Automated segmentation and tracking for large-scale analysis of focal adhesion dynamics.

Cell adhesion, a process mediated by the formation of discrete structures known as focal adhesions (FAs), is pivotal to many biological events including cell motility. Much is known about the molecular composition of FAs, although our knowledge of the spatio-temporal recruitment and the relative occupancy of the individual components present in the FAs is still incomplete. To fill this gap, an essential prerequisite is a highly reliable procedure for the recognition, segmentation and tracking of FAs. Although manual segmentation and tracking may provide some advantages when done by an expert, its performance is usually hampered by subjective judgement and the long time required in analysing large data sets. Here, we developed a model-based segmentation and tracking algorithm that overcomes these problems. In addition, we developed a dedicated computational approach to correct segmentation errors that may arise from the analysis of poorly defined FAs. Thus, by achieving accurate and consistent FA segmentation and tracking, our work establishes the basis for a comprehensive analysis of FA dynamics under various experimental regimes and the future development of mathematical models that simulate FA behaviour.

Computer-aided classification of colorectal polyps based on vascular patterns: a pilot study.

BACKGROUND AND STUDY AIMS: Recent studies have shown that narrow-band imaging (NBI) is a powerful diagnostic tool for differentiating between neoplastic and nonneoplastic colorectal polyps. The aim of the present study was to develop and evaluate a computer-based method for automated classification of colorectal polyps on the basis of vascularization features. PATIENTS AND METHODS: In a prospective pilot study with 128 patients who were undergoing zoom NBI colonoscopy, 209 detected polyps were visualized and subsequently removed for histological analysis. The proposed computer-based method consists of image preprocessing, vessel segmentation, feature extraction, and classification. The results of the automated classification were compared to those of human observers blinded to the histological gold standard. RESULTS: Consensus decision between the human observers resulted in a sensitivity of 93.8 % and a specificity of 85.7 %. A "safe" decision, i. e., classifying polyps as neoplastic in cases when there was interobserver discrepancy, yielded a sensitivity of 96.9 % and a specificity of 71.4 %. The overall correct classification rates were 91.9 % for the consensus decision and 90.9 % for the safe decision. With ideal settings the computer-based approach achieved a sensitivity of approximately 90 % and a specificity of approximately 70 %, while the overall correct classification rate was 85.3 %. The computer-based classification showed a specificity of 61.2 % when a sensitivity of 93.8 % was selected, and a 53.1 % specificity with a sensitivity of 96.9 %. CONCLUSIONS: Automated classification of colonic polyps on the basis of NBI vascularization features is feasible, but classification by observers is still superior. Further research is needed to clarify whether the performance of the automated classification system can be improved.

Sensor, signal, and image informatics - state of the art and current topics.

OBJECTIVES: The number of articles published annually in the fields of biomedical signal and image acquisition and processing is increasing. Based on selected examples, this survey aims at comprehensively demonstrating the recent trends and developments. METHODS: Four articles are selected for biomedical data acquisition covering topics such as dose saving in CT, C-arm X-ray imaging systems for volume imaging, and the replacement of dose-intensive CT-based diagnostic with harmonic ultrasound imaging. Regarding biomedical signal analysis (BSA), the four selected articles discuss the equivalence of different time-frequency approaches for signal analysis, an application to Cochlea implants, where time-frequency analysis is applied for controlling the replacement system, recent trends for fusion of different modalities, and the role of BSA as part of a brain machine interfaces. To cover the broad spectrum of publications in the field of biomedical image processing, six papers are focused. Important topics are content-based image retrieval in medical applications, automatic classification of tongue photographs from traditional Chinese medicine, brain perfusion analysis in single photon emission computed tomography (SPECT), model-based visualization of vascular trees, and virtual surgery, where enhanced visualization and haptic feedback techniques are combined with a sphere-filled model of the organ. RESULTS: The selected papers emphasize the five fields forming the chain of biomedical data processing: (1) data acquisition, (2) data reconstruction and pre-processing, (3) data handling, (4) data analysis, and (5) data visualization. Fields 1 and 2 form the sensor informatics, while fields 2 to 5 form signal or image informatics with respect to the nature of the data considered. CONCLUSIONS: Biomedical data acquisition and pre-processing, as well as data handling, analysis and visualization aims at providing reliable tools for decision support that improve the quality of health care. Comprehensive evaluation of the processing methods and their reliable integration in routine applications are future challenges in the field of sensor, signal and image informatics.

A technique to detect and to quantify fasciocutaneous blood vessels in small laboratory animals ex vivo.

PURPOSE: A microangiographical technique is described, which allows visualization of small and capillary blood vessels and quantification of fasciocutaneous blood vessels by means of digital computer analysis in very small laboratory animals. MATERIALS AND METHODS: The left carotid artery of 20 nu/nu mice was cannulated (26 gauge) and a mixture of gelatin, bariumsulfate, and green ink was injected according to standardized protocol. Fasciocutaneous blood vessels were visualized by digital mammography and analyzed for vessel length and vessel surface area as standardized units [SU] by computer program. RESULTS: With the described microangiography method, fasciocutaneous blood vessels down to capillary size level can be clearly visualized. Regions of interest (ROIs) can be defined and the containing vascular network quantified. Comparable results may be obtained by calculating the microvascular area index (MAI) and the microvascular length index (MLI), related to the ROIs size. Identical ROIs showed a high reproducibility for measured [SU] < 0.01 +/- 0.0012%. CONCLUSION: Combining microsurgical techniques, pharmacological knowledge, and modern digital image technology, we were able to visualize small and capillary blood vessels even in small laboratory animals. By using our own computer analytical program, quantification of vessels was reliable, highly reproducible, and fast.

[A microangiography technique to quantify fasciocutaneous blood vessels in small laboratory animals]. / Eine mikroangiographische Technik zur Quantifizierung fasziokutaner Blutgefässe am kleinen Versuchstier.

PURPOSE: A microangiographic technique is described, which allows visualization of small blood vessels with a diameter of approximately 20 microm and quantification of fasciocutaneous blood vessels by means of digital computer analysis in very small laboratory animals. METHOD: The left carotid artery of 45 nu/nu mice was cannulated (26 gauge) and a mixture of gelatine, barium sulfate and green ink was injected according to standardized protocol. Fasciocutaneous blood vessels were visualized by digital mammography and analyzed for vessel length and vessel surface area as standardized units (pixel) by computer program. RESULTS: With the described microangiography method fasciocutaneous blood vessels can be clearly visualized. Regions of interest (ROIs) can be defined and the containing vascular network quantified. Identical ROIs showed a high reproducibility for measured unit (pixel) < 6.5 +/- 2.4 %. By the use of digital image, processing the quantification of vessels was reliable, reproducible and fast. CONCLUSION: Combining microsurgical techniques, pharmacological knowledge and modern computer imaging analysis systems, we were able to visualize and quantify blood vessels with a diameter of approximately 20 microm even in small laboratory animals.

Analysis of nerve fibers and their distribution in histologic sections of the human brain.

The field of quantitative analysis and subsequent mapping of the cerebral cortex has developed rapidly. New powerful tools have been applied to investigate large regions of complex folded gyrencephalic cortices in order to detect structural transition regions that might partition different cortical fields of disjunct neuronal functions. We have developed a new mapping approach based on axoarchitectonics, a method of cortical visualization that previously has been used only indirectly with regard to myeloarchitectonics. Myeloarchitectonic visualization has the disadvantage of producing strong agglomerative effects of closely neighbored nerve fibers. Therefore, single and neurofunctional-relevant parameters such as axonal branchings, axon areas, and axon numbers have not been determinable with satisfying precision. As a result, different staining techniques had to be explored in order to achieve a suitable histologic staining for axon visualization. The best results were obtained after modifying the Naoumenko-Feigin staining for axons. From these contrast-rich stained histologic sections, videomicroscopic digital image tiles were generated and analyzed using a new fiber analysis framework. Finally, the analysis of histologic images provided topologic ordered parameters of axons that were transferred into parameter maps. The axon parameter maps were analyzed further via a recently developed traverse generating algorithm that calculated test lines oriented perpendicular to the cortical surface and white matter border. The gray value coded parameters of the parameter maps were then transferred into profile arrays. These profile arrays were statistically analyzed by a reliable excess mass approach we recently developed. We found that specific axonal parameters are preferentially distributed throughout granular and agranular types of cortex. Furthermore, our new procedure detected transition regions originally defined by changes of cytoarchitectonic layering. Statistically significant inhomogeneities of the distribution of certain axon quantities were shown to indicate a subparcellation of areas 4 and 6. The quantification techniques established here for the analysis of spatial axon distributions within larger regions of the cerebral cortex are suitable to detect inhomogeneities of laminar axon patterns. Hence, these techniques can be recommended for systematic and observer-supported cortical area mapping and parcellation studies.

Human cerebral perfusion analysis with ultrasound contrast agent constant infusion: a pilot study on healthy volunteers.

With ultrasound (US) contrast agent (UCA) continuous infusion providing a steady state, mean tissue microbubble velocity can be assessed by analyzing the reappearance rate after microbubble destruction with US energy (refill kinetics). In this study, we investigated this new approach for the assessment of human cerebral perfusion. A total of 12 healthy volunteers were investigated transtemporally with increasing pulsing intervals (250, 500, 750, 1000, 1250, 1500, 2000, 3000 and 4000 ms) and two UCA infusion rates (0.5 and 1.0 mL/min of Optison). Intensity vs. pulsing interval curves were analyzed using an exponential curve fit and parameters of the curve (plateau echo enhancement, A, representing the microbubble concentration within the interrogated tissue; rate constant, beta, which is related to blood flow and their product, F = Abeta) were compared. For 20/20 investigations being available for further analysis, it was possible to generate a typical exponential intensity vs. pulsing interval curve from the ipsilateral thalamus. The plateau echo enhancement A showed a significant (p = 0.02), and the beta as well as the F values displayed a nonsignificant (p = 0.06, both), increase with infusion rate. The qualitative analysis of beta and F parameter images displayed the most homogeneous visualisation of perfusion in the ipsilateral thalamus and main territory of the middle cerebral artery. In conclusion, it is possible to display the UCA refill kinetics in human cerebral microcirculation after microbubble destruction by transcranial US. Grey-scale harmonic imaging allows a quantitative approach to cerebral perfusion with a large interindividual variation of the parameters.

Digital radiography enhancement by nonlinear multiscale processing.

Today's digital radiography systems mostly use unsharp maskinglike enhancement algorithms based on splitting input images into two or three frequency channels. This method allows fine detail enhancement as well as processing of global contrast (harmonization). However, structures of medium size are not accessible. In extension of a standard algorithm of such type, we develop and test a new enhancement algorithm based on hierarchically repeated unsharp masking, resulting in a multiscale architecture allowing consistent access to structures of all sizes. Our algorithm decomposes a radiograph by a pyramid-architecture, dividing it into eight or more channels representing structures of different sizes, known as "scales." At each scale, weakly contrasting structures are then enhanced by suitable nonlinear processing. We emphasize two points: first, backward compatibility to the standard algorithm which is used routinely in clinical practice. This allows reuse of current parametrization know-how as well as a smooth transition from current to new processing. Second, our enhancement is noise-resistant in the sense that it prevents unacceptable noise amplification. A prototype implementation of the algorithm is undergoing trials in the clinical routine of radiology departments of major German hospitals. Results strongly indicate the superior performance and high acceptance of the new processing.

Coding of segmented images using shape-independent basis functions.

An important issue in object-based image coding is the efficient description of image segments having an arbitrary shape. This paper outlines a solution to this task using basic principles of transform image coding that are generalized for the case of arbitrarily shaped image segments. The texture inside each region is successively approximated using two-dimensional (2-D) shape-independent basis functions defined on a rectangle circumscribing the given image segment. The resulting texture description exhibits a high energy compactness and is well suited for low bit rate image coding. Unlike other approaches aimed at segment-oriented image coding, the proposed concept does not couple texture description with contour coding. The computational load is kept low, especially for the decoding process.