Automated detection of brain abnormalities in neonatal hypoxia ischemic injury from MR images.

We compared the efficacy of three automated brain injury detection methods, namely symmetry-integrated region growing (SIRG), hierarchical region splitting (HRS) and modified watershed segmentation (MWS) in human and animal magnetic resonance imaging (MRI) datasets for the detection of hypoxic ischemic injuries (HIIs). Diffusion weighted imaging (DWI, 1.5T) data from neonatal arterial ischemic stroke (AIS) patients, as well as T2-weighted imaging (T2WI, 11.7T, 4.7T) at seven different time-points (1, 4, 7, 10, 17, 24 and 31 days post HII) in rat-pup model of hypoxic ischemic injury were used to assess the temporal efficacy of our computational approaches. Sensitivity, specificity, and similarity were used as performance metrics based on manual ('gold standard') injury detection to quantify comparisons. When compared to the manual gold standard, automated injury location results from SIRG performed the best in 62% of the data, while 29% for HRS and 9% for MWS. Injury severity detection revealed that SIRG performed the best in 67% cases while 33% for HRS. Prior information is required by HRS and MWS, but not by SIRG. However, SIRG is sensitive to parameter-tuning, while HRS and MWS are not. Among these methods, SIRG performs the best in detecting lesion volumes; HRS is the most robust, while MWS lags behind in both respects

Image similarity in medical images

Recent experiments have indicated a strong influence of the substrate grain orientation on the self-ordering in anodic porous alumina. Anodic porous alumina with straight pore channels grown in a stable, self-ordered manner is formed on (001) oriented Al grain, while disordered porous pattern is formed on (101) oriented Al grain with tilted pore channels growing in an unstable manner. In this work, numerical simulation of the pore growth process is carried out to understand this phenomenon. The rate-determining step of the oxide growth is assumed to be the Cabrera-Mott barrier at the oxide/electrolyte (o/e) interface, while the substrate is assumed to determine the ratio β between the ionization and oxidation reactions at the metal/oxide (m/o) interface. By numerically solving the electric field inside a growing porous alumina during anodization, the migration rates of the ions and hence the evolution of the o/e and m/o interfaces are computed. The simulated results show that pore growth is more stable when β is higher. A higher β corresponds to more Al ionized and migrating away from the m/o interface rather than being oxidized, and hence a higher retained O:Al ratio in the oxide. Experimentally measured oxygen content in the self-ordered porous alumina on (001) Al is indeed found to be about 3% higher than that in the disordered alumina on (101) Al, in agreement with the theoretical prediction. The results, therefore, suggest that ionization on (001) Al substrate is relatively easier than on (101) Al, and this leads to the more stable growth of the pore channels on (001) Al

Biomedical image segmentation using geometric deformable models and metaheuristics

International audienceThis paper describes a hybrid level set approach for medical image segmentation. This new geometric deformable model combines region-and edge-based information with the prior shape knowledge introduced using deformable registration. Our proposal consists of two phases: training and test. The former implies the learning of the level set parameters by means of a Genetic Algorithm, while the latter is the proper segmentation, where another metaheuristic, in this case Scatter Search, derives the shape prior. In an experimental comparison, this approach has shown a better performance than a number of state-of-the-art methods when segmenting anatomical structures from different biomedical image modalities

Meta-optimization of Bio-inspired Techniques for Object Recognition

Il riconoscimento di oggetti consiste nel trovare automaticamente un oggetto all'interno di un'immagine o in una sequenza video. Questo compito è molto importante in molti campi quali diagnosi mediche, assistenza di guida avanzata, visione artificiale, sorveglianza, realtà aumentata. Tuttavia, questo compito può essere molto impegnativo a causa di artefatti (dovuti al sistema di acquisizione, all'ambiente o ad altri effetti ottici quali prospettiva, variazioni di illuminazione, etc.) che possono influenzare l'aspetto anche di oggetti facili da identificare e ben definiti . Una possibile tecnica per il riconoscimento di oggetti consiste nell'utilizzare approcci basati su modello: in questo scenario viene creato un modello che rappresenta le proprietà dell'oggetto da individuare; poi, vengono generate possibili ipotesi sul posizionamento dell'oggetto, e il modello viene trasformato di conseguenza, fino a trovare la migliore corrispondenza con l'aspetto reale dell'oggetto. Per generare queste ipotesi in maniera intelligente, è necessario un buon algoritmo di ottimizzazione. Gli algoritmi di tipo bio-ispirati sono metodi di ottimizzazione che si basano su proprietà osservate in natura (quali cooperazione, evoluzione, socialità). La loro efficacia è stata dimostrata in molte attività di ottimizzazione, soprattutto in problemi di difficile soluzione, multi-modali e multi-dimensionali quali, per l'appunto, il riconoscimento di oggetti. Anche se queste euristiche sono generalmente efficaci, esse dipendono da molti parametri che influenzano profondamente le loro prestazioni; pertanto, è spesso richiesto uno sforzo significativo per capire come farle esprimere al massimo delle loro potenzialità. Questa tesi descrive un metodo per (i) individuare automaticamente buoni parametri per tecniche bio-ispirate, sia per un problema specifico che più di uno alla volta, e (ii) acquisire maggior conoscenza sul ruolo di un parametro in questi algoritmi. Inoltre, viene mostrato come le tecniche bio-ispirate possono essere applicate con successo in diversi ambiti nel riconoscimento di oggetti, e come è possibile migliorare ulteriormente le loro prestazioni mediante il tuning automatico dei loro parametri.Object recognition is the task of automatically finding a given object in an image or in a video sequence. This task is very important in many fields such as medical diagnosis, advanced driving assistance, image understanding, surveillance, virtual reality. Nevertheless, this task can be very challenging because of artefacts (related with the acquisition system, the environment or other optical effects like perspective, illumination changes, etc.) which may affect the aspect even of easy-to-identify and well-defined objects. A possible way to achieve object recognition is using model-based approaches: in this scenario a model (also called template) representing the properties of the target object is created; then, hypotheses on the position of the object are generated, and the model is transformed accordingly, until the best match with the actual appearance of the object is found. To generate these hypotheses intelligently, a good optimization algorithm is required. Bio-inspired techniques are optimization methods whose foundations rely on properties observed in nature (such as cooperation, evolution, emergence). Their effectiveness has been proved in many optimization tasks, especially in multi-modal, multi-dimensional hard problems like object recognition. Although these heuristics are generally effective, they depend on many parameters that strongly affect their performances; therefore, a significant effort must be spent to understand how to let them express their full potentialities. This thesis describes a method to (i) automatically find good parameters for bio-inspired techniques, both for a specific problem and for more than one at the same time, and (ii) acquire more knowledge of a parameter's role in such algorithms. Then, it shows how bio-inspired techniques can be successfully applied to different object recognition tasks, and how it is possible to further improve their performances by means of automatic parameter tuning

Innovative techniques to devise 3D-printed anatomical brain phantoms for morpho-functional medical imaging

Introduction. The Ph.D. thesis addresses the development of innovative techniques to create 3D-printed anatomical brain phantoms, which can be used for quantitative technical assessments on morpho-functional imaging devices, providing simulation accuracy not obtainable with currently available phantoms. 3D printing (3DP) technology is paving the way for advanced anatomical modelling in biomedical applications. Despite the potential already expressed by 3DP in this field, it is still little used for the realization of anthropomorphic phantoms of human organs with complex internal structures. Making an anthropomorphic phantom is very different from making a simple anatomical model and 3DP is still far from being plug-and-print. Hence, the need to develop ad-hoc techniques providing innovative solutions for the realization of anatomical phantoms with unique characteristics, and greater ease-of-use. Aim. The thesis explores the entire workflow (brain MRI images segmentation, 3D modelling and materialization) developed to prototype a new complex anthropomorphic brain phantom, which can simulate three brain compartments simultaneously: grey matter (GM), white matter (WM) and striatum (caudate nucleus and putamen, known to show a high uptake in nuclear medicine studies). The three separate chambers of the phantom will be filled with tissue-appropriate solutions characterized by different concentrations of radioisotope for PET/SPECT, para-/ferro-magnetic metals for MRI, and iodine for CT imaging. Methods. First, to design a 3D model of the brain phantom, it is necessary to segment MRI images and to extract an error-less STL (Standard Tessellation Language) description. Then, it is possible to materialize the prototype and test its functionality. - Image segmentation. Segmentation is one of the most critical steps in modelling. To this end, after demonstrating the proof-of-concept, a multi-parametric segmentation approach based on brain relaxometry was proposed. It includes a pre-processing step to estimate relaxation parameter maps (R1 = longitudinal relaxation rate, R2 = transverse relaxation rate, PD = proton density) from the signal intensities provided by MRI sequences of routine clinical protocols (3D-GrE T1-weighted, FLAIR and fast-T2-weighted sequences with ≤ 3 mm slice thickness). In the past, maps of R1, R2, and PD were obtained from Conventional Spin Echo (CSE) sequences, which are no longer suitable for clinical practice due to long acquisition times. Rehabilitating the multi-parametric segmentation based on relaxometry, the estimation of pseudo-relaxation maps allowed developing an innovative method for the simultaneous automatic segmentation of most of the brain structures (GM, WM, cerebrospinal fluid, thalamus, caudate nucleus, putamen, pallidus, nigra, red nucleus and dentate). This method allows the segmentation of higher resolution brain images for future brain phantom enhancements. - STL extraction. After segmentation, the 3D model of phantom is described in STL format, which represents the shapes through the approximation in manifold mesh (i.e., collection of triangles, which is continuous, without holes and with a positive – not zero – volume). For this purpose, we developed an automatic procedure to extract a single voxelized surface, tracing the anatomical interface between the phantom's compartments directly on the segmented images. Two tubes were designed for each compartment (one for filling and the other to facilitate the escape of air). The procedure automatically checks the continuity of the surface, ensuring that the 3D model could be exported in STL format, without errors, using a common image-to-STL conversion software. Threaded junctions were added to the phantom (for the hermetic closure) using a mesh processing software. The phantom's 3D model resulted correct and ready for 3DP. Prototyping. Finally, the most suitable 3DP technology is identified for the materialization. We investigated the material extrusion technology, named Fused Deposition Modeling (FDM), and the material jetting technology, named PolyJet. FDM resulted the best candidate for our purposes. It allowed materializing the phantom's hollow compartments in a single print, without having to print them in several parts to be reassembled later. FDM soluble internal support structures were completely removable after the materialization, unlike PolyJet supports. A critical aspect, which required a considerable effort to optimize the printing parameters, was the submillimetre thickness of the phantom walls, necessary to avoid distorting the imaging simulation. However, 3D printer manufacturers recommend maintaining a uniform wall thickness of at least 1 mm. The optimization of printing path made it possible to obtain strong, but not completely waterproof walls, approximately 0.5 mm thick. A sophisticated technique, based on the use of a polyvinyl-acetate solution, was developed to waterproof the internal and external phantom walls (necessary requirement for filling). A filling system was also designed to minimize the residual air bubbles, which could result in unwanted hypo-intensity (dark) areas in phantom-based imaging simulation. Discussions and conclusions. The phantom prototype was scanned trough CT and PET/CT to evaluate the realism of the brain simulation. None of the state-of-the-art brain phantoms allow such anatomical rendering of three brain compartments. Some represent only GM and WM, others only the striatum. Moreover, they typically have a poor anatomical yield, showing a reduced depth of the sulci and a not very faithful reproduction of the cerebral convolutions. The ability to simulate the three brain compartments simultaneously with greater accuracy, as well as the possibility of carrying out multimodality studies (PET/CT, PET/MRI), which represent the frontier of diagnostic imaging, give this device cutting-edge prospective characteristics. The effort to further customize 3DP technology for these applications is expected to increase significantly in the coming years