Volker J. Schmid

Ludwig-Maximilians-University of Munich | LMU · Institut für Statistik

This paper aims to solve the arterial input function (AIF) determination in dynamic contrast-enhanced MRI (DCE-MRI), an important linear ill-posed inverse problem, using the maximum entropy technique (MET) and regularization functionals. In addition, estimating the pharmacokinetic parameters from a DCE-MR image investigations is an urgent need to o...

Background: For the kinetic models used in contrast-based medical imaging, the assignment of the arterial input function named AIF is essential for the estimation of the physiological parameters of the tissue via solving an optimization problem. Objective: In the current study, we estimate the AIF relayed on the modified maximum entropy method. The...

Genome-based functions are inseparable from the dynamic higher-order architecture of the cell nucleus. In this context, the repair of DNA damage is coordinated by precise spatiotemporal controls that target and regulate the repair machinery required to maintain genome integrity. However, the mechanisms that pair damaged DNA with intact template for...

Introduction In Germany, the regional settlement structure is heterogenous, ranging from densely populated cities with a tight network of vascular healthcare to large regions in which access to healthcare is limited in terms of space and time. Therefore, the aim of this secondary data analysis was to investigate the association between the settleme...

Background: Obesity, as a risk factor for many noncommunicable diseases, is a common public health problem in developed and developing countries. Among Iranian children and adolescents, the prevalence of being overweight has increased by almost 50% in the past two decades. Aims: To visualize the geographic differences in general and abdominal ob...

Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture, linked to nuclear functions, is less well understood. Using live-cell and super-resolved 3D microscopy, here we find that cohesin depletion in a human colon cancer derived cell line results in endomitosis and a single multilobula...

Background: The German quality assurance guideline on abdominal aortic aneurysm (AAA) was implemented by the Joint Federal Committee (Gemeinsamer Bundesausschuss, G-BA) in 2008. The aims of this study were to verify the association between hospital case volume and outcome and to assess the hypothetical effect of minimum caseload requirements. Met...

Co-localization analysis is a popular method for quantitative analysis in fluorescence microscopy imaging. The localization of marked proteins in the cell nucleus allows a deep insight into biological processes in the nucleus. Several metrics have been developed for measuring the co-localization of two markers, however, they depend on subjective th...

Background: Abdominal aortic aneurysms (AAA) can be treated by either open surgery (OAR) or endovascular aortic repair (EVAR). The aim of this study was to analyze regional variations in application of (EVAR) and in-hospital mortality after intact AAA (iAAA) repair. Methods: Using data provided by the German Federal Statistical Office, a nationwide...

Background: Abdominal aortic aneurysms (AAA) can be treated by either open surgery (OAR) or endovascular aortic repair (EVAR). The aim of this study was to analyze regional variations in application of (EVAR) and in-hospital mortality after intact AAA (iAAA) repair. Methods: Using data provided by the German Federal Statistical Office, a nationwide...

The human genome forms thousands of "contact domains", which are intervals of enhanced contact frequency. Some, called "loop domains" are thought to form by cohesin-mediated loop extrusion. Others, called "compartmental domains", form due to the segregation of active and inactive chromatin into A and B compartments. Recently, Hi-C studies revealed...

Purpose: Considering the increase in incidence of breast and cervix uteri cancers in Iran, this study investigates spatio-temporal patterns of the incidence of these two cancers by estimating the step changes between pairs of adjacent regions and between the Iranian women from 2004 to 2009. Methods: Using an adaptive smoothing model, spatio-temp...

Background For Germany, regional variation of procedure rates of carotid endarterectomy (CEA) and carotid artery stenting (CAS) performed for carotid stenosis have so far not been analyzed at a national level. The aim of this study was to assess small area estimates of procedure rates among German regions, and to identify regional characteristics,...

Cervical cancer in women is one of the most common cancers and breast cancer has grown dramatically in recent years. The purpose of this study was to map the incidence of breast and cervix uteri cancer among Iranian women over a 6-year period (2004-2009) searching for trend changes and risk factors. Cancer incidence data were extracted from the ann...

Background For Germany, regional variation of procedure rates of carotid endarterectomy (CEA) and carotid artery stenting (CAS) performed for carotid stenosis have so far not been analyzed at a national level. The aim of this study was to assess small area estimates of procedure rates among German regions, and to identify regional characteristics,...

Objective: This study aimed to analyze the spatial distribution and regional variation of the hospital incidence and in hospital mortality of abdominal aortic aneurysms (AAA) in Germany. Methods: German DRG statistics (2011-2014) were analysed. Patients with ruptured AAA (rAAA, I71.3, treated or not) and patients with non-ruptured AAA (nrAAA, I7...

Objectives: The aim of this study was to analyse the association between annual hospital procedural volume and post-operative outcomes following repair of abdominal aortic aneurysms (AAA) in Germany. Methods: Data were extracted from nationwide Diagnosis Related Group (DRG) statistics provided by the German Federal Statistical Office. Cases with...

Background The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an ‘open’ local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explor...

Background: Among the proposals for joint disease mapping, the shared component model has become more popular. Another advance to strengthen inference of disease data is the extension of purely spatial models to include time aspect. We aim to combine the idea of multivariate shared components with spatio-temporal modelling in a joint disease mappin...

Complex statistical models often require strong assumptions to overcome the issue of non-identifiability. While in theory it is well understood that model assumptions can strongly influence the results, this seems to be underappreciated in practice. We address the impact of model assumptions in the case of scalar-on-image regression. This paper giv...

Background: Aim of this study was to analyze hospital incidence, type of treatment, and hospital mortality rates of patients with abdominal aortic aneurysm (AAA) in Germany from 2005 to 2014. Methods: Microdata of the diagnosis-related group (DRG) statistics compiled by the German Federal Statistical Office for the years 2005-2014 were analyzed....

Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow...

Background: In the estimation of physiological kinetic parameters from Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) data, the determination of the arterial input function (AIF) plays a key role. Objectives: This paper proposes a Bayesian method to estimate the physiological parameters of DCE-MRI along with the AIF in situations...

Fitting regression models can be challenging when regression coefficients are high-dimensional. Especially when large spatial or temporal effects need to be taken into account the limits of computational capacities of normal working stations are reached quickly. The analysis of images with several million pixels, where each pixel value can be seen...

Since manual object detection is very inaccurate and time consuming, some automatic object detection tools have been developed in recent years. At the moment, there is no image analysis software available which provides an automatic, objective assessment of 3D foci which is generally applicable. Complications arise from discrete foci which are very...

Utilizing 3D structured illumination microscopy, we investigated the quality and quantity of nuclear invaginations and the distribution of nuclear pores during rabbit early embryonic development and identified the exact time point of nucleoporin 153 (NUP153) association with chromatin during mitosis. Contrary to bovine early embryonic nuclei, featu...

Background: For the statistical analysis of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) data, compartment models are a commonly used tool. By these models, the observed uptake of contrast agent in some tissue over time is linked to physiologic properties like capillary permeability and blood flow. Up to now, models of different...

The present study demonstrates a major remodeling of the nuclear envelope and its underlying lamina during bovine preimplantation development. Up to the onset of major embryonic genome activation (MGA) at the 8-cell stage nuclei showed a non-uniform distribution of nuclear pore complexes (NPCs). NPCs were exclusively present at sites where DNA cont...

Advances in clinical medical imaging have brought about the routine production of vast numbers of medical images that need to be analyzed. As a result, an enormous amount of computer vision research effort has been targeted at achieving automated medical image analysis. This has proved to be an elusive goal in many cases. The complexity of the prob...

This chapter reviews the basics of genetic algorithms (GAs), briefly describes the schema theorem and the building block hypothesis, and explains feature selection based on GAs, as one of the most important applications of GAs. GAs differ from classical optimization and search procedures: (1) direct manipulation of a coding, (2) search from a popul...

The analysis of perfusion MRI data by unsupervised clustering methods provides the advantage that it does not imply speculative presumptive knowledge on contrast agent dilution models, but strictly focuses on the observed complete MRI signal time-series. In this chapter, the applicability of clustering techniques is demonstrated as tools for the an...

Feature extraction methods encompass, besides the traditional transformed and nontransformed signal characteristics and texture, structural and graph descriptors. The feature selection methods described in this chapter are the exhaustive search, branch and bound algorithm, max–min feature selection, sequential forward and backward selection, and al...

In this chapter, we present the theory of 2-D discrete wavelet transforms, and of biorthogonal wavelets, and we show several applications of the wavelet transform in medical imaging. The most remarkable applications are: (a) ability of the WT to make visible simple objects in a noisy background, which were previously considered to be invisible to a...

Breast cancer is the most common cancer among women, but has an encouraging cure rate if diagnosed at an early stage. Thus, early detection of breast cancer continues to be the key for effective treatment. The success of CAD in conventional X-ray mammography motivated the research of automated diagnosis techniques in breast MRI to expedite diagnost...

This chapter presents some of the most important neural architectures relevant to bioimaging and their applications to several bioimaging tasks. In general, medical image patterns either possess a circular symmetric shape—such as nodules—or appear as small objects with a variety of geometric patterns—such as calcifications. Neural networks have dem...

This chapter covers spatial approaches for three different types of temporal models: linear, nonlinear, and nonparametric models. Assuming a global spatial smoothness is typically not appropriate for medical images and locally adaptive smoothing allows to retain sharp features and borders in the images.

This chapter gives an overview about the most important approaches in statistical and syntactic pattern recognition and their application to biomedical imaging. Parametric and nonparametric estimation methods and binary decision trees form the basis for most classification problems related to bioimaging while grammatical inference and graphical met...

This chapter reviews the basics of subband coding and presents the different types of wavelet transforms in great detail. Subband coding means a transformation created by filtering and subsampling. The signal is separated approximately into frequency bands for efficient coding. The subband signals are quantized such that the objective measure is ma...

Neural networks are excellent candidates for feature extraction and selection, and also for signal separation. The underlying architectures are mostly employing unsupervised learning algorithms and are viewed as nonlinear dynamical systems. The material in this chapter is organized in three parts: the first part describes the neurodynamical aspects...

In a medical imaging system, uncertainties can be present at any point resulting from incomplete or imprecise input information, ambiguity in medical images, ill-defined or overlapping boundaries among the disease classes or regions, and indefiniteness in extracting features and relations among them. A patient can have a set of symptoms, which can...

Medical imaging deals with the interaction of all forms of radiation with tissue and the design of technical systems to extract clinically relevant information, which is then represented in image format. Medical images range from the simplest such as a chest X-ray to sophisticated images displaying temporal phenomena such as the functional magnetic...

Abstract The binding behavior of molecules in nuclei of living cells can be studied through the analysis of images from fluorescence recovery after photobleaching experiments. However, there is still a lack of methodology for the statistical evaluation of FRAP data, especially for the joint analysis of multiple dynamic images. We propose a hierarch...

Nuclear invaginations carrying nuclear pores may facilitate increased mRNA export and protein import to areas inside the nucleus remote from the nuclear border. In this study on rabbit embryos, we investigated whether large early embryonic nuclei and the increased import/export demands around major embryonic genome activation (MGA) at the 8-cell st...

Abstract Nuclear landscapes were studied during preimplantation development of bovine embryos, generated either by in vitro fertilization (IVF), or generated as cloned embryos by somatic cell nuclear transfer (SCNT) of fetal bovine fibroblasts, using three-dimensional confocal laser scanning microscopy (3D-CLSM) and structured illumination microsco...

Background Coronary Heart Disease (CHD) remains a major cause of mortality in the United Kingdom. Yet predictions of future CHD mortality are potentially problematic due to population ageing and increase in obesity and diabetes. Here we explore future projections of CHD mortality in England & Wales under two contrasting future trend assumptions. M...

Background A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quantitative image analysis, we compared its ultrastructure with active chromosome territories (CTs) in human and mouse somatic cells,...

Background: Although the rate of death (mortality) from Coronary Heart Disease (CHD) has halved since the 1970s, CHD remains a major cause of all-cause mortality in the UK. Furthermore, population ageing plus recent increases in obesity and diabetes may soon increase total CHD deaths. Predictions of future CHD mortality are thus potentially problem...

Competing compartment models of different complexities have been used for the quantitative analysis of dynamic contrast-enhanced magnetic resonance imaging data. We present a spatial elastic net approach that allows to estimate the number of compartments for each voxel such that the model complexity is not fixed a priori. A multi-compartment approa...

Medical imaging is one of the heaviest funded biomedical engineering research areas. The second edition of Pattern Recognition and Signal Analysis in Medical Imaging brings sharp focus to the development of integrated systems for use in the clinical sector, enabling both imaging and the automatic assessment of the resultant data. Since the first ed...

Background: Breast cancer is the most frequently diagnosed cancer in women and estimating its relative risks and trends of incidence at the area-level is helpful for health policy makers. However, traditional methods of estimation which do not take spatial heterogeneity into account suffer from drawbacks and their results may be misleading, as the...

In the quantitative analysis of dynamic contrast-enhanced magnetic resonance imaging compartment models allow the uptake of contrast medium to be described with biologically meaningful kinetic parameters. As simple models often fail to describe adequately the observed uptake behaviour, more complex compartment models have been proposed. However, th...

Aiming at iron-related T2-hypointensity, which is related to normal aging and neurodegenerative processes, we here present two practicable approaches, based on Bayesian inference, for preprocessing and statistical analysis of a complex set of structural MRI data. In particular, Markov Chain Monte Carlo methods were used to simulate posterior distri...