image‐based modeling
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The paper describes a set of approaches and routines designed to improve results in CT based 3D subtractive angiography of lower extremities via better global locally defined image data registration. Starting from the generic concept of 3D disparity-based flexible registration, modifications of this idea are made founded on prior anatomical knowledge, as segmentation into individual bone areas, their rigid registration followed by constrained flexible registration, and flexible registration of soft tissue volumes. After final subtraction, fusion of the individually derived volumes into the full volume of extremities provides the medically assessable results. The level of detail in minor vessels, and continuity of vessels including those in direct contact with the bones, have been found much better clinically than those achieved by standard contemporary commercial software.
- MeSH
- algoritmy MeSH
- artefakty MeSH
- biologické modely MeSH
- digitální subtrakční angiografie metody MeSH
- lidé MeSH
- počítačová rentgenová tomografie metody MeSH
- rentgenový obraz - interpretace počítačová metody MeSH
- reprodukovatelnost výsledků MeSH
- rozpoznávání automatizované metody MeSH
- senzitivita a specificita MeSH
- subtrakční technika MeSH
- vylepšení rentgenového snímku metody MeSH
- zobrazování trojrozměrné metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
Colposcopy is a well-established method to detect and diagnose intraepithelial lesions and uterine cervical cancer in early stages. During the exam color and texture changes are induced by the application of a contrast agent (e.g.3-5% acetic acid solution or iodine). Our aim is to densely quantify the change in the acetowhite decay level for a sequence of images captured during a colposcopy exam to help the physician in his diagnosis providing new tools that overcome subjectivity and improve reproducibility. As the change in acetowhite decay level must be calculated from the same tissue point in all images, we present an elastic image registration scheme able to compensate patient, camera and tissue movement robustly in cervical images. The image registration is based on a novel multi-feature entropy similarity criterion. Temporal features are then extracted using the color properties of the aligned image sequence and a dual compartment tissue model of the cervix. An example of the use of the temporal features for pixel-wise classification is presented and the results are compared against ground truth histopathological annotations.
- MeSH
- algoritmy MeSH
- cervix uteri patologie MeSH
- databáze faktografické MeSH
- diagnóza počítačová metody MeSH
- dospělí MeSH
- kolposkopie metody MeSH
- kyselina octová chemie MeSH
- lidé středního věku MeSH
- lidé MeSH
- nádory děložního čípku diagnóza MeSH
- počítačové zpracování obrazu metody MeSH
- reprodukovatelnost výsledků MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
During pregnancy, oxygen diffuses from maternal to fetal blood through villous trees in the placenta. In this paper, we simulate blood flow and oxygen transfer in feto-placental capillaries by converting three-dimensional representations of villous and capillary surfaces, reconstructed from confocal laser scanning microscopy, to finite-element meshes, and calculating values of vascular flow resistance and total oxygen transfer. The relationship between the total oxygen transfer rate and the pressure drop through the capillary is shown to be captured across a wide range of pressure drops by physical scaling laws and an upper bound on the oxygen transfer rate. A regression equation is introduced that can be used to estimate the oxygen transfer in a capillary using the vascular resistance. Two techniques for quantifying the effects of statistical variability, experimental uncertainty and pathological placental structure on the calculated properties are then introduced. First, scaling arguments are used to quantify the sensitivity of the model to uncertainties in the geometry and the parameters. Second, the effects of localized dilations in fetal capillaries are investigated using an idealized axisymmetric model, to quantify the possible effect of pathological placental structure on oxygen transfer. The model predicts how, for a fixed pressure drop through a capillary, oxygen transfer is maximized by an optimal width of the dilation. The results could explain the prevalence of fetal hypoxia in cases of delayed villous maturation, a pathology characterized by a lack of the vasculo-syncytial membranes often seen in conjunction with localized capillary dilations.
- MeSH
- biologické modely * MeSH
- choriové klky embryologie MeSH
- difuze MeSH
- kapiláry metabolismus fyziologie MeSH
- krevní oběh * MeSH
- kyslík metabolismus MeSH
- lidé MeSH
- placenta krevní zásobení MeSH
- plod krevní zásobení MeSH
- těhotenství MeSH
- zobrazování trojrozměrné * MeSH
- Check Tag
- lidé MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Evoked neural responses to sensory stimuli have been extensively investigated in humans and animal models both to enhance our understanding of brain function and to aid in clinical diagnosis of neurological and neuropsychiatric conditions. Recording and imaging techniques such as electroencephalography (EEG), magnetoencephalography (MEG), local field potentials (LFPs), and calcium imaging provide complementary information about different aspects of brain activity at different spatial and temporal scales. Modeling and simulations provide a way to integrate these different types of information to clarify underlying neural mechanisms. In this study, we aimed to shed light on the neural dynamics underlying auditory evoked responses by fitting a rate-based model to LFPs recorded via multi-contact electrodes which simultaneously sampled neural activity across cortical laminae. Recordings included neural population responses to best-frequency (BF) and non-BF tones at four representative sites in primary auditory cortex (A1) of awake monkeys. The model considered major neural populations of excitatory, parvalbumin-expressing (PV), and somatostatin-expressing (SOM) neurons across layers 2/3, 4, and 5/6. Unknown parameters, including the connection strength between the populations, were fitted to the data. Our results revealed similar population dynamics, fitted model parameters, predicted equivalent current dipoles (ECD), tuning curves, and lateral inhibition profiles across recording sites and animals, in spite of quite different extracellular current distributions. We found that PV firing rates were higher in BF than in non-BF responses, mainly due to different strengths of tonotopic thalamic input, whereas SOM firing rates were higher in non-BF than in BF responses due to lateral inhibition. In conclusion, we demonstrate the feasibility of the model-fitting approach in identifying the contributions of cell-type specific population activity to stimulus-evoked LFPs across cortical laminae, providing a foundation for further investigations into the dynamics of neural circuits underlying cortical sensory processing.
- MeSH
- akustická stimulace metody MeSH
- elektroencefalografie metody MeSH
- Haplorrhini MeSH
- lidé MeSH
- počítačová simulace MeSH
- sluchové evokované potenciály fyziologie MeSH
- sluchové korové centrum * fyziologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Research Support, N.I.H., Extramural MeSH
Motivation: Whole genome expression profiling of large cohorts of different types of cancer led to the identification of distinct molecular subcategories (subtypes) that may partially explain the observed inter-tumoral heterogeneity. This is also the case of colorectal cancer (CRC) where several such categorizations have been proposed. Despite recent developments, the problem of subtype definition and recognition remains open, one of the causes being the intrinsic heterogeneity of each tumor, which is difficult to estimate from gene expression profiles. However, one of the observations of these studies indicates that there may be links between the dominant tumor morphology characteristics and the molecular subtypes. Benefiting from a large collection of CRC samples, comprising both gene expression and histopathology images, we investigated the possibility of building image-based classifiers able to predict the molecular subtypes. We employed deep convolutional neural networks for extracting local descriptors which were then used for constructing a dictionary-based representation of each tumor sample. A set of support vector machine classifiers were trained to solve different binary decision problems, their combined outputs being used to predict one of the five molecular subtypes. Results: A hierarchical decomposition of the multi-class problem was obtained with an overall accuracy of 0.84 (95%CI=0.79-0.88). The predictions from the image-based classifier showed significant prognostic value similar to their molecular counterparts. Contact: popovici@iba.muni.cz. Availability and Implementation: Source code used for the image analysis is freely available from https://github.com/higex/qpath . Supplementary information: Supplementary data are available at Bioinformatics online.
- MeSH
- kolorektální nádory diagnóza genetika metabolismus patologie MeSH
- lidé MeSH
- nádorové biomarkery * MeSH
- neuronové sítě * MeSH
- počítačové zpracování obrazu metody MeSH
- prognóza MeSH
- regulace genové exprese u nádorů MeSH
- support vector machine MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The performance of a pharmaceutical formulation, such as the drug (API) release rate, is significantly influenced by the properties of the materials used, the composition of the final product and the tablet compression process parameters. However, in some cases, the knowledge of these input parameters does not necessarily provide a reliable description or prediction of tablet performance. Therefore, the knowledge of tablet microstructure is desirable to understand such formulations. Commonly used analytical techniques, such as X-ray tomography and intrusion mercury porosimetry, are not widely used in pharmaceutical companies due to their price and/or toxicity, and therefore, efforts are made to develop a tool for fast and easy microstructure description. In this work, we have developed an image-based method for microstructure description and applied it to a model system consisting of ibuprofen and CaHPO4∙2H2O (API and excipient with different deformability). The obtained parameter, the quadratic mean of the equivalent diameter of the non-deformable, brittle excipient CaHPO4∙2H2O, was correlated with tablet composition, compression pressure and API release rate. The obtained results demonstrate the possibility of describing the tablet dissolution performance in the presented model system based on the microstructural parameter, providing a possible model system for compressed solid dosage forms in which a plastic component is present and specific API release is required.
- MeSH
- biologické modely * MeSH
- ibuprofen chemie MeSH
- pomocné látky * chemie MeSH
- příprava léků MeSH
- tablety chemie MeSH
- Publikační typ
- časopisecké články MeSH
A key requirement for precision medicine is the accurate identification of patients that would respond to a specific treatment or those that represent a high-risk group, and a plethora of molecular biomarkers have been proposed for this purpose during the last decade. Their application in clinical settings, however, is not always straightforward due to relatively high costs of some tests, limited availability of the biological material and time, and procedural constraints. Hence, there is an increasing interest in constructing tissue-based surrogate biomarkers that could be applied with minimal overhead directly to histopathology images and which could be used for guiding the selection of eventual further molecular tests. In the context of colorectal cancer, we present a method for constructing a surrogate biomarker that is able to predict with high accuracy whether a sample belongs to the "BRAF-positive" group, a high-risk group comprising V600E BRAF mutants and BRAF-mutant-like tumors. Our model is trained to mimic the predictions of a 64-gene signature, the current definition of BRAF-positive group, thus effectively identifying histopathology image features that can be linked to a molecular score. Since the only required input is the routine histopathology image, the model can easily be integrated in the diagnostic workflow.
Computed tomography (CT) is an effective diagnostic modality for three-dimensional imaging of bone structures, including the geometry of their defects. The aim of the study was to create and optimize 3D geometrical and real plastic models of the distal femoral component of the knee with joint surface defects. Input data included CT images of stifle joints in twenty miniature pigs with iatrogenic osteochondrosis-like lesions in medial femoral condyle of the left knee. The animals were examined eight and sixteen weeks after surgery. Philips MX 8000 MX and View workstation were used for scanning parallel plane cross section slices and Cartesian discrete volume creation. On the average, 100 slices were performed in each stifle joint. Slice matrices size was 512 x 512 with slice thickness of 1 mm. Pixel (voxel) size in the slice plane was 0.5 mm (with average accuracy of +/-0.5 mm and typical volume size 512 x 512 x 100 voxels). Three-dimensional processing of CT data and 3D geometrical modelling, using interactive computer graphic system MediTools formerly developed here, consisted of tissue segmentation (raster based method combination and 5 % of manual correction), vectorization by the marching-cubes method, smoothing and decimation. Stifle- joint CT images of three individuals of different body size (small, medium and large) were selected to make the real plastic models of their distal femurs from plaster composite using rapid prototyping technology of Zcorporation. Accuracy of the modeling was +/- 0.5 mm. The real plastic models of distal femurs can be used as a template for developing custom made press and fit scaffold implants seeded with mesenchymal stem cells that might be subsequently implanted into iatrogenic joint surface defects for articular cartilage-repair enhancement.
- MeSH
- anatomické modely * MeSH
- design s pomocí počítače MeSH
- femur radiografie MeSH
- kolenní kloub u koně, psa radiografie MeSH
- kultivované buňky MeSH
- mezenchymální kmenové buňky * MeSH
- miniaturní prasata MeSH
- modely nemocí na zvířatech MeSH
- osteochondritida radiografie MeSH
- počítačová rentgenová tomografie * MeSH
- prasata MeSH
- protézy - design MeSH
- rentgenový obraz - interpretace počítačová MeSH
- tkáňové inženýrství * MeSH
- tkáňové podpůrné struktury * MeSH
- zobrazování trojrozměrné * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
PURPOSE: Dynamic Contrast-Enhanced (DCE) MRI with 2nd generation pharmacokinetic models provides estimates of plasma flow and permeability surface-area product in contrast to the broadly used 1st generation models (e.g. the Tofts models). However, the use of 2nd generation models requires higher frequency with which the dynamic images are acquired (around 1.5 s per image). Blind deconvolution can decrease the demands on temporal resolution as shown previously for one of the 1st generation models. Here, the temporal-resolution requirements achievable for blind deconvolution with a 2nd generation model are studied. METHODS: The 2nd generation model is formulated as the distributed-capillary adiabatic-tissue-homogeneity (DCATH) model. Blind deconvolution is based on Parker's model of the arterial input function. The accuracy and precision of the estimated arterial input functions and the perfusion parameters is evaluated on synthetic and real clinical datasets with different levels of the temporal resolution. RESULTS: The estimated arterial input functions remained unchanged from their reference high-temporal-resolution estimates (obtained with the sampling interval around 1 s) when increasing the sampling interval up to about 5 s for synthetic data and up to 3.6-4.8 s for real data. Further increasing of the sampling intervals led to systematic distortions, such as lowering and broadening of the 1st pass peak. The resulting perfusion-parameter estimation error was below 10% for the sampling intervals up to 3 s (synthetic data), in line with the real data perfusion-parameter boxplots which remained unchanged up to the sampling interval 3.6 s. CONCLUSION: We show that use of blind deconvolution decreases the demands on temporal resolution in DCE-MRI from about 1.5 s (in case of measured arterial input functions) to 3-4 s. This can be exploited in increased spatial resolution or larger organ coverage.
