An overview of state-of-the-art image restoration in electron microscopy.

In Life Science research, electron microscopy (EM) is an essential tool for morphological analysis at the subcellular level as it allows for visualization at nanometer resolution. However, electron micrographs contain image degradations such as noise and blur caused by electromagnetic interference, electron counting errors, magnetic lens imperfections, electron diffraction, etc. These imperfections in raw image quality are inevitable and hamper subsequent image analysis and visualization. In an effort to mitigate these artefacts, many electron microscopy image restoration algorithms have been proposed in the last years. Most of these methods rely on generic assumptions on the image or degradations and are therefore outperformed by advanced methods that are based on more accurate models. Ideally, a method will accurately model the specific degradations that fit the physical acquisition settings. In this overview paper, we discuss different electron microscopy image degradation solutions and demonstrate that dedicated artefact regularisation results in higher quality restoration and is applicable through recently developed probabilistic methods.

Automatic identification of Caenorhabditis elegans in population images by shape energy features.

Experiments on model organisms are used to extend the understanding of complex biological processes. In Caenorhabditis elegans studies, populations of specimens are sampled to measure certain morphological properties and a population is characterized based on statistics extracted from such samples. Automatic detection of C. elegans in such culture images is a difficult problem. The images are affected by clutter, overlap and image degradations. In this paper, we exploit shape and appearance differences between C. elegans and non-C. elegans segmentations. Shape information is captured by optimizing a parametric open contour model on training data. Features derived from the contour energies are proposed as shape descriptors and integrated in a probabilistic framework. These descriptors are evaluated for C. elegans detection in culture images. Our experiments show that measurements extracted from these samples correlate well with ground truth data. These positive results indicate that the proposed approach can be used for quantitative analysis of complex nematode images.

Skeletonization method for vessel delineation of arteriovenous malformation.

Cerebral arteriovenous malformation (AVM) presents a great health threat due to its high probability of rupture that can cause severe brain damage. Image segmentation alone is not sufficient to support AVM embolization procedure. In order to successfully navigate the catheter and perform embolization, the segmented blood vessels need to be classified into feeding arteries, draining veins and the AVM nidus. For this reason we address here the AVM localization and vessel decomposition problem. We propose in this paper a novel AVM localization and vessel delineation method using ordered thinning-based skeletonization. The main focus of vessel delineation is the delineation of draining veins since it is essential for the embolization procedure. The main contribution is a graph-based method for exact extraction of draining veins which, in combination with our earlier work on AVM detection, allows the AVM decomposition into veins, arteries and the nidus (with an emphasis on the draining veins). We validate the proposed approach on blood vessel phantoms representing the veins and the AVM structure, as well as on cerebral 3D digital rotational angiography (3DRA) images before and after embolization, paired with digital subtraction angiography (DSA) images. Results on AVM delineation show high correspondence to the ground truth structures and indicate potentials for use in surgical planning.

An imaging system with calibrated color image acquisition for use in dermatology.

We propose a novel imaging system useful in dermatology, more precisely, for the follow-up of patients with an increased risk of skin cancer. The system consists of a Pentium PC equipped with an RGB frame grabber, a three-chip charge coupled devices (CCD) camera controlled by the serial port and equipped with a zoom lens and a halogen annular light source. Calibration of the imaging system provides a way to transform the acquired images, which are defined in an unknown color space, to a standard, well-defined color space called sRGB. sRGB has a known relation to the CIE1 XYZ and CIE L*a*b* colorimetric spaces. These CIE color spaces are based on the human vision, and they allow the computation of a color difference metric called CIE deltaE*ab, which is proportional to the color difference, as seen by a human observer. Several types of polynomial RGB to sRGB transforms will be tried, including some optimized in perceptually uniform color spaces. The use of a standard and well-defined color space also allows meaningful exchange of images, e.g., in teledermatology. The calibration procedure is based on 24 patches with known color properties, and it takes about 5 minutes to perform. It results in a number of settings called a profile that remains valid for tens of hours of operation. Such a profile is checked before acquiring images using just one color patch, and is adjusted on the fly to compensate for short-term drift in the response of the imaging system. Precision or reproducibility of subsequent color measurements is very good with (deltaE*ab) = 0.3 and deltaE*ab < 1.2. Accuracy compared with spectrophotometric measurements is fair with (deltaE*ab) = 6.2 and deltaE*ab < 13.3.

ECG data compression with time-warped polynomials.

This paper presents a new adaptive compression method for ECG's. The method represents each R-R interval by an optimally time-warped polynomial. It achieves a high-quality approximation at less than 250 bits/s. The article shows that the corresponding rates for other transform based schemes (the DCT and the DLT) are always higher. Also, the new method is less sensitive to errors in QRS detection and it removes more (white) noise from the signal. The reconstruction errors are distributed more uniformly in the new scheme and the peak error is usually lower. The reconstruction method is also useful for adaptive filtering of noisy ECG signals.

Adaptive noise removal from biomedical signals using warped polynomials.

This paper presents the time-warped polynomial filter (TWPF), a new interval-adaptive filter for removing stationary noise from nonstationary biomedical signals. The filter fits warped polynomials to large segments of such signals. This can be interpreted as low-pass filtering with a time-varying cut-off frequency. In optimal operation, the filter's cut-off frequency equals the local signal bandwidth. However, the paper also presents an iterative filter adaptation algorithm, which does not rely on the (complicated) computation of the local bandwidth. The TWPF has some important advantages over existing adaptive noise removal techniques: it reacts immediately to changes in the signal's properties, independently of the desired noise reduction; it does not require a reference signal and can be applied to nonperiodical signals. In case of quasiperiodical signals, applying the TWPF to the individual signal periods leads to an optimal noise reduction. However, the TWPF can also be applied to intervals of fixed size, at the expense of a slightly lower noise reduction. This is the way nonquasiperiodical signals are filtered. The paper presents experimental results which demonstrate the usefulness of the interval-adaptive filter in several biomedical applications: noise removal from ECG, respiratory and blood pressure signals, and base line restoration of electro-encephalograms (EEG's).

Data compression of ECG's by high-degree polynomial approximation.

A method for the compression of ECG data is presented. The method is based on high-degree polynomial expansions. Data rates of about 350 bits per second are achievable at an acceptable signal quality. The high compression is obtained by a carefully selected subdivision of the ECG signal into intervals that make optimal use of the special properties of the polynomial base functions. Each interval corresponds to one ECG period. The method is compared to the discrete cosine transform and is found to yield a significantly higher data compression for a given signal quality (quantified by mean squared error and peak error).

Corrections to "JPEG dequantization array for regularized decompression".

An error in the theoretical derivations leading up to the main equation of the above correspondence by Prost et al. is pointed out, and corrections are presented. Due to the error, the experimentally obtained "optimal" parameters are really only suboptimal.

Lossless quantization of Hadamard transform coefficients.

This paper shows that an n x 1 integer vector can be exactly recovered from its Hadamard transform coefficients, even when 0.5 n log(2)(n) of the (less significant) bits of these coefficients are removed. The paper introduces a fast "lossless" dequantization algorithm for this purpose. To investigate the usefulness of the procedure in data compression, the paper investigates an embedded block image coding technique called the "LHAD" based on the algorithm. The results show that lossless compression ratios close to the state of the art can be achieved, but that techniques such as CALIC and S+P still perform better.

Quantitative analysis of the neonatal brain by ultrasound.

Clinical research has shown a clear correlation between white matter disorders of the neonatal brain and neuromotoric handicap at a later age. Ultrasound imaging is a proven method to detect the white matter damage at an early stage. However, since subjective visual examination of the images by neonatologists not always leads to an unambiguous diagnosis, a need for quantitative characterization is felt. Reproducibility is the first requirement in order to be able to perform objective quantitative analysis. This paper proposes a software-based method to compensate for variable acquisition factors that negatively affect the reproducibility of the measurements. The results of some basic experiments will illustrate the usefulness of the developed compensation algorithm.

State-of-the-art techniques for lossless compression of 3D medical image sets.

This paper explains the basic principles of lossless two-dimensional (2D) and three-dimensional (3D) image coding at a high level of abstraction. It discusses also a new inter-frame technique for lossless video coding based on intra-frame prediction and inter-frame context modelling. The performance of this technique is compared to that of state-of-the-art 2D coders on CT and MRI data sets from the Visual Human Project. The results show that the inter-frame technique outperforms state-of-the-art intra-frame coders, i.e. Calic and JPEG-LS. The improvement in compression ratio is significant in the case of CT data but is rather small in the case of MRI data.

Generalized pixel profiling and comparative segmentation with application to arteriovenous malformation segmentation.

Extraction of structural and geometric information from 3-D images of blood vessels is a well known and widely addressed segmentation problem. The segmentation of cerebral blood vessels is of great importance in diagnostic and clinical applications, with a special application in diagnostics and surgery on arteriovenous malformations (AVM). However, the techniques addressing the problem of the AVM inner structure segmentation are rare. In this work we present a novel method of pixel profiling with the application to segmentation of the 3-D angiography AVM images. Our algorithm stands out in situations with low resolution images and high variability of pixel intensity. Another advantage of our method is that the parameters are set automatically, which yields little manual user intervention. The results on phantoms and real data demonstrate its effectiveness and potentials for fine delineation of AVM structure.

Interstitial cells of Cajal and their role in veterinary gastrointestinal pathologies.

This study highlights the importance of interstitial cells of Cajal (ICs) in gastrointestinal disease. Human research is already considering IC pathologies but in veterinary research IC pathologies are rarely studied. Nevertheless, recent studies of ICs show a growing interest in the pathophysiology of gastrointestinal diseases and emphasize the consideration of this cell type in the pathophysiology of veterinary gastrointestinal malfunctions.

Simultaneous degradation estimation and restoration of confocal images and performance evaluation by colocalization analysis.

A novel method for joint restoration and estimation of the degradation of confocal microscope images is presented. The observed images are degraded due to two sources: blurring due to the band-limited nature of the optical system [modelled by the point spread function (PSF)], and Poisson noise contaminates the observations due to the discrete nature of the photon detection process. The proposed method iterates noise reduction, blur estimation and deblurring, and applies these steps in two phases, i.e. a training phase and a restoration phase. In the first phase, these three steps are iterated until the blur estimation converges. Noise reduction and blur estimation are performed using steerable pyramids, and the deblurring is performed by the Richardson-Lucy algorithm. The second phase is the actual restoration. From then on, the blur estimation is used as a criterion to measure the image quality. The iterations are stopped when this measure converges, a result that is guaranteed. The integrated method is completely automatic, and no prior information on the image is required. The method has been given the name SPERRIL (Steerable Pyramid-based Estimation and Regularized Richardson-Lucy restoration). Compared with existing techniques by both objective measures and visual observation, in the SPERRIL-restored images noise is better suppressed.

Intermittent positive pressure ventilation and high frequency ventilation in dogs with experimental bronchopleural fistulae.

This study evaluated respiratory and cardiovascular responses of canines in whom bilateral bronchopleural fistulae were created surgically, and in whom ventilation was varied between intermittent positive pressure ventilation (IPPV) and high frequency ventilation (HFV). An Emerson prototype ventilator was used for HFV at rates of 300-1400/min at driving pressures of 2.5, 5.0, and 10 psi. Gas exchange was judged by arterial and mixed venous blood gases. Cardiac performance was measured by cardiac index, heart rate, stroke index, stroke work index, systemic and pulmonary vascular pressures and resistances. Ventilation during IPPV with the fistula open resulted in a statistically significant increase in PaCO2 and a decrease in PaO2 when compared to both HFV modes. Variations in cardiac function in these open-chested animals were insignificant for all variables tested except pulmonary artery pressures which rose significantly in the IPPV group.

Limits to maximal performance in individuals with spinal cord injury.

The purpose of this study was to examine the effect of four conditions that might improve oxygen transport and/or utilization during maximal exercise performance in individuals with spinal cord injury (SCI). Five males with tetraplegia (TP) and four males with paraplegia (PR) performed maximal arm cranking exercise in the following positions: 1) sitting; 2) supine; and 3) sitting with the addition of a) anti-gravity suit (anit-G), b) elastic stockings and abdominal binder, and c) functional electrical stimulation (FES) of the paralysed leg muscles. Peak power output (PO peak), peak oxygen uptake (VO2peak), peak heart rate (HR peak) and maximal systolic blood pressure were significantly lower in TP compared to PR for all conditions. A significant decrease in HR peak for PR, and a significant increase in VO2peak/kg for TP was seen during the supine compared to sitting condition. Respiratory exchange ratio (R) decreased significantly during the FES compared to the sitting condition in TP. No other changes were observed for any of the other conditions in either group. Improvements in central circulation previously reported during submaximal exercise for these four conditions did not result in a concomitant rise in maximal exercise performance. The results of this study suggest that the limitation in VO2peak for individuals with SCI is located peripherally (small active muscle mass) rather than centrally (heart or lungs).

A case of childhood sarcoidosis.

Cutaneous sarcoidosis is rare in children. We report a case of a 5-year-old Bangladeshi girl who presented with fever, a papular eruption on the lower limbs and trunk, malaise, anorexia and weight loss. There was multisystem involvement with marked hepatosplenomegaly, generalized lymphadenopathy, parotid fullness and chronic uveitis. Pulmonary infiltrates were seen on the chest X-ray. Histology of a skin biopsy showed naked noncaseating granulomata and PCR for Mycobacterium tuberculosis was negative. A clinical diagnosis of sarcoidosis was made. The patient was treated with oral prednisolone (2 mg/kg per day). An excellent clinical response with resolution of the rash and improvement of extracutaneous signs was noted within 3 months and she remains well on low-dose prednisolone on alternate days. We discuss the presentation and management of sarcoidosis in children, and highlight the potential difficulty in differentiating this from disseminated tuberculosis.