionality and coordinate system used by MIPAV, the data types MIPAV supports, the header offset information, endianness, and how to view and edit image attributes.It also provides a basic information about image file formats supported by MIPAV. More information about graphic file formats and the formats that MIPAV supports can be found in Appendix C: "Supported formats" .
Supported graphic formats overview
MIPAV supports three categories of graphic file formats: vector (i.e., volume of interest, or VOI), bitmap (i.e., 2D to 5D grayscale or RGB images), and 3D images.
Vector file formats are usually used to store line-based elements. These elements can be geometric shapes, such as polygons, curves, or splines. MIPAV can read and generate several vector-formatted file types including the MIPAV lookup table (LUT), MIPAV MTX, MIPAV Graphics Plot (PLT), and MIPAV VOI. See also Appendix C: "Supported formats" .
Bitmap file formats are usually used to store real-world graphics data e.g., photographs or medical images such as CT scans. The data portion of bitmap files contains numerical data that indicates the color of each pixel or voxel in the image. MIPAV can read and generate a number of bitmap formatted file types, such as Adobe Photoshop (PSD), Graphics Interchange File (GIF), Sun Raster (RS), Tagged Image File Format (TIFF), and Truevision Graphics Adapter (TGA).
</font>MIPAV uses 3D graphic formatted files to store descriptions of the color and shape of 3D models of real-world and imaginary objects.
To support the wide range of image-processing needs of the NIH intramural research community, MIPAV reads and writes the image file types indicated in Table 1, refer to Appendix C: "Supported formats".
Understanding the MIPAV dimensionality and coordinate system
The voxel in the upper left-most position is considered the origin of the dataset. (A volumetric dataset is a set of cross-sectional images). Ideally, each voxel would be isotropic (i.e., cubic), but clinical datasets are often acquired in such a manner that the resolution in the x and y dimensions is greater than the resolution in the z dimension, thus producing rectangular voxels (elongated in the z direction). This voxel anisotropy is taken into account in the execution of the algorithms found in MIPAV.
Because MIPAV's image storage buffer is n-dimensional, it can store 2D, 3D, and 4D medical images. CT and MRI are examples of 3D medical images where the three dimensions (x, y, and z) are spatial dimensions. Other 3D datasets include fluoroscopy volumes, where the first two dimensions are spatial and the third dimension is time.
Data types
Data type
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Description
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Boolean
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1 bit per pixel/voxel (1 on, 0 off)
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Signed byte
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1 byte per pixel/voxel (-128, 127)
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Unsigned byte
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1 byte per pixel/voxel (0, 255)
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Signed short
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2 bytes per pixel/voxel (-32768, 32767)
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Unsigned short
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2 bytes per pixel/voxel (0, 65535)
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Integer
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4 bytes per pixel/voxel (-231, 231-1)
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Long
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8 bytes per pixel/voxel (-9.22E18, 9.22E18)
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Float
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4 bytes per pixel/voxel (-3.4E38, 3.4E38)
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Double
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8 bytes per pixel/voxel (-1.8E308, 1.8E308)
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Color 32
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3 bytes per pixel/voxel, plus 1 byte; 8 bits per color channel (alpha, red, green, and blue)
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Headers
Endianness
Viewing and editing image attributes
The Image Attributes window displays the name of the image file and information about the resolution of the image. The About Image window displays more detailed information about the image, such as the orientation of the image or the number of bits per pixel or voxel.
Viewing image attributes
Editing image attributes
By default, the General page always appears first when the Image Attributes dialog box opens.
Image Attributes dialog box
Apply | applies the changes to the current image, but doesn't close the dialog box. | |
OK | applies the changes to the current image and closes the dialog box. | |
Close | closes the dialog box without applying the changes to the image. | |
Help | opens the on-line help. | |
General tab | ||
Image name (without suffix) | displays the name of the current image. You can change the image's name here. | |
Image modality | shows image modality. You can change the modality by selecting it from the list. | |
The list includes: | Unknown Modality, Biomagnetic Imaging, Color Flow Doppler, Computed Radiography, Computed Tomography, Diaphanography, Digital Radiography, Duplex Doppler, Endoscopy, External Camera Photography, FA, General Microscopy, Hardcody, ICG, Intraoral Radiography, Laser Surface Scan, Magnetic Resonance Angiography, Mammography, Magnetic Resonance, Nuclear Medicine, Other, Positron Emission Tomography, Panoramic X-ray, Radio Fluoroscophy, Radiographic Imaging, Radiotherapy Dose, Radiotherapy Image, Radiotherapy Plane, Radiotherapy Record, Radiotherapy Structure Set, Red Free, Slide Microscopy, Single Photon Emission Computer Tomography, Thermography, Ultrasound, and X-ray Angiography. | |
Image endian order | Here, use the appropriate radio button to set the image endiannes. | |
Resolutions tab | ||
1-5 dimension | shows resolution for each dimension. | |
Slice thickness | shows the slice thickness. | |
Units of measure | displays the units of measure used in the image. | |
Orientation/Origin tab | ||
Image Orientation | Medical image data are stored in a variety of ways. In order to orient a two-dimensional image slice or three-dimensional volume in space, one needs to know how the order of the image data relates to a standard set of axes. For medical imaging, these axes are generally chosen to correspond to the directions posterior/anterior'superior/inferior [[1]]. This information could be found from the image header. To change image orientation, select one from the list: Axial, Coronal, Sagittal, or Unknown. See also "About medical image coordinate systems." | |
X-axis orientation (image left to right) Y-axis orientation (image top to bottom) Z-axis orientation (into the screen) |
To specify X, Y, or Z -axis orientation, select one from the list: Unknown, Patient Right to Left, Patient Left to Right, Patient Anterior to Posterior, Patient Posterior to Anterior, Patient Inferior to Superior, Patient Superior to Inferior. Here, the head end is referred to as the superior end, while the feet are referred to as the inferior end. Anteriorrefers to the "front" of the individual, similarly, posterior refers to the "back" of the individual. Left and right are self explanatory. | |
X-axis origin Y-axis origin Z-axis origin |
The image origin is generally at the corner of the image, often the upper left, the axis directions are: the X- axis is across, Y -axis is down, and Z-axis goes into the screen. Usually, it differs from matrix coordinates and Cartesian coordinates. E.g. for the above image, the origin coordinates shown in the dialog box are as follows: x=0,z=0, and y=-239.0625, which corresponds to the scanner frame of reference and scanner origin coordinates. If you mouse over the image, MIPAV will show you the coordinates from the image frame of reference. | |
4-th dimension | For 4D images, it specifies the units and values used for the 4-th dimension. | |
Transform matrix | ||
Matrix | displays a list of transformation matrix for the chosen image. | |
Transform. ID | displays transformation ID type for the chosen image. To change the current transformation matrix, select a new transform ID first, and then click Replace. This will replace the transformation matrix. | |
Replace | replaces a current transformation matrix to a new one that you choose. | |
Add a New | adds a transformation matrix that has been selected from the Transform ID list to the image. | |
Rename | renames a transformation matrix. | |
Copy | copies the current transformation matrix to the Clipboard. | |
Paste | pastes a copied transformation matrix | |
Load | loads a transformation matrix (from a file with the *.mtx | |
Save | saves a transformation matrix to a file. | |
Identity | transforms the current transformation matrix to an identity matrix. | |
Invert | inverts the current transformation matrix. | |
Composite | TBD. | |
Decompose | TBD. | |
Talairach | ||
Shows ACPC and Talairach transformation matrices. | ||
Include Talairach - displays a Talairach transformation matrix for the image. | ||
Load -loads a new matrix. | ||
Save - saves a matrix to a file. | ||
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What's the Difference Between Clicking Apply or Clicking OK? Click Apply when you want the dialog box or window to remain open after it makes the change so that you can make further modifications. If instead you click OK, the dialog box or window closes immediately after making the current change.
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