Imaging Systems: Transforms & System Theory

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Questions and Answers

Which of the following best describes what a transform does in the context of image analysis?

  • It always converts a color image to grayscale.
  • It directly enhances the resolution of an image.
  • It removes all noise from the image.
  • It maps image data from one mathematical space to another. (correct)

Orthogonal basis images are preferred in image transforms because they introduce redundant information.

False (B)

What key parameter does the Modulation Transfer Function (MTF) quantify in imaging systems?

contrast

The Nyquist criterion dictates the minimum ______ frequency required to avoid losing information during digitization.

<p>sampling</p>
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Match the following imaging modalities with their primary strengths:

<p>Computed Tomography (CT) = Excellent for imaging bone and detecting bleeding or trauma. Magnetic Resonance Imaging (MRI) = Superior for visualizing soft tissues and neurological structures. Ultrasound (US) = Useful for real-time imaging, non-invasive, and safe for imaging fluid paths. Nuclear Medicine (PET/SPECT) = Strength is functional imaging and is used extensively in heart and bone marrow imaging.</p>
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What is the purpose of applying digital pulses to the gates in CCD (Charge-Coupled Device) image sensors?

<p>To shift charges from one pixel to another towards a serial output register. (D)</p>
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Photomultiplier Tubes (PMTs) store electric changes, making them less ideal for extremely fast events compared to CCDs.

<p>False (B)</p>
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What type of distribution do detected photons follow, which is important for understanding noise characteristics?

<p>poisson</p>
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In fluorescence, the emission of light occurs at a ______ energy (larger wavelength) compared to the absorbed light.

<p>lower</p>
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Which of the following is a key advantage of using 2-photon excitation microscopy?

<p>It provides deeper tissue penetration and less photobleaching. (A)</p>
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X-rays are considered non-ionizing radiation, making them safe for all types of clinical imaging.

<p>False (B)</p>
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What is the appropriate probe wavelength length requirement for achieving adequate resolution?

<p>short</p>
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What is the order of relative X-ray absorption in the human body (from least to most absorption)?

<p>Air &lt; Fatty tissue &lt; Connective tissue &lt; Bones (A)</p>
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The goal during image reconstruction of the inner structure is to recover it from the ______.

<p>projections</p>
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Radiation exposure creates a unique cancer risk readily distinguished from cancer risk due to other environmental factors.

<p>False (B)</p>
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Which type of image compression is generally recommended when it is especially important to preserve all of the original image data?

<p>Lossless Compression (D)</p>
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According to the FDA's suggestion, what should be done before analysis of images to reduce file archiving demands?

<p>compression</p>
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Match the following terms with their definitions related to Fourier Transforms:

<p>Spatial Domain = The space where images are represented by pixels. Frequency Domain = The space where the rate of change in image intensity is represented. Basis Images = The sinusoidal terms used in Fourier transforms for image decomposition.</p>
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What are the two different methods used for visualizing 3D image data?

<p>Surface Rendering vs Volume Rendering (B)</p>
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Stereotactic intervention utilizes a ______ dimensional coordinate system to accurately locate targets in the body

<p>Three</p>
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In computer graphics, the procedure involves linking points to display mathematical curves and areas?

<p>True (A)</p>
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What type of information is attributed to points, edges, and areas when forming polygons in polygonal modeling?

<p>geometrical information</p>
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One limitation of Polygonal Modeling is that it has difficulty rendering ______ lines and patches.

<p>curved</p>
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Match the definition with the correct term:

<p>Bernstein-Polynomial = Polynomial of order n Bezier-Curve = Curve of order n with control points Approximation Method = Mathematical method</p>
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Surface triangulation involves creating a topological skeleton of an object?

<p>False (B)</p>
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What is the term for the process of assigning colors to different sections of an image based on depth?

<p>color depth coding</p>
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A ______ is the three-dimensional equivalent of a pixel.

<p>voxel</p>
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Which of the following features are associated with volume rendition?

<p>All of the above (D)</p>
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Image Order Rendering uses orthogonal projection to create images?

<p>False (B)</p>
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What are the two types of intensities that are handled in Volume Rendering?

<p>mean and maximum</p>
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Blending controls transparency or ______ by color, the color is a RGB-vector.

<p>opacity</p>
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Which parameter is NOT used in the additional control of brightness?

<p>Values (B)</p>
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3-D image processing is same as slice-by-slice image filtering.

<p>False (B)</p>
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The cubes of voxels of what size are analyzed with the Marching Cube?

<p>2x2x2</p>
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For proper implant fitting into 3D Image Volume, ______ geometry is used.

<p>embedded</p>
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Which of the following is a surface rendering technique?

<p>Marching Cubes (B)</p>
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Optical Tomography includes an increase, but not a reduction of blurr.

<p>False (B)</p>
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In the diagram, what is the name of the step following topology in the overall workflow options?

<p>triangulation</p>
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______ is required for quantitive assesment in volume rendering.

<p>Segmentation</p>
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Which of the following is a benefit of surface rendering over volume rendering?

<p>Facilitates geometric measurement (D)</p>
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In Object Order Rendering, the process goes from the back to the front.

<p>True (A)</p>
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Name the type of projection that Object Order Rendering focuses on.

<p>orthogonal</p>
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In stereoscopic CRT display systems, there is ______ multiplexed and time parallel.

<p>time</p>
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What is a key advantage of Volume Rendering over Surface Rendering?

<p>Visual Control (B)</p>
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What is increased with optical tomography?

<p>resolution</p>
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In the surface rendering workflow, ______ geometry is used.

<p>embedded</p>
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Which parameter is used with Image Order Rendering?

<p>all of the above (D)</p>
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Which of the following is a characteristic of surface rendering?

<p>photorealistic views (D)</p>
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What is surface triangulation?

<p>technique of creating surfaces using triangles (C)</p>
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What is one advantage of surface rendering?

<p>data compression (A)</p>
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What is one benefit of Object Ordering Rendering?

<p>Uses Orthogonal Projection (B)</p>
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What is one use of Surface Rendering?

<p>facilitates geometric measurement (A)</p>
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What is color depth coding?

<p>assigning colors based on depth (A)</p>
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Which of the following techniques is used in 3D Visualization process?

<p>Both A and B are correct (A)</p>
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What are the benifits to Non-invasive Serial Sectioning?

<p>None of the above (D)</p>
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What is a limitation of Surface Rendering?

<p>No Intensity Measurements (C)</p>
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What is a key point about Virtual Reality in 3-D Visualization?

<p>Feedback Sensor (B)</p>
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Which of the following is a limitation of polygonal modeling in 3D imaging?

<p>Difficulty in rendering curved lines and patches. (C)</p>
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In volume rendering, 'Image Order Rendering' projects voxels orthogonally onto the screen.

<p>False (B)</p>
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What is the primary function of blending in Volume Rendering regarding voxel intensities?

<p>controlling transparency or opacity</p>
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In 3D imaging, a pixel in a 2D image is analogous to a ______ in a 3D volume.

<p>voxel</p>
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Match the following steps to create a visualization:

<p>Acquisition = The process of capturing raw data from a source. This could involve scanning, imaging, or other data collection methods. 2-D preprocessing = Initial processing of acquired 2D data slices to enhance quality and prepare for 3D operations, such as noise reduction. Contouring = Tracing outlines in 2D slices to define structures, providing a basis for building 3D models. 3-D Filtering = Applying filters to 3D data to reduce noise, improve contrast, or enhance features within the volume.</p>
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What is considered the basic cellular unit of the brain?

<p>Neuron (B)</p>
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Extracellular recordings can only record the activity of a single neuron at a time.

<p>False (B)</p>
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Invasive recordings that use sharp or patch electrodes are known as ______ recordings.

<p>intracellular</p>
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Which of the following materials is NOT typically used for electrodes in extracellular recordings?

<p>Gold (B)</p>
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Intracellular recordings can measure subthreshold responses in neurons.

<p>True (A)</p>
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What term is used to describe the emission of light by an organism as the result of a chemical reaction?

<p>Bioluminescence</p>
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What happens when a molecule undergoes fluorescence?

<p>It emits light at a lower energy (larger wavelength) to return to its original state. (C)</p>
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In fluorescence, the emitted light has a smaller wavelength than the absorbed light.

<p>False (B)</p>
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The process where a molecule absorbs a high-energy photon, placing it in a higher energy state, is a key step in ______.

<p>fluorescence</p>
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Voltage-sensitive dyes are used to:

<p>Detect changes in membrane potential. (B)</p>
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Voltage-sensitive dyes need to be genetically encoded to be used in neurons.

<p>False (B)</p>
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In the context of voltage-sensitive dyes, what does PeT stand for?

<p>Photoinduced electron transfer</p>
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A major challenge with using dyes for imaging is the need to ______ to the specific neurons of interest.

<p>deliver dye</p>
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What is the primary advantage of using genetically encoded indicators over synthetic dyes?

<p>They do not require delivery to specific neurons. (C)</p>
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The use of GFP in cells allows for the cell itself to ______ the protein, which eliminates the need to inject synthetic dyes.

<p>generate</p>
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Which of the following is a limitation of using fluorescent proteins alone for imaging neural activity?

<p>They do not directly indicate neural activity. (A)</p>
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Name one type of sensor, other than calcium sensors, that can be combined with fluorescent proteins to image neural activity.

<p>Transmembrane voltage sensors</p>
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To image neural activity, fluorescent proteins are combined with proteins that change conformation in response to that activity, such as calcium sensors or ______ sensors.

<p>transmembrane voltage</p>
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What is the purpose of combining fluorescent proteins with other proteins to image neural activity?

<p>To modulate the emission in proportion to neuronal activity. (C)</p>
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Fluorescent proteins can act as indicators for neuronal activity all by themselves.

<p>False (B)</p>
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What does GECI stand for in the context of neural imaging?

<p>Genetically encoded calcium indicators</p>
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GCaMP is an example of a ______ indicator used in neural imaging.

<p>calcium</p>
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Which of the following is a well-known type of genetically encoded calcium indicator (GECI)?

<p>GCaMP (C)</p>
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In two-photon microscopy, two photons combine to have the same effect as multiple lower energy photons.

<p>False (B)</p>
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Name the technique that permits deeper tissue penetration and minimizes photobleaching by exciting fluorescent proteins only at the focal point where two photons interact.

<p>Two-photon microscopy</p>
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In two-photon microscopy, excitation of fluorescent proteins occurs only where two photons ______, reducing photobleaching.

<p>interact</p>
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Which of the following is a key advantage of two-photon microscopy over single-photon microscopy?

<p>Reduced photobleaching and deeper tissue penetration. (B)</p>
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Two-photon microscopy results in more photobleaching than one-photon microscopy.

<p>False (B)</p>
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What is the proposed function of the Drosophila central complex?

<p>Navigation (A)</p>
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The Drosophila central complex is thought to be involved in visual processing.

<p>False (B)</p>
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Light sheet microscopy allows you to image neural activity in an organism.

<p>True (A)</p>
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In light sheet microscopy, are samples illuminated from only one side?

<p>Yes</p>
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In microscopy, light ______ is a method in which samples are illuminated with just a 'sheet' of light.

<p>sheet</p>
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Light sheet microscopy is useful to image neural activity for what reason?

<p>Samples are only illuminated from one side. (A)</p>
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What is the primary advantage of using genetically encoded indicators, like GFP, for imaging neural activity, compared to synthetic dyes?

<p>Genetically encoded indicators do not require delivery into neurons; the cells produce them. (D)</p>
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Extracellular recordings utilize sharp electrodes to record subthreshold responses from neurons.

<p>False (B)</p>
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What property of a molecule is key to fluorescence?

<p>emission of light at a lower energy (larger wavelength) after absorbing light at a higher energy (smaller wavelength)</p>
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Two-photon microscopy reduces photobleaching because excitation occurs only where two ______ interact.

<p>photons</p>
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Which type of microscopy is particularly useful for imaging deeper into tissue with reduced photobleaching?

<p>Two-photon microscopy (B)</p>
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Match each voltage indicator with its correct description:

<p>ASAP2s = A type of voltage sensor ASAP3 = A type of voltage sensor JEDI-2P = A type of voltage sensor</p>
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Which of the following is a limitation of imaging with dyes?

<p>Dyes have to be delivered to neurons of interest. (B)</p>
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Fluorescent proteins can directly act as indicators of neural activity without needing additional components.

<p>False (B)</p>
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In the context of fluorescence, what happens when a molecule absorbs a high-energy photon?

<p>It enters a higher energy state. (C)</p>
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What is the basic cellular unit of the brain?

<p>neuron</p>
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Which of the following is NOT typically considered an area of use for clinical imaging methods?

<p>Cosmetic enhancement evaluation (A)</p>
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In X-ray imaging, increasing the radiation dose always leads to a decrease in the signal-to-noise ratio (SNR).

<p>False (B)</p>
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State the absorption law used in X-ray imaging.

<p>I = Ioe^(-md)</p>
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In X-ray imaging, contrast is based on differential ________ of radiation by different tissues.

<p>absorption</p>
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Match the following tissue types with their relative absorption of X-rays, from lowest to highest:

<p>Air = Lowest absorption Fatty Tissue = Low absorption Connective Tissue = Medium absorption Bones = Highest absorption</p>
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What is a primary disadvantage of projection X-ray imaging?

<p>Loss of depth information (C)</p>
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Perfusion imaging techniques can only be CT-based.

<p>False (B)</p>
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Name two parameters measured by sophisticated post-processing software in perfusion imaging.

<p>Cerebral Blood Volume (CBV) and Cerebral Blood Flow (CBF)</p>
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The development of _________ in imaging allowed for true 3D imaging.

<p>Computerized Tomography (CT)</p>
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Which of the following describes a key requirement for a probe used in medical imaging?

<p>It must have a wavelength short enough for adequate resolution. (A)</p>
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Ultrasound imaging uses electromagnetic (EM) energy.

<p>False (B)</p>
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Give one advantage and one disadvantage of ultrasound imaging.

<p>Advantage: Real-time imaging. Disadvantage: Severe distortions at air or bone interface.</p>
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In ultrasound imaging, resolution is proportional to _________.

<p>wavelength</p>
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Which of the following best describes how X-ray imaging generates an image?

<p>Measures line integrals of attenuation coefficient (B)</p>
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Magnetic Resonance (MR) imaging is generally considered unsafe due to the use of ionizing radiation.

<p>False (B)</p>
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What physical property does ultrasound measure to create images?

<p>Acoustic reflectivity or reflectivity</p>
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In Magnetic Resonance imaging, the signal, M(x,y,z), is proportional to _________.

<p>p(x,y,z) and T1, T2</p>
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Which imaging modality is generally the first choice for Neuro/Head assessment of bone structures?

<p>X-Ray (D)</p>
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Ultrasound is generally considered an excellent imaging modality for visualizing structures within the abdomen, regardless of air or gas interference.

<p>False (B)</p>
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Which modality could be merged with CT for extensive use in the heart?

<p>Nuclear</p>
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For cardiovascular imaging, X-ray imaging is excellent when combined with ________ contrast.

<p>catheter-injected</p>
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Which imaging modality provides functional information on perfusion in the skeletal system?

<p>Nuclear (A)</p>
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MRI is considered not useful for imaging the cardiovascular system.

<p>False (B)</p>
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For skeletal/muscular imaging, which modality is strong for viewing the skeletal system?

<p>CT or X-Ray</p>
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Which of the following lists the modalities in order of capital cost, from lowest to highest?

<p>Ultrasound, CT, MRI (C)</p>
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Which of the following is a primary reason for using image compression?

<p>To reduce the number of bits needed to represent an image. (B)</p>
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All images benefit equally from compression techniques, regardless of their content.

<p>False (B)</p>
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What type of redundancy is exploited when compressing neighboring pixels that are not independent but correlated?

<p>spatial redundancy</p>
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The difference between information and data is that data includes ______ data.

<p>redundant</p>
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In the context of image compression, what does 'quantization' refer to?

<p>Reducing the number of color levels in an image. (C)</p>
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Increasing the number of quantization levels always results in better image compression.

<p>False (B)</p>
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Name one factor, besides storage space, that makes image compression necessary.

<p>bandwidth</p>
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The uncompressed bit rate of digital cinema data can exceed 1 ______ per second.

<p>gbps</p>
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In image compression, 'spatial redundancy' refers to:

<p>The correlation between neighboring pixels. (D)</p>
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Spatial redundancy is about similarities that exist across multiple frames in a video sequence.

<p>False (B)</p>
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What term is used to describe the bits needed to represent an image?

<p>bit rate</p>
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Image compression exploits the fact that all images are not equally ______.

<p>likely</p>
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Which type of redundancy considers how the human eye perceives visual information when compressing images?

<p>Psychovisual redundancy (A)</p>
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Psychovisual redundancy relies on similarities that exist across frames in a video sequence.

<p>False (B)</p>
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What equation represents the composition of data in terms of information and redundancy?

<p>data = information + redundant data</p>
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In the equation Bit Rate = NQF, N represents the number of ______.

<p>pixels</p>
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What does decreasing 'Q' (Quantization bits/pixel) in the equation Bit Rate = NQF create?

<p>Contouring (artifacts) (B)</p>
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Decreasing frame rate will increase resolution

<p>False (B)</p>
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What is a primary goal in image compression, besides reducing file size?

<p>maximize image quality</p>
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Modern image processing is typically performed in the ______ domain.

<p>digital</p>
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Which of these is true of lossless compression?

<p>It can reproduce exactly the original image. (D)</p>
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Lossy image compression techniques guarantee perfect image data reconstruction upon decompression.

<p>False (B)</p>
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What type of coding is used by lossless compression?

<p>entropy coding</p>
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JPEG is an example of a ______ image compression method.

<p>lossy</p>
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Which of these file formats is typically associated with lossless compression?

<p>GIF (B)</p>
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JPEG files are best suited for logos and textual graphics.

<p>False (B)</p>
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What term describes the artifacts that can appear in an image from excessive compression?

<p>blocking artifacts</p>
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In JPEG encoding, the 2D forward ______ is applied to preprocess the image.

<p>dct</p>
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What comes after image preprocessing in JPEG encoding steps?

<p>Apply 2D forward DCT (C)</p>
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After Quantization, apply 2D forward DCT.

<p>False (B)</p>
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In the JPEG Block Diagram, what immediately precedes the Entropy Encoder?

<p>quantizer</p>
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In JPEG compression, color transformation is ______.

<p>optional</p>
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What is the main purpose of applying the Forward DCT (Discrete Cosine Transform) in image compression?

<p>To convert the image from the spatial domain to the frequency domain. (C)</p>
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DFT is preferred over DCT for better approximations.

<p>False (B)</p>
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The intensity values in each color plane often change how?

<p>slowly</p>
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______ is when the resulting image is 'close' to the original image.

<p>resulting image</p>
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According to the provided text, what should be done if in doubt about whether to use lossy or lossless compression?

<p>Always use lossless, for better fidelity. (C)</p>
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Image compression is a new field with lots of room for improvement.

<p>False (B)</p>
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What type of redundancy describes predictions along motion trajectories?

<p>temporal redundancy</p>
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_____DPCM is used to remove temporal redundancy first.

<p>temporal</p>
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Which of the following accurately describes a primary reason for employing image compression techniques?

<p>To reduce the storage space required for image data, addressing limitations in storage capacity and bandwidth. (B)</p>
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Spatial redundancy in images refers to the independence of neighboring pixels, meaning the value of one pixel does not correlate with the values of adjacent pixels.

<p>False (B)</p>
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Briefly explain how image compression exploits the characteristics of images to reduce file size.

<p>Image compression reduces file size by removing redundant data (spatial and temporal redundancy). It exploits the fact that not all information is equally likely or perceptible.</p>
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In the context of image compression, the two main categories are ______ compression, which can reproduce the original data exactly, and ______ compression, which sacrifices some data to achieve higher compression ratios.

<p>lossless, lossy</p>
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Match the following image compression concepts with their descriptions:

<p>Spatial Redundancy = Correlation between neighboring pixels in an image. Temporal Redundancy = Redundancy across consecutive frames in a video. Lossless Compression = Compression technique that allows the original data to be perfectly reconstructed. Lossy Compression = Compression technique where some data is sacrificed to achieve higher compression ratios.</p>
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Flashcards

What is a Transform?

A mathematical mapping process; provides info on rate of gray level change within an image (spatial frequency).

What is Point Spread Function (PSF)?

Describes how a single point of light is distributed or spread out by the imaging system.

What is Modulation Transfer Function (MTF)?

Quantifies how well an imaging system preserves contrast at different spatial frequencies; relates to detail transmission.

What is Noise in imaging?

Reduces information content; can be thermal or from electronic amplification; may not be independent of the signal.

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What is Resolution?

The ability of an imaging system to distinguish fine details or closely spaced objects.

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What is the Nyquist Criterion?

Minimum sampling frequency required to avoid losing information during digitization (twice the cutoff frequency).

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What is image sampling?

Converting an optical image (light photons) into a digital data stream (electrical signal).

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What are CCD Image Sensors?

Electronic devices that transform a light pattern (image) into an electronic charge pattern.

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What are Photomultiplier Tubes (PMTs)?

Extremely sensitive light detectors used in the ultraviolet, visible, and near-infrared range, utilizing the photoelectric effect.

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What are Computerized Tomography (CT) methods?

Measure the attenuation of X-rays from many different angles to reconstruct an organ in cross-sections.

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What is Ultrasound (US)?

Measuring acoustic reflectivity; safe, used where there is a complete soft tissue/fluid path, but suffers distortions.

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What is Nuclear (PET/SPECT) imaging?

Involves a radioactive isotope attached to a metabolic marker; good for functional imaging, especially heart and bone marrow.

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What are Fluorescence techniques?

Techniques crucial for imaging neural activity by visualizing changes in fluorescent indicators.

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What is Image Compression?

Compression that reduces the number of bits needed to represent an image; necessary because of storage and bandwidth.

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What is Lossless Compression?

Allows the stored image data to reproduce the original image exactly; uses entropy coding. Examples: BMP, TIFF, and GIF.

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What is Lossy Compression?

Reproduces something that looks close to the original image; uses quantization, entropy coding, and a frequency transform. Example: JPEG.

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What does Fourier Transform do?

Map image data from the spatial domain to the frequency domain.

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What are Reconstructions from Projections?

Measuring X-ray attenuation from different angles to reconstruct images.

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Compare Surface vs Volume rendering.

Surface vs Volume rendering: Surface better for measurements, volume for fuzzy structures and cuttings.

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What are Stereotactic interventions?

Utilizing a 3D coordinate system to accurately locate targets in the body and perform surgery.

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Computer Graphics

Creating visual representations from computer-generated data, differing from direct image acquisition.

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Polygonal Modeling

Representing objects by defining the points, edges, and areas that make up their surfaces with geometrical data.

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Bézier-Polynomial

Approximates curves by using polynomials to describe their shape.

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Bézier-Curves

A parametric curve defined by control points. Varying these influences the curve's shape.

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Topological Interpretation

A diagram that shows how the different components within an image connect (or intersect) with each other.

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Surface Triangulation

Approximation of a surface using triangles.

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Marching Cubes

A method for finding surfaces in a 3D dataset by analyzing cubes formed by voxels.

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Optical Tomography

Imaging by capturing and measuring the characteristics and behavior of photons.

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Non-invasive serial sectioning

Creating successive images of slices through a sample without physical cutting.

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Color depth coding

Representing depth in an image by assigning colors to image sections corresponding to their distance.

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Voxel

The 3D equivalent of a pixel, representing a value on a regular grid in three-dimensional space.

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Volume Rendering

A technique for creating a 2D image from a 3D dataset by integrating values along viewing rays through the volume.

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Artificial lightning

Using computer-generated light and shadows to improve the perception and analysis of volume-rendered images.

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Image Order Rendering

Determining the order in which image elements are processed based on their position relative to the viewer.

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Object Order Rendering

Determining the order in which elements are processed based on their spatial coordinates/location within the scene.

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Blending of intensities

Adjusting how much each voxel contributes to the final image brightness.

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Segmentation

An image processing technique used to isolate areas of interest based on similar characteristics.

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Region of Interest (ROI)

A defined spatial zone in imaging analysis. Essential in many visualization workflows.

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Embedded Geometry

Superimposing different data sets or models into a 3D scene or image to view them jointly.

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Topology

The study of spatial relationships between objects that remain unchanged by continuous deformations.

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Neuron

The basic cellular unit of the brain, responsible for transmitting information.

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Invasive Recordings

Using electrodes to record electrical activity either inside (intracellular) or outside (extracellular) of neurons.

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Intracellular Recording

A type of invasive recording where electrodes are placed directly inside a neuron to measure its electrical activity.

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Extracellular Recording

A type of invasive recording where electrodes are placed outside the neuron to measure its electrical activity.

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Fluorescence

A phenomenon where a molecule absorbs a high-energy photon, and then emits a lower-energy photon to return to its original state.

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Bioluminescence

A light is produced by a chemical reaction within a living organism.

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Dye Delivery

Delivering synthetic dyes to neurons of interest to track them.

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Aequorea victoria

A jellyfish species where Green Fluorescent Protein was derived from.

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Green Fluorescent Protein (GFP)

A protein that emits green light when exposed to blue light.

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Fluorescent Proteins

Proteins that can be genetically engineered to fluoresce and are used to visualize biological processes.

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Voltage Sensitive Dyes

Dyes that change their fluorescence properties in response to changes in voltage across a cell membrane.

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Calcium/Transmembrane voltage sensors

Fluorescent proteins combined with proteins to change conformation in response to neural activity.

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Genetically Encoded Calcium Indicators (GECIs)

Engineered proteins that change their fluorescence in response to calcium levels, indicating neural activity.

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cpGFP voltage sensors

Using proteins containing a voltage sensor domain (VSD) and a circularly permuted GFP (cpGFP) to track transmembrane voltage

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Light Sheet Microscopy

Microscopy techniques that capture high-resolution images of biological samples by illuminating them with a thin sheet of light.

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Two-Photon Microscopy

Microscopy where two photons contribute to the excitation of fluorophores. Benefits: deeper penetration, less photobleaching.

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Diagnostic Imaging

Verifies/supports a diagnosis using clinical imaging.

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Screening Imaging

Investigates disease at a large scale to prevent it

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Therapy Control Imaging

Controls treatment (drug, chemo-therapy) or monitors healing.

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Intervention Imaging

Imaging used for planning and controlling interventions.

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Basic Biomedical Research Imaging

Imaging focused on system micro-versions, to advance knowledge.

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Radiation Dosis

An important consideration for medical imaging.

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Costs and Time (Imaging)

The total finances and time expended.

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Medical Imaging Limitations

Restrictions or constraints on use/image type.

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(Physical) Resolution

Detail discernible in the image

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(Time) Resolution

Temporal image acquisition rate

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Image Matrix

Describes the image's size and sampling frequency.

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Imaging Measurement

Quantitative analysis of image features.

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Signal-to-Noise Ratio (SNR)

Quantifies signal strength to background noise

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X-ray Divergence

Intensity decreases quadratically with distance.

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X-ray Penetration

How deeply X-rays can pass through a substance.

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X-ray Absorption Law

Describes X-ray absorption based on material thickness.

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X-ray Contrast

Based on varying tissue absorption of X-rays.

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X-Ray Imaging

Uses line integrals of attenuation coefficient for imaging.

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Contrast Agent

Agent used to improve clinical imaging quality.

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Perfusion Imaging

CT or MR based with post-processing software.

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3D Imaging

True three dimensional imaging, like CT.

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Necessary Probe Properties

Semi-Transparency of the body to a probe.

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X-ray Modality

Measure line integrals of attenuation coefficient

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CT modality

Builds images tomographically

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Ultrasound modality

Measuring acoustic refectivity

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What is Bit Rate Reduction?

Minimizing number of bits to represent an image.

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How does image compression work?

Exploiting that images are not equally likely.

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What are energy gaps?

Redundancy in image data.

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What is spatial redundancy?

Redundancy due to pixel correlation in images.

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What is temporal redundancy?

Redundancy in video frames over time.

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Psychovisual redundancy

Redundancy not perceived by human vision.

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What is Bandwidth Compression?

Algorithm to reduce bits needed for an image.

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What is the main goal of image compression?

The goal is to store images efficiently and ensure quality.

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What is the digital domain?

Modern image manipulation exists in this domain.

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Reducing N,Q,F

Needs more sophisticated approaches of reducing certain properties.

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What is BMP (Bitmap)?

Image format using 3 bytes per pixel (R,G,B).

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Graphic Interchange Format (GIF)

Maximum colors is 256 from 24-bit RGB color.

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What is JPEG?

File format good for containing photos.

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What are 'Blocking Artifacts'?

Artifacts around sharp image block changes.

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What are the JPEG encoding steps?

Preprocess, DCT, Quantize, apply RLE, Entropy Encoding.

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What is color transformation?

Down-sampling chrominance components.

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What is Forward DCT?

Convert spatial to frequency domain.

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Why DCT not DFT?

DCT gives better image approximation with fewer coefficients.

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What is Reconstruction Error?

Resulting close image relative to original.

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Temporal DPCM

DPCM is used to remove temporal redundancy.

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Motion estimation influence?

The accuracy of estimation for motion.

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What is Motion Compensated Prediction?

Taking a first and comparing it to what change in the second.

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Study Notes

Image Compression

  • Image compression reduces the number of bits needed to represent an image or its information.
  • It exploits the fact that all images are not equally likely and energy gaps in the signal.

Why Compression is Needed

  • Requirements may exceed the anticipated increase of storage space and bandwidth.
  • Data storage and transmission, video conferencing, and printers benefit from compression.
  • The bitrate of uncompressed digital cinema data exceeds 1 Gbps.
  • Video streams require compression.

Why Compression Works

  • Spatial redundancy exists because neighboring pixels are not independent, but correlated.
  • Temporal redundancy.

Psychovisual Redundancy

  • Quantization is an example.
  • Adds a small pseudo-random number to each pixel before quantization.

Information vs. Data

  • Data = Information + Redundant Data.

Image Model

  • The picture size is one unit wide by one unit high.
  • M = number of samples.
  • D = spacing between samples = 1/√M
  • Correlation between adjacent samples = e^D = e^(1/√M)

Compression and Image Content

  • Portrait (fills 1/2 frame) has a correlation distance^-1 of 6.3.
  • Typical (moderate detail) has a correlation distance^-1 of 16.7.
  • 100 people has a correlation distance^-1 of 50.
  • 2000 people has a correlation distance^-1 of 150.

Interframe and Intraframe Processing

  • Interframe processing involves point-to-point predictive encoding and line-to-line encoding.
  • Intraframe Processing

Bit Rate

  • Bit Rate = NQF.
  • N = Number of pixels.
  • Q = Quantization bits/pixel.
  • F = Frame rate.
  • Compression Ratio = 10 LOG [Channel Bit Rate / NQF].

Reducing Parameters

  • Reducing N results in reduced resolution.
  • Reducing Q results in contouring (artifacts).
  • Reducing F results in image blur.
  • More sophisticated approaches are needed.

Goal of Image Compression

  • Storing image data as efficiently as possible.
  • Maximizing image quality and minimizing storage space and processing resources.
  • Trade-offs are necessary because you can't have the best of both.

Digital vs. Analog

  • Modern image processing is done in the digital domain.
  • Analog source images get converted to digital format before processing.

Lossless Compression

  • Stored image data can reproduce the original image exactly.
  • Lossless compression typically takes more storage space.
  • Lossless compression only uses entropy coding or none at all.
  • Examples: BMP, TIFF, GIF.

Lossy Compression

  • Stored image data can reproduce something that looks "close" to the original image.
  • Lossy Compression uses both quantization and entropy coding.
  • Lossy Compression involves transform into frequency or other domain.
  • Examples: JPEG, JPEG-2000.

BMP (Bitmap)

  • Uses 3 bytes per pixel: one each for R, G, and B.
  • Can represent up to 2^24 = 16.7 million colors.
  • No entropy coding.
  • File size in bytes = 3 * length * height, which can be very large.
  • Can use fewer than 8 bits per color, but need to store the color palette.
  • Works well with ZIP, RAR, etc.

GIF (Graphics Interchange Format)

  • Can use up to 256 colors from 24-bit RGB color space.
  • If a source image contains more than 256 colors, reprocessing is needed to reduce the image to fewer colors.
  • Suitable for simpler images such as logos and textual graphics, not photographs.
  • Uses LZW lossless data compression.

JPEG (Joint Photographic Experts Group)

  • Dominant image format today.
  • Typical file size is about 10% of BMP (can vary depending on quality settings).
  • Unlike GIF, JPEG is suitable for photographs, not logos and textual graphics.

JPEG Encoding Steps

  • Preprocess image.
  • Apply 2D forward DCT.
  • Quantize DCT coefficients.
  • Apply RLE, then entropy encoding.

Color Transformation

  • (Optional) Down-sample chrominance components to compress without loss of quality in color space as an option
  • Examples include: YUV 4:2:2 or 4:1:1
  • 640 x 480 RGB to YUV 4:1:1 example consists of: Y is 640x480, U is 160x120, and V is 160x120.

Forward DCT

  • Convert from spatial to frequency domain.
  • Convert the intensity function into a weighted sum of periodic basis (cosine) functions.
  • Identify bands of spectral information that can be thrown away without loss of quality.
  • Intensity values in each color plane often change slowly.

Why DCT Not DFT

  • DCT is similar to DFT, but can provide a better approximation with fewer coefficients.
  • The coefficients of DCT are real-valued instead of complex-valued in DFT.

Understanding DCT

  • In R^3, we can write (5, 2, 9) as the sum of a set of basis vectors: [(1,0,0), (0,1,0), (0,0,1)].
  • (5,2,9) = 5*(1,0,0) + 2*(0,1,0) + 9*(0,0,1).
  • DCT is the same process in the function domain.

DCT Basis Functions

  • Decompose the intensity function into a...

Reconstruction Error

  • The resulting image is "close" to the original image.
  • Closeness measures use MSE (Mean Squared Error) and PSNR (Peak Signal to Noise Ratio).
  • Desire low MSE and high PSNR.

Image Compression in Regulated Environments

  • Previously employed image acquisition, analysis, compression.
  • Image Compression utilizes, Image acquisition, compression, analysis.

Image Formats in Regulated Studies

  • JPEG compression does not alter the accuracy or reliability to reproduce individual data point measurements, except at the highest compression level.
  • If acquired with TIFF and saved as JPEG, there may be discordance.
  • If the original and features extracted from a JPEG-compressed file, high confidence in the reproducibility of individual measures.

Quantitative Analysis and Compression

  • High-quality classifications can be obtained with JPEG compression ratios up to 10:1 or higher.
  • High compression tends to eliminate much of the pixel-to-pixel detail.
  • Training on compressed imagery could raise the training site accuracy, but did not raise the percentage of pixels matching the original classification.
  • The maximum-likelihood classifier degraded faster than other classifiers due to specific assumptions about class statistics.
  • Data tends to become uncorrelated with high compression, ruining its statistics.

What is MPEG

  • "Motion Picture Expert Group" was established in 1990 to create standards for the delivery of audio and video.
  • MPEG-1 targets VHS quality on a CD-ROM(320x240 + CD audio @ 1.5 Mbit/sec).

MPEG (Interframe Coding)

  • Temporal DPCM removes temporal redundancy first.
  • Motion compensated error is coded with DCT+Run length Huffman entropy coding.
  • Spatial Compression(Image compression)
  • Termporal Compression.(Sequence compression)
  • MPEG-2 has a ratio of 100:1
  • MPEG-4 has a ratio of 200:1

MPEG Temporal Redundancy

  • Prediction along the motion trajectories (motion compensation prediction).

Motion Estimation

  • The accuracy of motion estimation has a big influence on coding efficiency.
  • Motion estimation is time-consuming.
  • Fast algorithms are needed.

MPEG-1 Frame Types

  • I frame is an intra-coded frame.
  • P frame is an inter-coded or predicted frame.

Conclusion

  • Image compression can be done lossy or lossless.
  • Use lossless if in doubt.
  • The degree of noise will impact the amount of compression.
  • Image compression is nearly mature, but there is always room for improvement.

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