Three-dimensional histological specimen preparation for accurate imaging and spatial reconstruction of the middle and inner ear

Parameterisation and Prediction of Intra-canal Cochlear Structures

Accurate 3D models of the cochlea are useful tools for research in the relationship between the electrode array and nerve fibres. The internal geometry of the cochlear canal plays an important role in understanding and quantifying that relationship. Predicting the location and shapes of the geometry is done by measuring histologic sections and fitting equations that can be used to predict parameters that fully define the geometry. A parameter sensitivity analysis is employed to prove that the size and location of the spiral lamina are the characteristics that most influence current distribution along target nerve fibres. The proposed landmark prediction method more accurately predicts the location of the points defining the spiral lamina in the apical region of the cochlea than methods used in previous modelling attempts. Thus, this technique can be used to generate 2D geometries that can be expanded to 3D models when high-resolution imaging is not available.

Spatial correlation of 2D hard-tissue histology with 3D microCT scans through 3D printed phantoms

Hard-tissue histology-the analysis of thin two-dimensional (2D) sections-is hampered by the opaque nature of most biological specimens, especially bone. Therefore, the cutting process cannot be assigned to regions of interest. In addition, the applied cutting-grinding method is characterized by significant material loss. As a result, relevant structures might be missed or destroyed, and 3D features can hardly be evaluated. Here, we present a novel workflow, based on conventual microCT scans of the specimen prior to the cutting process, to be used for the analysis of 3D structural features and for directing the sectioning process to the regions of interest. 3D printed fiducial markers, embedded together with the specimen in resin, are utilized to retrospectively register the obtained 2D histological images into the 3D anatomical context. This not only allows to identify the cutting position, but also enables the co-registration of the cell and extracellular matrix morphological analysis to local 3D information obtained from the microCT data. We have successfully applied our new approach to assess hard-tissue specimens of different species. After matching the predicted microCT cut plane with the histology image, we validated a high accuracy of the registration process by computing quality measures namely Jaccard and Dice similarity coefficients achieving an average score of 0.90 ± 0.04 and 0.95 ± 0.02, respectively. Thus, we believe that the novel, easy to implement correlative imaging approach holds great potential for improving the reliability and diagnostic power of classical hard-tissue histology.

Quantitative Evaluation of the 3D Anatomy of the Human Osseous Spiral Lamina Using MicroCT

PURPOSE

The osseous spiral lamina (OSL) is an inner cochlear bony structure that projects from the modiolus from base to apex, separating the cochlear canal into the scala vestibuli and scala tympani. The porosity of the OSL has recently attracted the attention of scientists due to its potential impact on the overall sound transduction. The bony pillars between the vestibular and tympanic plates of the OSL are not always visible in conventional histopathological studies, so imaging of such structures is usually lacking or incomplete. With this pilot study, we aimed, for the first time, to anatomically demonstrate the OSL in great detail and in 3D.

METHODS

We measured width, thickness, and porosity of the human OSL by microCT using increasing nominal resolutions up to 2.5-µm voxel size. Additionally, 3D models of the individual plates at the basal and middle turns and the apex were created from the CT datasets.

RESULTS

We found a constant presence of porosity in both tympanic plate and vestibular plate from basal turn to the apex. The tympanic plate appears to be more porous than vestibular plate in the basal and middle turns, while it is less porous in the apex. Furthermore, the 3D reconstruction allowed the bony pillars that lie between the OSL plates to be observed in great detail.

CONCLUSION

By enhancing our comprehension of the OSL, we can advance our comprehension of hearing mechanisms and enhance the accuracy and effectiveness of cochlear models.

Current Approaches for Image Fusion of Histological Data with Computed Tomography and Magnetic Resonance Imaging

Classical analysis of biological samples requires the destruction of the tissue's integrity by cutting or grinding it down to thin slices for (Immuno)-histochemical staining and microscopic analysis. Despite high specificity, encoded in the stained 2D section of the whole tissue, the structural information, especially 3D information, is limited. Computed tomography (CT) or magnetic resonance imaging (MRI) scans performed prior to sectioning in combination with image registration algorithms provide an opportunity to regain access to morphological characteristics as well as to relate histological findings to the 3D structure of the local tissue environment. This review provides a summary of prevalent literature addressing the problem of multimodal coregistration of hard- and soft-tissue in microscopy and tomography. Grouped according to the complexity of the dimensions, including image-to-volume (2D ⟶ 3D), image-to-image (2D ⟶ 2D), and volume-to-volume (3D ⟶ 3D), selected currently applied approaches are investigated by comparing the method accuracy with respect to the limiting resolution of the tomography. Correlation of multimodal imaging could position itself as a useful tool allowing for precise histological diagnostic and allow the a priori planning of tissue extraction like biopsies.

The Use of Clinically Measurable Cochlear Parameters in Cochlear Implant Surgery as Indicators for Size, Shape, and Orientation of the Scala Tympani

OBJECTIVES

(1) To assess variations of the human intracochlear anatomy and quantify factors which might be relevant for cochlear implantation (CI) regarding surgical technique and electrode design. (2) Search for correlations of these factors with clinically assessable measurements.

DESIGN

Human temporal bone study with micro computed tomography (μCT) data and analysis of intracochlear geometrical variations: μCT data of 15 fresh human temporal bones was generated, and the intracochlear lumina scala tympani (ST) and scala vestibuli were manually segmented using custom software specifically designed for accurate cochlear segmentation. The corresponding datasets were processed yielding 15 detailed, three-dimensional cochlear models which were investigated in terms of the scalae height, cross-sectional size, and rotation as well as the interrelation of these factors and correlations to others.

RESULTS

The greatest anatomical variability was observed within the round window region of the cochlea (basal 45°), especially regarding the cross-sectional size of the ST and its orientation relative to the scala vestibuli, which were found to be correlated (p < 0.001). The cross-sectional height of the ST changes substantially for both increasing cochlear angles and lateral wall distances. Even small cochleae were found to contain enough space for all commercially available CI arrays. Significant correlations of individual intracochlear parameters to clinically assessable ones were found despite the small sample size.

CONCLUSION

While there is generally enough space within the ST for CI, strong intracochlear anatomical variations could be observed highlighting the relevance of both soft surgical technique as well as a highly flexible and self-adapting cochlear implant electrode array design. Cochlear dimensions (especially at the round window) could potentially be used to indicate surgically challenging anatomies.

Synchrotron Radiation-Based Reconstruction of the Human Spiral Ganglion: Implications for Cochlear Implantation

OBJECTIVE

To three-dimensionally reconstruct Rosenthal's canal (RC) housing the human spiral ganglion (SG) using synchrotron radiation phase-contrast imaging (SR-PCI). Straight cochlear implant electrode arrays were inserted to better comprehend the electro-cochlear interface in cochlear implantation (CI).

DESIGN

SR-PCI was used to reconstruct the human cochlea with and without cadaveric CI. Twenty-eight cochleae were volume rendered, of which 12 underwent cadaveric CI with a straight electrode via the round window (RW). Data were input into the 3D Slicer software program and anatomical structures were modeled using a threshold paint tool.

RESULTS

The human RC and SG were reproduced three-dimensionally with artefact-free imaging of electrode arrays. The anatomy of the SG and its relationship to the sensory organ (Corti) and soft and bony structures were assessed.

CONCLUSIONS

SR-PCI and computer-based three-dimensional reconstructions demonstrated the relationships among implanted electrodes, angular insertion depths, and the SG for the first time in intact, unstained, and nondecalcified specimens. This information can be used to assess stimulation strategies and future electrode designs, as well as create place-frequency maps of the SG for optimal stimulation strategies of the human auditory nerve in CI.

Synchrotron radiation X-ray microtomography for the visualization of intra-cochlear anatomy in human temporal bones implanted with a perimodiolar cochlear implant electrode array

Recently, synchrotron radiation computed microtomography (SRµCT) has emerged as a promising tool for non-destructive, in situ visualization of cochlear implant electrode arrays inserted into a human cochlea. Histological techniques have been the `gold standard' technique for accurate localization of cochlear implant electrodes but are suboptimal for precise three-dimensional measurements. Here, an SRµCT experimental setup is proposed that offers the benefit of a high spatial and contrast resolution (isotropic voxel size = 4.95 µm and propagation-based phase-contrast imaging), while visualizing the soft-tissue structures and electrode array of the cochlear implant simultaneously. In this work, perimodiolar electrode arrays have been tested, which incorporate thick and closely spaced platinum-iridium contacts and wiring. These data can assist cochlear implant and hearing research, can be used to verify electrode segmentation techniques for clinical computed tomography or could be utilized to evaluate cochlear implant electrode array designs.

diceCT: A Valuable Technique to Study the Nervous System of Fish

Contrast-enhanced X-ray imaging provides a non-destructive and flexible approach to optimizing contrast in soft tissues, especially when incorporated with Lugol's solution (aqueous I₂KI), a technique currently referred to as diffusible iodine-based contrast-enhanced computed tomography (diceCT). This stain exhibits high rates of penetration and results in excellent contrast between and within soft tissues, including the central nervous system. Here, we present a staining method for optimizing contrast in the brain of a cartilaginous fish, the brownbanded bamboo shark, Chiloscyllium punctatum, and a bony fish, the common goldfish, Carassius auratus, using diceCT. The aim of this optimization procedure is to provide suitable contrast between neural tissue and background tissue(s) of the head, thereby facilitating digital segmentation and volumetric analysis of the central nervous system. Both species were scanned before staining and were rescanned at time (T) intervals, either every 48 h (C. punctatum) or every 24 h (C. auratus), to assess stain penetration and contrast enhancement. To compare stain intensities, raw X-ray CT data were reconstructed using air and water calibration phantoms that were scanned under identical conditions to the samples. Optimal contrast across the brain was achieved at T = 240 h for C. punctatum and T = 96 h for C. auratus Higher resolution scans of the whole brain were obtained at the two optimized staining times for all the corresponding specimens. The use of diceCT provides a new and valuable tool for visualizing differences in the anatomic organization of both the central and peripheral nervous systems of fish.

Reprint of Corrosion casting of the temporal bone: Review of the technique

The temporal bone has the most sophisticated anatomy of the whole skeleton. Its study is a challenge for students and surgeons. An inverse model of the visually obscured cavities and canals can facilitate better three-dimensional orientation and investigation. This can be made by means of corrosion casting, which is an established technique first documented on the temporal bone at the beginning of the nineteenth century. The prepared specimens are suitable not only for teaching purposes but also for research on the fascinating topography of the osseous labyrinth and the whole temporal bone. Many important studies on temporal bone anatomy are based on this technique. An extensive review of the pertinent literature is provided in relation to each method available.

Corrosion casting of the temporal bone: Review of the technique

The temporal bone has the most sophisticated anatomy of the whole skeleton. Its study is a challenge for students and surgeons. An inverse model of the visually obscured cavities and canals can facilitate better three-dimensional orientation and investigation. This can be made by means of corrosion casting, which is an established technique first documented on the temporal bone at the beginning of the nineteenth century. The prepared specimens are suitable not only for teaching purposes but also for research on the fascinating topography of the osseous labyrinth and the whole temporal bone. Many important studies on temporal bone anatomy are based on this technique. An extensive review of the pertinent literature is provided in relation to each method available.

Investigation of inner ear anatomy in mouse using X-ray phase contrast tomography

A thorough understanding of inner ear anatomy is important for investigators. However, investigation of the mouse inner ear is difficult due to the limitations of imaging techniques. X-ray phase contrast tomography increases contrast 100-1,000 times compared with conventional X-ray imaging. This study aimed to investigate inner ear anatomy in a fresh post-mortem mouse using X-ray phase contrast tomography and to provide a comprehensive atlas of microstructures with less tissue deformation. All experiments were performed in accordance with our institution's guidelines on the care and use of laboratory animals. A fresh mouse cadaver was scanned immediately after sacrifice using an inline phase contrast tomography system. Slice images were reconstructed using a filtered back-projection (FBP) algorithm. Standardized axial and coronal planes were adjusted with a multi-planar reconstruction method. Some three-dimensional (3D) objects were reconstructed by surface rendering. The characteristic features of microstructures, including otoconia masses of the saccular and utricular maculae, superior and inferior macula cribrosae, single canal, modiolus, and osseous spiral lamina, were described in detail. Spatial positions and relationships of the vestibular structures were exhibited in 3D views. This study investigated mouse inner ear anatomy and provided a standardized presentation of microstructures. In particular, otoconia masses were visualized in their natural status without contrast for the first time. The comprehensive anatomy atlas presented in this study provides an excellent reference for morphology studies of the inner ear.

Histology Strategies for Medical Implants and Interventional Device Studies

Histology of medical devices poses a variety of unique challenges. Comprehensive histologic assessment of medical devices often requires spatial context and high-quality retention of the device–tissue interface. However, the composition of many medical devices is often not amenable to traditional paraffin embedding and thus alternative specialized methodologies such as hard resin embedding must be used. Hard resin embedding requires specialized laboratory technical expertise and equipment, and the fixation techniques and resin composition used markedly impact the feasibility of immunohistochemistry. For the continuity of spatial context during histologic evaluation, additional imaging methods such as macrophotography, radiography, micro-Computerized Tomography (microCT), or magnetic resonance imaging (MRI) can be used to guide sectioning and to complement histologic findings. Although standardized approaches are scarce for medical devices, important considerations specific to medical device histology are discussed, including general specimen preparation, special considerations for devices by organ system, and the challenges of immunohistochemistry. Histologic preparation of medical devices must be thoughtful, thorough, and tailored to achieve optimal histologic outcomes for complex, valuable, and often limited implant specimens.

Enhanced contrast in X-ray microtomographic images of the membranous labyrinth using different X-ray sources and scanning modes

The vestibular system, located in the inner ear, plays a crucial role in balance and gaze stabilisation by sensing head movements. The interconnected tubes with membranous walls of the vestibular system are located in the skull bone (the 'membranous labyrinth'). Unfortunately, these membranes are very hard to visualise using three-dimensional (3D) X-ray imaging techniques. This difficulty arises due to the embedment of the membranes in the dense skull bone, the thinness of the membranes, and the small difference in X-ray absorption between the membranes and the surrounding fluid. In this study, we compared the visualisation of very small specimens (lizard heads with vestibular systems smaller than 3 mm) by X-ray computed micro-tomography (μCT) based on synchrotron radiation and conventional sources. A visualisation protocol using conventional X-ray μCT would be very useful thanks to the ease of access and lower cost. Careful optimisation of the acquisition parameters enables detection of the membranes by using μCT scanners based on conventional microfocus sources, but in some cases a low contrast-to-noise ratio (CNR) prevents fast and reliable segmentation of the membranes. Synchrotron radiation μCT proved to be preferable for the visualisation of the small samples with very thin membranes, because of their high demands for spatial and contrast resolution. The best contrast was obtained by using synchrotron radiation μCT working in phase-contrast mode, leading to up to twice as high CNRs than the best conventional μCT results. The CNR of the synchrotron radiation μCT scans was sufficiently high enough to enable the construction of a 3D model by the means of semi-automatic segmentation of the membranous labyrinth. Membrane thickness was found to range between 2.7 and 36.3 μm. Hence, the minimal membrane thickness was found to be much smaller than described previously in the literature (between 10 and 50 μm).

Visualizing the 3D cytoarchitecture of the human cochlea in an intact temporal bone using synchrotron radiation phase contrast imaging

The gold standard method for visualizing the pathologies underlying human sensorineural hearing loss has remained post-mortem histology for over 125 years, despite awareness that histological preparation induces severe artifacts in biological tissue. Historically, the transition from post-mortem assessment to non-invasive clinical biomedical imaging in living humans has revolutionized diagnosis and treatment of disease; however, innovation in non-invasive techniques for cellular-level intracochlear imaging in humans has been difficult due to the cochlea's small size, complex 3D configuration, fragility, and deep encasement within bone. Here we investigate the ability of synchrotron radiation-facilitated X-ray absorption and phase contrast imaging to enable visualization of sensory cells and nerve fibers in the cochlea's sensory epithelium in situ in 3D intact, non-decalcified, unstained human temporal bones. Our findings show that this imaging technique resolves the bone-encased sensory epithelium's cytoarchitecture with unprecedented levels of cellular detail for an intact, unstained specimen, and is capable of distinguishing between healthy and damaged epithelium. All analyses were performed using commercially available software that quickly reconstructs and facilitates 3D manipulation of massive data sets. Results suggest that synchrotron radiation phase contrast imaging has the future potential to replace histology as a gold standard for evaluating intracochlear structural integrity in human specimens, and motivate further optimization for translation to the clinic.

Visualizing the 3D cytoarchitecture of the human cochlea in an intact temporal bone using synchrotron radiation phase contrast imaging

The gold standard method for visualizing the pathologies underlying human sensorineural hearing loss has remained post-mortem histology for over 125 years, despite awareness that histological preparation induces severe artifacts in biological tissue. Historically, the transition from post-mortem assessment to non-invasive clinical biomedical imaging in living humans has revolutionized diagnosis and treatment of disease; however, innovation in non-invasive techniques for cellular-level intracochlear imaging in humans has been difficult due to the cochlea's small size, complex 3D configuration, fragility, and deep encasement within bone. Here we investigate the ability of synchrotron radiation-facilitated X-ray absorption and phase contrast imaging to enable visualization of sensory cells and nerve fibers in the cochlea's sensory epithelium in situ in 3D intact, non-decalcified, unstained human temporal bones. Our findings show that this imaging technique resolves the bone-encased sensory epithelium's cytoarchitecture with unprecedented levels of cellular detail for an intact, unstained specimen, and is capable of distinguishing between healthy and damaged epithelium. All analyses were performed using commercially available software that quickly reconstructs and facilitates 3D manipulation of massive data sets. Results suggest that synchrotron radiation phase contrast imaging has the future potential to replace histology as a gold standard for evaluating intracochlear structural integrity in human specimens, and motivate further optimization for translation to the clinic.

Generating standardized image data for testing and calibrating quantification of volumes, surfaces, lengths, and object counts in fibrous and porous materials using X-ray microtomography

Quantification of the structure and composition of biomaterials using micro-CT requires image segmentation due to the low contrast and overlapping radioopacity of biological materials. The amount of bias introduced by segmentation procedures is generally unknown. We aim to develop software that generates three-dimensional models of fibrous and porous structures with known volumes, surfaces, lengths, and object counts in fibrous materials and to provide a software tool that calibrates quantitative micro-CT assessments. Virtual image stacks were generated using the newly developed software TeIGen, enabling the simulation of micro-CT scans of unconnected tubes, connected tubes, and porosities. A realistic noise generator was incorporated. Forty image stacks were evaluated using micro-CT, and the error between the true known and estimated data was quantified. Starting with geometric primitives, the error of the numerical estimation of surfaces and volumes was eliminated, thereby enabling the quantification of volumes and surfaces of colliding objects. Analysis of the sensitivity of the thresholding upon parameters of generated testing image sets revealed the effects of decreasing resolution and increasing noise on the accuracy of the micro-CT quantification. The size of the error increased with decreasing resolution when the voxel size exceeded 1/10 of the typical object size, which simulated the effect of the smallest details that could still be reliably quantified. Open-source software for calibrating quantitative micro-CT assessments by producing and saving virtually generated image data sets with known morphometric data was made freely available to researchers involved in morphometry of three-dimensional fibrillar and porous structures in micro-CT scans.

Panel 2: Anatomy (Eustachian Tube, Middle Ear, and Mastoid-Anatomy, Physiology, Pathophysiology, and Pathogenesis)

Objective In this report, we review the recent literature (ie, past 4 years) to identify advances in our understanding of the middle ear-mastoid-eustachian tube system. We use this review to determine whether the short-term goals elaborated in the last report were achieved, and we propose updated goals to guide future otitis media research. Data Sources PubMed, Web of Science, Medline. Review Methods The panel topic was subdivided, and each contributor performed a literature search within the given time frame. The keywords searched included middle ear, eustachian tube, and mastoid for their intersection with anatomy, physiology, pathophysiology, and pathology. Preliminary reports from each panel member were consolidated and discussed when the panel met on June 11, 2015. At that meeting, the progress was evaluated and new short-term goals proposed. Conclusions Progress was made on 13 of the 20 short-term goals proposed in 2011. Significant advances were made in the characterization of middle ear gas exchange pathways, modeling eustachian tube function, and preliminary testing of treatments for eustachian tube dysfunction. Implications for Practice In the future, imaging technologies should be developed to noninvasively assess middle ear/eustachian tube structure and physiology with respect to their role in otitis media pathogenesis. The new data derived from these structure/function experiments should be integrated into computational models that can then be used to develop specific hypotheses concerning otitis media pathogenesis and persistence. Finally, rigorous studies on medical or surgical treatments for eustachian tube dysfunction should be undertaken.

Innovative 3D Model of the Human Middle Ear in High Resolution with a Histological Microgrinding Method: A Feasibility Study and Comparison with μCT

Conclusion. The development of a histological 3D model of the tympanic cavity visualizes the exact microanatomy of the sound conduction organ and is therefore essential for finite elements simulations and surgical training. Objectives. So far, no accurate histological 3D model of the sound conduction system existed in literature. For 3D reconstruction of the very fine structures inside and outside the auditory ossicles, a method based on histological slices allows a more differential analysis of both hard and soft tissues and could thus be superior to μCT. Method. A complete temporal bone was embedded in epoxy resin and microground in distances of about 34 μm. After photodocumentation of every plane, a 3D reconstruction was performed by using the Computer Aided Design (CAD) program Rhinoceros 5®. For comparison, a μCT of the same specimen resulted in a 3D model of the calcified structures in the middle ear. Results. The histological 3D model gives an excellent overview to all anatomical soft and bony tissues of the human auditory ossicles. Specifically the fine blood vessel system and the exact dimension of cartilage areas inside the ossicles can be illustrated much more precisely than with μCT data. The present technique also allows the evaluation of the fine connecting ligaments inside the tympanic cavity.

Insertion forces and intracochlear trauma in temporal bone specimens implanted with a straight atraumatic electrode array

The aim of the study was to evaluate insertion forces during manual insertion of a straight atraumatic electrode in human temporal bones, and post-implantation histologic evaluation of the samples to determine whether violation of intracochlear structures is related to insertion forces. In order to minimize intracochlear trauma and preserve residual hearing during cochlear implantation, knowledge of the insertion forces is necessary. Ten fresh frozen human temporal bones were prepared with canal wall down mastoidectomy. All samples were mounted on a one-axis force sensor. Insertion of a 16-mm straight atraumatic electrode was performed from different angles to induce "traumatic" insertion. Histologic evaluation was performed in order to evaluate intracochlear trauma. In 4 of 10 samples, dislocation of the electrode into scala vestibuli was observed. The mean insertion force for all 10 procedures was 0.003 ± 0.005 N. Insertion forces measured around the site of dislocation to scala vestibuli in 3 of 4 samples were significantly higher than insertion forces at the same location of the cochleae measured in samples without trauma (p < 0.04). Mean force during the whole insertion process of the straight atraumatic electrode is lower than reported by other studies using longer electrodes. Based on our study, insertion forces leading to basilar membrane trauma may be lower than the previously reported direct rupture forces.

Advanced Non-Destructive Ocular Visualization Methods by Improved X-Ray Imaging Techniques

Due to limited X-ray contrast, the use of micro-CT in histology is so far not as widespread as predicted. While specific staining procedures-mostly using iodine-address this shortcoming, long diffusion times restrict its use in the often time-constrained daily routine. Recently, a novel staining protocol has been proposed using a biochemical preconditioning step, which increases the permeability of the cells for the staining agent. This could enable the imaging of entire organs of small mammals at a yet unmatched image quality with reasonable preparation and scan times. We here propose an adaptation of this technique for virtual ophthalmology and histology by volumetrically assessing both human and porcine eyes. Hereby, we demonstrate that (contrast-enhanced) micro-CT can outperform conventional histology in the assessment of tumor entities, as well as functioning as a supplementary tool for surgeons in the positioning of intraocular implants in-vitro and as a general assessment tool for ophthalmologic specimens.

Insertion trauma of a cochlear implant electrode array with Nitinol inlay

The integration of a shape memory actuator is a potential mechanism to achieve a consistent perimodiolar position after electrode insertion during cochlear implant surgery. After warming up, and therefore activation of the shape memory effect, the electrode array will change from a straight configuration into a spiral shaped one leading to a final position close to the modiolus. The aim of this study was to investigate whether the integration of an additional thin wire (referred to as an "inlay") made of Nitinol, a well-established shape memory alloy, in a conventional hearing preservation electrode array will affect the insertion behaviour in terms of increased risk of insertion trauma. Six conventional Hybrid-L electrode arrays (Cochlear Ltd., Sydney, Australia) were modified to incorporate a wire inlay made of Nitinol. The diameter of the wires was 100 µm with a tapered tip region. Electrodes were inserted into human temporal bone specimens using a standard surgical approach. After insertion and embedding in epoxy resin, histological sections were prepared to evaluate insertion trauma. Insertion was straightforward and no difficulties were observed. The addition of a shape memory wire, thin but also strong enough to curl the electrode array, does not result in histologically detectable insertion trauma. Atraumatic insertion seems possible.

Reconstruction of cochlea based on micro-CT and histological images of the human inner ear

The study of the normal function and pathology of the inner ear has unique difficulties as it is inaccessible during life and, so, conventional techniques of pathologic studies such as biopsy and surgical excision are not feasible, without further impairing function. Mathematical modelling is therefore particularly attractive as a tool in researching the cochlea and its pathology. The first step towards efficient mathematical modelling is the reconstruction of an accurate three dimensional (3D) model of the cochlea that will be presented in this paper. The high quality of the histological images is being exploited in order to extract several sections of the cochlea that are not visible on the micro-CT (mCT) images (i.e., scala media, spiral ligament, and organ of Corti) as well as other important sections (i.e., basilar membrane, Reissner membrane, scala vestibule, and scala tympani). The reconstructed model is being projected in the centerline of the coiled cochlea, extracted from mCT images, and represented in the 3D space. The reconstruction activities are part of the SIFEM project, which will result in the delivery of an infrastructure, semantically interlinking various tools and libraries (i.e., segmentation, reconstruction, and visualization tools) with the clinical knowledge, which is represented by existing data, towards the delivery of a robust multiscale model of the inner ear.

Volume shrinkage of bone, brain and muscle tissue in sample preparation for micro-CT and light sheet fluorescence microscopy (LSFM)

Two methods are especially suited for tomographic imaging with histological detail of macroscopic samples that consist of multiple tissue types (bone, muscle, nerve or fat): Light sheet (based) fluorescence microscopy (LSFM) and micro-computed tomography (micro-CT). Micro-CT requires staining with heavy chemical elements (and thus fixation and sometimes dehydration) in order to make soft tissue imageable when measured alongside denser structures. LSMF requires fixation, decalcification, dehydration, clearing and staining with a fluorescent dye. The specimen preparation of both imaging methods is prone to shrinkage, which is often not mentioned, let alone quantified. In this paper the presence and degree of shrinkage are quantitatively identified for the selected preparation methods/stains. LSFM delivers a volume shrinkage of 17% for bone, 56% for muscle and 62% for brain tissue. The three most popular micro-CT stains (phosphotungstic acid, iodine with potassium iodide, and iodine in absolute ethanol) deliver a volume shrinkage ranging from 10 to 56% for muscle and 27-66% for brain, while bone does not shrink in micro-CT preparation.