Image Processing Ebooks Catalog
Van (1934) designed an instrument that could have identified single cells using a microscope and a photodetector. In the 1940s, George Papanicolaou demonstrated that he could identify cancerous cells from cervical smears by observing the staining patterns obtained using specifically designed stains (Papanicolaou and Traut 1941 Chapter 1). This suggested several opportunities for the identification of abnormal cells, primarily using image-analysis techniques. It proved to be quite difficult to create analytical technology based on the capability of computers and imaging technology at that time, and the result was a movement toward single-cell analysis, as opposed to image processing and recognition.
Sophisticated computer-based tools for product analysis and identification are available. Computer-controlled automated sampling procedures have been developed to predict noodle discoloration over time (16). Computer vision technology can be used as a quality control process for gauging, verification, flaw determination, recognition, and locating (17). Machine vision and image processing have been used to identify corn kernel shape (18). Grain kernels, nuts, and crackers have also been examined using computerized image analysis and classified with a neural network program (19). Snack and chips with varying morphological and texture features as input and sensory attributes as output were used to train a neural network for quality analysis. The program was validated with predicted output compared with a sensory evaluation panel (20). Computer-controlled shape and size grading and filleting in the seafood industry have been developed (21). Computer-simulated models of flavor loss due to...
Producing gene expression data using microarray technology is an elaborate process with many potential sources of variability. To maximize the scientific value of gene expression information derived from microarrays, we must make rigorous quality assessments throughout the process. Standard sample preparation protocols include a number of qualitative assessments meant to ensure that good quality RNA is used in the hybridization experiments. After hybridization and image processing, each microarray provides a wealth of information that can be used to assess the quality of the data. Recommended post-hybridization quality assessments include general image quality assessment and analysis of intensity measures of specialized probes (Afifymetrix, 2001). In this section, we suggest some methods to assess data quality based on the analysis of residuals from the models fitted to estimate gene expression. Departures from quality standards may be attributable to various sources RNA preparation,...
A 2D crystal of the 20S proteasome from Thermoplasma acidophilum produced by the negative staining-carbon film procedure, with 2 ammonium molybdate (pH 7) as the final negative stain. Image processing suggests that the unit cell may contain six molecules because of the specific rotational orientation of the heptameric proteasome within the crystal (modifed from Harris 2 ). Note the absence of individual and small groups of molecules from the 2D crystal lattice (arrowheads). Fig. 10. A 2D crystal of the 20S proteasome from Thermoplasma acidophilum produced by the negative staining-carbon film procedure, with 2 ammonium molybdate (pH 7) as the final negative stain. Image processing suggests that the unit cell may contain six molecules because of the specific rotational orientation of the heptameric proteasome within the crystal (modifed from Harris 2 ). Note the absence of individual and small groups of molecules from the 2D crystal lattice (arrowheads).
Images are preferably recorded on photographic film and subsequently digitized with a high-resolution scanner, because the current image processing methods benefit from large and coherently connected single crystal images, and the current generation of CCD cameras does not yet offer for higher acceleration voltages (200 kV and higher) a better transfer function at high resolution than the conventional Kodak SO 163 film (27).
(10) that can be used for these image processing steps. SAVR is a subset of programs within EMAN that has been developed based on Crowther's algorithm for icosahedral particle reconstruction. This method specifically takes advantage of the high symmetries of icosahedral viruses and is very efficient in computing. It is particularly useful for initial model building. Nevertheless, EMAN is a generic single particle image processing software package that also supports other symmetries in addition to performing icosahedral reconstruction. Adopting the generic single particle package, EMAN, offers additional benefits in that the same software can be used to determine structures of the non-ico-sahedral components in an icosahedral particle (36). Fig. 5. Schematic diagram of the image processing for icosahedral particles using EMAN. Fig. 5. Schematic diagram of the image processing for icosahedral particles using EMAN.
A system to predict crawfish molting based on color ratio was used to produce soft-shelled crawfish (13). The system used an IBM PC AT to control a Versa Module Eurocard (VME) image-processing system. A Pulmix CCD color camera with a polarizing filter was used to acquire the image. A system consisting of an optical scanner, a computer and image-processing system, and a robot water jet cutter was designed to produce fat-free steaks (14). The system uses a 3D laser scanner to obtain the image profile with up to 0.1 pixel. A digital signal processor (DSP) program enables the image-processing system to receive the product's volume and thus its mass. Another similar system using rotating blades instead of water jets combines image processing with a scale to define the shape, orientation, and mass of product to be cut into portions (Fig. 6). This process allows for maximum efficiency and minimum waste. These systems not only save on labor and add efficiency but also are more effective in...
The limit of resolution of traditional EM is about 5 nm. With advanced EM techniques, such as cryogenic EM (cryoEM, in which the sample is rapidly frozen instead of exposed to chemical fixatives), coupled with computer image processing, smaller structures (1-2 nm) can be resolved. However, X-ray crystallography is the only method that allows for atomic-level resolution. Small viruses that produce uniform particles can be crystallized. The first atomic-level structure of a virus, tomato bushy stunt virus, was solved in 1978.
Experimental characterization of coalescence can be carried out using a variety of experimental techniques, many of which are similar to those used to monitor flocculation (Section 7.4.3). The most direct approach is to observe droplet coalescence using an optical microscope (Mikula 1992). An emulsion is placed on a microscope slide and the change in the droplet size distribution is measured as a function of time, by counting the individual droplets manually or by using a computer with image-processing software. It is possible to observe individual coalescence events using a sufficiently rapid camera, but these events are often so improbable in food emulsions that they are difficult to follow directly (Dickinson 1992, Walstra 1996a).
Ultrasound is strongly reflected at the interface of different tissue structures. In coronary arteries these are the blood-intimal border and the external elastic membrane (EEM). Manual or computer aided planimetry of these two borders allows precise measurements of the lumen area, intima-media area, and EEM.1 In addition, the ultrasound signal backscattered from the arterial wall allows the various tissue components to be differentiated, including the atherosclerotic plaque. The visual appearance of IVUS images of atheroma describe a continuum from echodense (bright echo signal) to echolucent (faint echo signal).2 However, recent approaches using advanced image processing of the raw IVUS data such as radiofrequency analysis have improved characterisation of vessel wall characteristics.
For a DCE-MRI image processing and analysis (informatics) protocol, the steps include the definition of the region of interest (ROI) by a process of image segmentation definition of the arterial or vascular input function, calculation of pre-contrast T , and calculation of Ktrans or IAUC. If the analysis is performed voxelwise, the individual data points may be noisy, leading to fitting errors in compartmental models however, if analysis is confined to the total ROI then it is not possible to account for heterogeneity. There are several sources of variation in DCE-MRI of which two major sources of bias and subjectivity must be
We perform this step using Adobe Photoshop software, version 5.0 or higher. Some basic knowledge of this software is needed in order to mount the immuno-FISH pictures. The following instructions are one example of how to do it, but other procedures or imaging software may also be used. 3. In order to produce properly aligned color pictures, open all three files in Adobe Photoshop. Convert all images from Indexed Color to RGB color mode (Menu Image Mode). 5. Align the three image layers by moving the layer content by the arrow keys ( Move tool from the Photoshop toolbox) (see Note 9). The morphologically common details on all images, such as the chromosome contours, should coincide. Finally, crop the image to the zone of interest ( Crop tool from Photoshop toolbox) and save the file. 9. Alignment of the three image layers in the Photoshop compound image file is necessary in particular, in the case of separate immunostaining and FISH-staining image acquisition. However, this is often...
Although it is widely accepted that both 2D and 3D displays reveal important features for polyp diagnosis (Dachman et al. 1998), there is not yet a consensus on which 2D or 3D viewing modes provide for the most accurate and efficient diagnosis. Moreover, advances in image processing and computer graphics have led to a multitude of advanced 3D displays that go beyond conventional virtual endoscopy, defined as the 3D view created when a single virtual camera is positioned inside the colonic lumen. Once a virtual camera is positioned at a particular voxel, moving the camera's position to another voxel will result in a new 3D rendering of the surface. Sequential movement of the camera along the colon amounts to navigating its course, wherein the goal is to view the surface in an animated, fly-through format. Various research groups have developed software packages that make this process a semiautomatic, preprocessing step (Paik et al. 1998 Reed and Johnson 1997 Samara et al. 1999 Lorensen...
Because field topographies are typically diffuse, source estimation by eye is a rather inexact process. Some investigators have employed image processing techniques to allow for easier detection of features in the field topography. For example, computation ofthe spatial derivative (the Laplacean) of the observed magnetic field or potential topography tends to place maxima over the current sources. Indeed, one form of MEG sensor a first-order planar gradiometer effectively implements this transform in the detector coil configuration.
Grid technology has a key role in enabling the development of a European Research Area 1, 2 with the potential to allow querying across heterogeneous and distributed data sets if these can be integrated and represented in ways which are valid, usable and ethically and legally acceptable 3, 4 . In areas such as brain imaging, the opportunities and the challenges of integration have been particularly evident, requiring integration in multi-centre clinical studies of patients in early stages of psychiatric disorders, standardization of scanners and image processing techniques across mental health research networks as well as scalable integration of voxel-based image data at different levels of integration 5, 6 , and the development of shared ontologies and spatial
In an effort to provide quantitative criteria for the distinction of area V2 from other cortical areas, image-processing techniques have been used to assess the cytoarchitectonic and myeloarchitectonic organizations of area V2 and to compare them with those from areas V1 and V4. According to this approach, Nissl-stained sections are digitized and the profiles of cell bodies are segmented according to gray level. A gray level index is then used to quantify the areal fraction of cortex occupied by stained cell bodies. Figure 5A illustrates the gray level index in areas V1, V2, and V4.
Because these patients are impaired at grouping, they appear to be oversensitive to segmentation cues and to parse stimuli inappropriately into parts. In fact, grouping and segmentation are likely two sides of the same coin, with the grouping impairment leading to piecemeal and fragmented image processing. The integrative agnosia deficit appears to affect a stage of visual coding intermediate between basic shape coding and visual access to memory representations, concerned with parallel perceptual grouping and the integration of parts into wholes. It is revealed most strikingly under conditions when segmentation or grouping are stressed.
Earlier work with a model of the retina5657 showed that synchronous oscillations have characteristics that make computational vision models useful tools for image processing (Figure 2.7). The power of synchronous oscillations is proportional to the size of the stimulus, which makes them useful for noise filtering and for discriminating large-vs.-small objects as well as rapid segmentation. Depending upon the desired feature size, the sensitivity to noise can be set by the user. One of the key insights from this spiking-neuron model is that delayed inhibition is necessary for synchronous oscillations. So, by adjusting the gain and the time constant of the inhibition, one can control the power of the oscillations and thus the degree of filtering. The retinal model emphasizes adjacent pixels with roughly equivalent contrast by grouping them into synchronous blobs. Performance should improve for a model based on cortical V1 neurons.
In order to more thoroughly assess the possible utility of MR-based volume measurements of anteromedial temporal lobe neuroanatomic structures in the diagnosis of AD we undertook a study which employed a large number of control and AD patients, state-of-the-art image acquisition and image-processing techniques, and well-accepted neuroanatomic boundary criteria for the various medial temporal lobe structures that were measured (58). MR-based volume measurements of the hippocampus, parahippocampal gyrus
And have addressed item 1, that is, identifying imaging criteria that will help to establish the diagnosis of AD in individual subjects. However, items 2 and 3 provide an equally valid rationale for the use of imaging markers in AD. Items 2 and 3, however, necessitate longitudinal as opposed to cross-sectional study design. A particularly attractive use for quantitative MR imaging in AD might center on item 3 to assess the response to therapeutic intervention as an independent marker of the efficacy of a drug in the treatment of AD. The history of imaging markers of hemispheric and regional atrophy in AD has been that significant differences between groups are consistently found, but overlap exists between individual members of the control and the AD populations. While this is a substantial problem if the goal of the imaging marker is to make a clinical diagnosis in individual patients, overlap among individuals becomes less of a problem in the setting of a drug trial where the...
Thus, intelligent image understanding will require image processing, pattern recognition, and a knowledge base together with an appropriate control strategy, and all must be smoothly integrated. Like so much else in AI, image understanding beyond very limited and heavily constrained situations is currently beyond the state of the art.
A final point to emphasize is that VPSEM GSE and even BSE images typically lack the usual strong contrasts present in conventional SEM images. Primary electron beam scatter, sample charging, poor detector efficiencies and the lack of a metal (e.g. Au, Au Pd) surface coating contribute to this problem. It is usual practice to use image manipulation software to optimize image contrast and brightness after collection. Noise reduction and edge-enhancing unsharpen mask filters also are very useful as image enhancement tools. Remember that unedited (raw) images should always be archived.
In summary, there is a growing body of evidence supporting the development and use of quantitative MRI tumor microvascular bioassays, achievable through the application of macromolecular blood pool contrast media, to characterize individual tumors and non-neo-plastic disease processes that affect microvessels. It is reasonable to anticipate that the clinical introduction of a dynamic MMCM-enhanced MRI bioassay could lead to better definition of tumor biological properties including the more precise identification of malignancy, the grading of malignancy, the angiographic demarcation of tumor feeding vessels, the presence and degree of accelerated angiogenesis, and perhaps clinically most important, a means to rapidly and non-invasively evaluate tumor response to treatment. Critical to the realization of the full potential of MMCM-enhanced MRI will be the identification, development, and ultimately the governmental approval of macromolecular blood pool contrast agents that combine...
Multiresolution imaging is an extremely useful technique for understanding in detail the structure of large DNA viruses that do not yield to the requirements of protein crystallography. The methodology consists in fitting the atomic structures of capsid components, independently solved, to medium-resolution, 3D maps of the complete virion, obtained by cryoelectron microscopy and image processing. On combining the two kinds of imaging data, one must take into account their intrinsic differences, as they have different resolution, suffer from different imaging artifacts, and are at different scales. These efforts are rewarded by quasi-atomic resolution models that provide valuable information about protein-protein interactions in the capsid. Difference maps calculated by subtracting the quasi-atomic model from the cryoelectron microscopy map reveal the molecular envelope of those capsid components whose atomic structure is unknown. A better understanding of the complex interactions...
Shieh, Ph.D., is a clinical professor at the University of California Irvine Medical Center. His research interests include computer-aided diagnosis, medical image processing, and medical informatics. His research has been published in the Journal of Digital Imaging, the International Journal of Healthcare Technology Management, and ACME Transactions, among others.
Formats including simulated fluorescence, stereo pairs, red-green anaglyph projections, and two or three color stereo pairs. These approaches allowing the presentation of multichannel information sets providing a synthesis of large data sets for the readers examination. Additional approaches involve the application of 3D rendering of these data sets. Figure 6.11 provides an example of a series of images of an Elbe river floc showing four images, the reflection image of particulate matter in the floc, autofluorescence showing the presence of autotrophic algae and cyanobacteria, staining with the nucleic acid stain Syto 9 showing all bacteria, and staining with a lectin Triticum vulgaris-TRITC revealing the exopolymer matrix of the floc as single channel maximum intensity projection (MIP) and then combined as MIP and a rendering image all of the same floc. Finally, images are often adjusted in terms of color balance for publication using programs such as Photoshop (Adobe Systems Inc.,...
Before actual image processing to determine the orientation of all particles, the following preprocessing tasks should be completed. Individual good particles would be selected for the later image processing. Both manual and automated particle selection are available however, in practice, combined manual screening post automatic selection is the best practical approach to ensure high quality selection.
Background measured by the image processing software is usually removed by subtracting individual probe background from the probe signal value or by subtracting a local average background from each individual probe signal value. It is also recommended to define a detection-threshold limit for each array, which is the mean plus two standard deviations of negative control probes on the array, or another robust estimate for theoretically nonex-pressed probes on the array.
This device simply translates the captured image to usable bits. Speed is necessary here so that a response is given quickly. The speed will depend on the capacity of the computer, the complexity of the image, and the type and quantity of information desired from it. The system and software should be optimized for the specific application so that the necessary frame grabber programs, algorithms, accelerators that interface with the CPU, and application software are adequate. Among the software available are NeuroCheck, a general-purpose image-processing system for industrial quality control Eurosys, suitable for industrial machine vision HACCON, which is flexible and gives high performance for research and education and WiT, for image-processing development (2). WiT, along with VPE, ProtoPIPE, VPM, and Concept Vi, allow the user to pick the image-processing icon, drag it to the workspace canvas, connect I Os using links, and define operator-specific parameters (7).
The use of micro-electrodes is an invasive technique and colonies must be discarded after measurements have been taken. According to Malakar et al. (2000), the measurement itself might even influence the gradient. Therefore, they used fluorescence ratio imaging to study the formation of microgradients in immobilized bacterial colonies of Lactobacillus curvatus. This non-invasive technique is based on the fact that fluorescence (energy emitted as light), resulting from an excitation light energy, is environment dependent, and can thus be used as a probe of its immediate surroundings. A fluorescence microscope was used to capture the fluorescence intensity images, which were then processed with an image processing tool. The spatial resolution of the images was about 1.5 pm. This is about the scale of a bacterial cell, and therefore suitable for observing local effects in colonies. The pH gradients observed in these experiments were due to production of lactic acid by the Lactobacillus...
While descriptive parameters from T1-weighted images have been shown to be helpful, they are not readily transportable, and are affected by a range of factors including specific sequence parameters, instrumental parameters, inherent tissue T1 relaxation times, built in image processing. These can vary markedly between MR systems, and some may vary with hardware and software revision, or routine maintenance. Thus there are significant problems to be addressed in generalising such techniques across several centres for multi-centre trials.
Ribotyping is more reproducible than conventional RFLP analysis. As this is due in part to the specificity of the technique, the ribotype patterns obtained by a given method can give a higher reproducibility when a combination of several REs is used. 20 In the automated procedure, molecular markers and image optimization software are used to increase between-batch reproducibil-ity so that band patterns can be compared with archived patterns using a computerized similarity index.
Combining the use of tagging agents with a software-based removal of this material, Zalis and Hahn (2001) reported results of a process dubbed digital subtraction bowel cleansing. In this technique, specialized image processing algorithms remove the marked colon contents from the CT images as a postprocessing step, in effect cleaning the images rather than the patient. One potential advantage of this approach is that the 3D endoluminal evaluation of the colon is preserved for problem solving. In addition, the visually distracting tagged colon contents are removed from view during screening evaluation of the multiplanar images. In preliminary data obtained in a limited, enriched cohort of patients, two independent readers correctly identified all colonoscopy-confirmed polyps lower than 1 cm, suggesting performance comparable to standard CTC (Zalis et al. 2000 Zalis and Hahn 2001).
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