The full-field thickness distribution, three-dimensional surface model and general morphological data of six human tympanic membranes are presented. Cross-sectional images were taken perpendicular ...through the membranes using a high-resolution optical coherence tomography setup. Five normal membranes and one membrane containing a pathological site are included in this study. The thickness varies strongly across each membrane, and a great deal of inter-specimen variability can be seen in the measurement results, though all membranes show similar features in their respective relative thickness distributions. Mean thickness values across the pars tensa ranged between 79 and 97 μm; all membranes were thinnest in the central region between umbo and annular ring (50–70 μm), and thickness increased steeply over a small distance to approximately 100–120 μm when moving from the central region either towards the peripheral rim of the pars tensa or towards the manubrium. Furthermore, a local thickening was noticed in the antero–inferior quadrant of the membranes, and a strong linear correlation was observed between inferior–posterior length and mean thickness of the membrane. These features were combined into a single three-dimensional model to form an averaged representation of the human tympanic membrane. 3D reconstruction of the pathological tympanic membrane shows a structural atrophy with retraction pocket in the inferior portion of the pars tensa. The change of form at the pathological site of the membrane corresponds well with the decreased thickness values that can be measured there.
In order to improve realism in middle ear (ME) finite-element modeling (FEM), comprehensive and precise morphological data are needed. To date, micro-scale X-ray computed tomography (μCT) recordings ...have been used as geometric input data for FEM models of the ME ossicles. Previously, attempts were made to obtain these data on ME soft tissue structures as well. However, due to low X-ray absorption of soft tissue, quality of these images is limited. Another popular approach is using histological sections as data for 3D models, delivering high in-plane resolution for the sections, but the technique is destructive in nature and registration of the sections is difficult. We combine data from high-resolution μCT recordings with data from high-resolution orthogonal-plane fluorescence optical-sectioning microscopy (OPFOS), both obtained on the same gerbil specimen. State-of-the-art μCT delivers high-resolution data on the 3D shape of ossicles and other ME bony structures, while the OPFOS setup generates data of unprecedented quality both on bone and soft tissue ME structures. Each of these techniques is tomographic and non-destructive and delivers sets of automatically aligned virtual sections. The datasets coming from different techniques need to be registered with respect to each other. By combining both datasets, we obtain a complete high-resolution morphological model of all functional components in the gerbil ME. The resulting 3D model can be readily imported in FEM software and is made freely available to the research community. In this paper, we discuss the methods used, present the resulting merged model, and discuss the morphological properties of the soft tissue structures, such as muscles and ligaments.
We made a qualitative and quantitative comparison between a state-of-the-art implementation of micro-Computed Tomography (microCT) and the scanning Thin-Sheet Laser Imaging Microscopy (sTSLIM) ...method, applied to mouse cochleae. Both imaging methods are non-destructive and perform optical sectioning, respectively, with X-rays and laser light. MicroCT can be used on fresh or fixed tissue samples and is primarily designed to image bone rather than soft tissues. It requires complex back-projection algorithms to produce a two-dimensional image, and it is an expensive instrument. sTSLIM requires that a specimen be chemically fixed, decalcified, and cleared; but it produces high-resolution images of soft and bony tissues with minimum image postprocessing and is less expensive than microCT. In this article, we discuss the merits and disadvantages of each method individually and when combined.
Several well-established techniques are available to obtain 3-D image information of biomedical specimens, each with their specific advantages and limitations. Orthogonal plane fluorescence optical ...sectioning (OPFOS), or selective plane illumination microscopy (SPIM), are additional techniques which, after adequate specimen preparation, produce high quality, autoaligned sectional images in nearly real time, of bone as well as soft tissue. Up until now, slicing resolutions down to
have been obtained. We present a high resolution (HR) OPFOS method, which delivers images that approach the quality of histological sections. With our HROPFOS technique, we achieve in-plane resolutions of
and a slicing resolution of
. A region of interest within an intact and much larger object can be imaged without problems, and as the optical technique is nondestructive, the object can be measured in any slicing direction. We present quantitative measurements of resolution. A 3-D model reconstructed from our HROPFOS data is compared to SEM results, and the technique is demonstrated with section images and 3-D reconstructions of middle ear specimens.
A projection moiré profilometer is presented in which both projection and optical demodulation are realized with liquid crystal light modulators. The computer generated grids, realized on thin film ...transistor matrices, allow phase-stepping and discrete grid averaging without the need for any mechanically moving component. Spatial line pitch and phase steps can thus be readily adjusted to suit the measurement precision and object geometry. The device is able to perform topographic measurements with a height resolution of 15 microm on every pixel of the recording device.
High-resolution 3D morphology models of cat, gerbil, rabbit, rat and human ossicular chains are presented. The models are based on high-resolution CT measurements. The resolution of the CT images, ...from which the models are segmented, varies from 5.6 to 33.5 μm. Models are freely available in different formats at our website (http://www.ua.ac.be/bimef/models) for research and educational purposes.
► Three dimensional morphology models of ME of different species are presented. ► The resolution obtained from the CT images varies between 6 and 34 μm. ► The models are open access through our website (http://www.ua.ac.be/bimef/models).
The optimization of the Beetle readout ASIC and the performance of the software for the signal processing based on machine learning methods are presented. The Beetle readout chip was developed for ...the LHCb (Large Hadron Collider beauty) tracking detectors and was used in the VELO (Vertex Locator) during Run 1 and 2 of LHC data taking. The VELO, surrounding the LHC beam crossing region, was a leading part of the LHCb tracking system. The Beetle chip was used to read out the signal from silicon microstrips, integrating and amplifying it. The studies presented in this paper cover the optimization of its electronic configuration to achieve the lower power consumption footprint and the lower operational temperature of the sensors, while maintaining a good condition of the analogue response of the whole chip. The studies have shown that optimizing the operational temperature is possible and can be beneficial when the detector is highly irradiated. Even a single degree drop in silicon temperature can result in a significant reduction in the leakage current. Similar studies are being performed for the future silicon tracker, the Upstream Tracker (UT), which will start operating at LHC in 2021. It is expected that the inner part of the UT detector will suffer radiation damage similar to the most irradiated VELO sensors in Run 2. In the course of analysis we also developed a general approach for the pulse shape reconstruction using an ANN approach. This technique can be reused in case of any type of front-end readout chip.
Large-volume optical coherence tomography (OCT) setups employ scanning mirrors and suffer from geometric distortion artefacts in which the degree of distortion is determined by the maximum angles ...over which the mirrors rotate. In this note, we describe a straightforward coordinate transformation scheme to correct for these artefacts in three dimensions, creating an alternative to previously reported ray-tracing schemes. We demonstrate that this recalibration procedure can be applied in real time by implementing the proposed algorithm on the graphics card of a standard computer, making it useful for topography applications. The accuracy of the proposed calibration procedure is validated over an imaging volume of 12.35×10.13×2.36 mm3 using optical moiré measurements of a highly curved object.
Summary
Image acquisition is an important step in the study of cytoskeleton organization. As visual interpretations and manual measurements of digital images are prone to errors and require a great ...amount of time, a freely available software package named MicroFilament Analyzer (MFA) was developed. The goal was to provide a tool that facilitates high‐throughput analysis to determine the orientation of filamentous structures on digital images in a more standardized, objective and repeatable way. Here, the rationale and applicability of the program is demonstrated by analyzing the microtubule patterns in epidermal cells of control and gravi‐stimulated Arabidopsis thaliana roots. Differential expansion of cells on either side of the root results in downward bending of the root tip. As cell expansion depends on the properties of the cell wall, this may imply a differential orientation of cellulose microfibrils. As cellulose deposition is orchestrated by cortical microtubules, the microtubule patterns were analyzed. The MFA program detects the filamentous structures on the image and identifies the main orientation(s) within individual cells. This revealed four distinguishable microtubule patterns in root epidermal cells. The analysis indicated that gravitropic stimulation and developmental age are both significant factors that determine microtubule orientation. Moreover, the data show that an altered microtubule pattern does not precede differential expansion. Other possible applications are also illustrated, including field emission scanning electron micrographs of cellulose microfibrils in plant cell walls and images of fluorescent actin.
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