Improving biomedical image quality with computers

Computerized image enhancement techniques used on biomedical radiographs and photomicrograph

XNet: A convolutional neural network (CNN) implementation for medical X-Ray image segmentation suitable for small datasets

X-Ray image enhancement, along with many other medical image processing applications, requires the segmentation of images into bone, soft tissue, and open beam regions. We apply a machine learning approach to this problem, presenting an end-to-end solution which results in robust and efficient inference. Since medical institutions frequently do not have the resources to process and label the large quantity of X-Ray images usually needed for neural network training, we design an end-to-end solution for small datasets, while achieving state-of-the-art results. Our implementation produces an overall accuracy of 92%, F1 score of 0.92, and an AUC of 0.98, surpassing classical image processing techniques, such as clustering and entropy based methods, while improving upon the output of existing neural networks used for segmentation in non-medical contexts. The code used for this project is available online.Comment: 11 pages, 5 figures, 2 table

Characterization of tissue properties on the sub-micron scale in human bone by means of synchrotron radiation CT

Gesunder humaner Knochen unterliegt einem permanenten Umbau, um sich den mechanischen Anforderungen anzupassen, Mikrofrakturen zu reparieren und das Mineraliengleichgewicht zu erhalten. Dieser Umbauprozess wird durch Osteoblasten- und Osteoklastenaktivität realisiert, den knochenbildenden bzw. knochenresorbierenden Zellen. Gesteuert wird dieser Prozess durch Osteozyten, dessen Netzwerk mechanosensorische Fähigkeiten zugesprochen werden. Bisphosphonate (BP), hemmen die Osteoklastenaktivität und erhöhen somit die Knochenumsatzzeit. Im ersten Teil dieser Arbeit wurden morphologische Eigenschaften der Osteozyten-Lakunen (OL) in humanem Knochen mittels Synchrotron-µCT untersucht. Dabei wurden sowohl gesunde als auch mit BP behandelte Spender verglichen. Anschließend haben wir Synchrotron-Nano-CT in Kombination mit Phasenkontrast angewandt, um unsere Untersuchungen auf die Morphologie des lakuno-kanalikulären Netzwerkes (LKN) und die Gewebeeigenschaften in der Umgebung des LKN auszuweiten. Wir nahmen an, dass der sekundäre Mineralisierungsprozess mittels eines Diffusionsprozesses durch die Grenzfläche der extrazellulären Flüssigkeit im LKN stattfindet, was zu Gradienten der Massendichte in der Umgebung des LKN führen sollte. Unsere Untersuchungen haben gezeigt, dass sowohl in der Umgebung der OL als auch der Kanäle Massendichtegradienten existieren. Daraus schließen wir, dass der Mineralienaustausch zwischen der extrazellulären Flüssigkeit und der mineralisierten Matrix an der gesamten Oberfläche des LKN stattfindet. Wir schätzten, dass die Kapazität, unter Berücksichtigung des gesamten LKN, Mineralien auszutauschen etwa eine Größenordnung höher ist, gegenüber der Annahme, dass der Austausch lediglich an den Grenzflächen der OL stattfindet. Zukünftige Studien sollten nicht nur die peri-LKN Gewebeeigenschaften während der sekundären Mineralisierung untersuchen, sondern auch Schwankungen der Mineralienkonzentration bei hohen Kalziumanforderungen des Körpers berücksichtigen.Under healthy conditions human bone undergoes permanent remodeling to adjust to mechanical demands, to repair micro-cracks and to maintain mineral homeostasis. This process of remodeling is performed by osteoblasts and osteoclasts: bone-forming and bone-resorbing cells. The activity of osteoclasts and osteoblasts is triggered by osteocytes, the most frequently occurring type of bone cell, via mechanosensation processes. Bisphosphonates (BP) prescribed during treatment for osteoporosis or bone metastasis inhibit osteoclast activity and thus decrease the bone turnover. In this work, the distribution and morphology of osteocyte lacunae of human cortical jaw bone was investigated in 3D, and a comparison between healthy and BP-treated donors was performed using synchrotron radiation (SR) µCT. In a second approach, we used SR nano-CT with phase contrast to investigate the morphology of the canalicular network and the bone tissue properties in the vicinity of the lacuna-canalicular network of human jaw bone, originating from both healthy subjects and patients treated with BPs. We hypothesized that secondary mineralization takes place via a diffusion process through the fluid-matrix interface at both the lacunar and the canalicular surfaces. This should result in mass density gradients with respect to the distance to the pore boundary. Such mass density gradients were indeed observed at both lacunar and canalicular interfaces. We concluded that mineral exchange between extracellular fluid and mineralized matrix occurs at all bone surfaces, including the canaliculi. Our data suggested that the capacity of the pore network to exchange mineral with the bone matrix would increase by one order of magnitude if the canalicular surface is taken into account. However, more studies should be performed, targeting not only the changes of tissue properties during secondary mineralization, but also during fluctuations of mineral concentration in periods of high mineral demand

Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: a validation study

The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting). Casting can be quantified with magnetic resonance imaging (MRI) technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS) and 9 plastic sample vials (film containers) to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98%) (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm). The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/–2.18 mm based on voxel (three-dimensional pixel) dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb

Validation of numerical prediction of bone ingrowth into cementless implants

Total joint replacement was pioneered by John Charnley in the late 1950's, and has since revolutionised the management of arthritis sufferers. By 1991, an estimated 5 million people had undergone hip replacements. Although relatively successful, the cemented components had some problems, and this led to the development of cementless implants. These implants depend on the ingrowth of bone into a porous coating, to produce a durable method of implant fixation which the normal bone turnover process will maintain. One of the problems with cementless implants is that the type and extent of tissue ingrowth into the porous coating is unpredictable. Movement of the implant relative to the surrounding bone may result in the formation of an interfacial fibrous tissue layer. Hence, numerical modelling has been used to predict tissue ingrowth into such implants. Numerical simulation has the advantage that comprehensive data can be extracted relatively quickly. The finite element method is a powerful tool that has become the preferred method of analysis, and takes into account critical factors such as implant design, bone properties, and loading conditions. However, these models have not been tested extensively. Little attention has been given to comparing numerical models with the actual findings of retrieval studies or radiological imaging studies. This study thus evaluates the potential of one such numerical model. Most numerical models analyse the stress patterns of a particular state of bone ingrowth (i.e. a static case). This model considered the development of the ingrowing material - a dynamic analysis of tissue changes over a period of time. A 2-dimensional, plane stress finite element model was used to predict the ingrowth of bone into the porous coating of the femoral stem of a hip implant. A side plate was incorporated to mimic 3-dimensional characteristics. The evaluation was achieved by comparing the predictions of the numerical model with plane X-ray images of seven patients with Zimmer Anatomic cementless hip implants. The X-rays were scanned at a high resolution, so as to be able to "magnify" the regions to be examined. Several algorithms were developed to analyse the images, and provide a quantitative assessment of the X-ray images. The algorithms were designed to identify regions of bony and fibrous tissue. This involved the identification of the interface between the implant and the surrounding bone, and the extraction of the grayscale values of the X-rays at this interface. Thereafter, various radiographic signs that indicate the presence of fibrous tissue or bony tissue were identified, and these were used to enhance the original grayscale plot. The resulting graph was then modified slightly so as to make its presentation comparable with the numerical model. Plane X-rays proved to be suitable for the task of identifying tissue types. These data were then compared with the predictions of the numerical model. A qualitative correlation was used, as this was deemed to be most appropriate. Several authors in the literature also found a quantitative approach to have limitations. Some agreement between the experimental findings and the numerical simulation was found to exist, although this was limited. The agreement was judged to be less than the "reasonable agreement'' that several studies in the literature concluded. The correlation is better described by "some agreement". Nevertheless, the finite element method was assessed as being a tool with great potential, and modifications to the present model may provide more reliable results. A time study was also undertaken, whereby the tissue density was evaluated at various periods after the operation. The study provided insight into the evolution of the implant-bone interface after surgery, and correlated well with the literature. The phases of repair and remodelling were evident, and it was assessed as being a valuable contribution to this work. The time study may prove to be a more useful method than those used in assessing the "static" images, and could even provide a prognostic tool in assessing implant stability over time

CT diagnosis of early stroke : the initial approach to the new CAD tool based on multiscale estimation of ischemia

Background: Computer aided diagnosis (CAD) becomes one of the most important diagnostic tools for urgent states in cerebral stroke and other life-threatening conditions where time plays a crucial role. Routine CT is still diagnostically insufficient in hyperacute stage of stroke that is in the therapeutic window for thrombolytic therapy. Authors present computer assistant of early ischemic stroke diagnosis that supports the radiologic interpretations. A new semantic-visualization system of ischemic symptoms applied to noncontrast, routine CT examination was based on multiscale image processing and diagnostic content estimation. Material/Methods: Evaluation of 95 sets of examinations in patients admitted to a hospital with symptoms suggesting stroke was undertaken by four radiologists from two medical centers unaware of the final clinical findings. All of the consecutive cases were considered as having no CT direct signs of hyperacute ischemia. At the first test stage only the CTs performed at the admission were evaluated independently by radiologists. Next, the same early scans were evaluated again with additional use of multiscale computer-assistant of stroke (MulCAS). Computerized suggestion with increased sensitivity to the subtle image manifestations of cerebral ischemia was constructed as additional view representing estimated diagnostic content with enhanced stroke symptoms synchronized to routine CT data preview. Follow-up CT examinations and clinical features confirmed or excluded the diagnosis of stroke constituting 'gold standard' to verify stroke detection performance. Results: Higher AUC (area under curve) values were found for MulCAS -aided radiological diagnosis for all readers and the differences were statistically significant for random readers-random cases parametric and non-parametric DBM MRMC analysis. Sensitivity and specificity of acute stroke detection for the readers was increased by 30% and 4%, respectively. Conclusions: Routine CT completed with proposed method of computer assisted diagnosis provided noticeable better diagnosis efficiency of acute stroke according to the rates and opinions of all test readers. Further research includes fully automatic detection of hypodense regions to complete assisted indications and formulate the suggestions of stroke cases more objectively. Planned prospective studies will let evaluate more accurately the impact of this CAD tool on diagnosis and further treatment in patients suffered from stroke. It is necessary to determine whether this method is possible to be applied widely

Bone fracture detection through X-ray using Edge detection Algorithms

Human beings are highly prone to bone fractures, to a great extent as an outcome of accidents or other factors such as bone cancer. Manual fracture detection takes a lengthy time and comes with a considerable chance of error. As a result, establishing a computer-based method to reduce fracture bone diagnosis time and risk of error is critical. The most common method for segmenting images based on sharp changes in intensity is edge detection. Sobel, Robert, Canny, Prewitt, and LoG (Laplacian of Gaussian) are some of the edge detection approaches that are examined for the study of bone fracture detection. The focal point of this paper is an endeavor to study, analyze and compare the Sobel, Canny, and Prewitt Techniques for detecting edges and identifying the fracture

Implementation of a metal artifact reduction methods for small-animal CT

In the recent years, because of the constantly increasing knew discoveries in the fields of genomics and molecular biology and the development of new technologies, the use of animal models of human diseases has become more frequent. This combined with improvements in biomedical instrumentation and medical imaging has led to the development of micro CT systems enabling noninvasive investigations on animals. The work included in this thesis is framed on one of the lines of research carried out by the Biomedical Imaging and Instrumentation Group (BIIG) from the Bioengineering and Aerospace Department of Universidad Carlos III de Madrid working jointly with the Gregorio Marañón Hospital. This multidisciplinary group has developed a micro-CT system for small animals, which is used in different preclinical research lines within the group. One of these research lines focuses on the use of brain stimulation as Parkinson disease treatment. Rats have stainless electrodes implanted and fixed with screws in the lateral hypothalamus, through stereotaxic surgery. The CT subsystem of ARGUS is used then to corroborate the surgery was correct and the position of the electrodes is the right one. The presence of metallic objects creates severe streak artifacts in CT images affecting image quality and hindering the correct representation of anatomy. The beam hardening correction method, already integrated in the ARGUS system results insufficient for the correction of the artifacts derived from the presence of metals. Motivated by this context, the objective of this thesis is to implement an algorithm for metal artifact correction to be included in ARGUS. After reviewing the methods proposed in the literature the one proposed by Meyer et. al. in 2012 was implemented in MATLAB. The implemented MAR method was evaluated using simulations and real studies acquired with the ARGUS scanner, based on visual assessment, intensity profiles and mean squared error before and after the correction. The results of the evaluation showed an efficient elimination of streaks even for very strong artifact, as it is the case of gold implants. In all cases, bone edges were preserved when correcting with MAR and the metal structures are clearly delimited after correction.Ingeniería Biomédic