Imaging anatomical features of the human brain at cellular resolution currently relies on series of physical sections with related slicing artefacts. So far, microtomography has been employed to image an entire human brain at a voxel size of 20µm and selected regions using 6µm. This study aims to demonstrate the feasibility of imaging the entire human brain with cellular resolution without the need for physical sectioning using hard x-ray computed tomography. 1.2mm high sections of two human brains, one embedded in ethanol, the other in paraffin, were imaged using microtomography at the P07 beamline at DESY, Hamburg, Germany with a monochromatic beam at 67keV. The extended field of view necessary to cover the ca. 10 cm wide specimens at 2.54µm voxel size was realized by projection tiling with eight to ten rings. The resulting reconstructed slices measured 39,000×39,000 voxels. This synchrotron radiation-based study shows the feasibility of employing x-ray tomography to image the entire human brain with isotropic voxels of 2.54µm resolution. Next, we need to tackle the vertical stitching of several 10,000 slices of 6GB each, posing the challenge of processing the big data of an entire PB-sized human brain and making it accessible to the research community.
Palatoplasty in infants with cleft palate aims to reconstruct the intricate three-dimensional anatomy and restore the velopharyngeal function, which is essential for swallowing, speech, and ventilation of the middle ear through the opening of the Eustachian tube. The non-destructive analysis of the microarchitecture around the pterygoid hamulus using hard x-rays should enhance the existing knowledge from dissection and histological studies. Specifically, the micro-anatomical relationship between the palatine aponeurosis, the tendon of the tensor veli palatini muscle, and the pterygoid hamulus must be characterized to understand their structural relationship and functional implications. At the cellular level, the arrangement of fibers within muscle fascicles needs to be clarified. The right half of a historical plastinated infant cadaveric head was examined with two laboratory-based micro computed tomography (μCT) systems: phoenix|xray nanotom® m for imaging of the entire specimen with a pixel size of 55μm; and Zeiss Xradia 610 Versa for local tomography with a pixel size of 3.4μm. Using synchrotron radiation-based microtomography, additional measurements were performed with a pixel size of 3.24μm. The resulting images were rigidly registered and analyzed. Automated threshold-based segmentation of bones and manual segmentation of muscles, tendons, and aponeurosis, were performed to visualize their topographic relationships in three dimensions. An unstained segment of a human gracilis muscle was examined using the Exciscope Polaris with a pixel size of 0.35μm, and the fiber architecture was visually inspected. Laboratory-based x-ray μCT systems are suitable for virtual-histology examination of soft tissues and visualization of subcellular structures therein. Synchrotron radiation-based μCT with phase retrieval provided additional contrast within the plastinated soft tissues. The findings of this study support the hypothesis that the palatal muscles form a complex muscle sling around the pterygoid hamulus, underscoring the importance of preserving this bony protuberance during cleft palate repair.
Transport of immune cells, nutrients and waste products via the cerebrospinal fluid (CSF) has been implicated in the development of neurological disorders. Using time-resolved in vivo microtomography, we investigated pulsatile motion of CSF spaces in the mouse brain as a potential driver of CSF flow. Here we present a method for detecting motion captured in murine brain images acquired in vivo at the European Synchrotron Radiation Facility. Anesthetized mice were placed in a heated holder that was designed to minimize head motion and maintain physiological body temperature. Contrast agent was infused into the ventricle to improve visibility of the CSF spaces. Projections were retrospectively sorted based on the ECG recording. Cardiac phase images were reconstructed in 10ms intervals from the ECG peak and automatically analyzed for decorrelation. Motion was automatically quantified by non-rigid registration. Regions with high intensity structures, large motion magnitudes, large improvements in image similarity due to registration, or at the contrast-enhanced ventricles were visually inspected for structures with motion artifacts prior to registration. We detected mainly motion in the nasopharynx, skin, ear channels, and bones in the range of 2.3 to 14.8µm magnitude. Small motion artifacts were detectable only for high-contrast structures. No misalignments were visible for the contrast-enhanced ventricles at a voxel resolution of 6.30 to 6.45µm. In the future, dedicated active gating to ensure regular sampling and local scans with improved spatial resolution will be used to investigate the limits to the detection of in vivo ventricular motion in mice.
The acquisition of large tomography volumes, exceeding the typical detector field-of-view, requires advanced acquisition techniques. Current approaches are the tiling of local reconstructed volumes or the tiling in projection space, also known as mosaic tomography. Reconstruction tiling has the advantage that standard reconstruction software can be used and acquisition can be interrupted and resumed relatively easily. The disadvantage is that there is the need for volume registration and transformation. Projection tiling is faster and more dose efficient, however a custom reconstruction pipeline is required, registration in projection space is challenging due to lower contrast, and there is a high sensitivity to mechanical instabilities. In this work we propose a third, hybrid approach, to profit from the advantages of projection tiling, but limit the risks. The volume to be imaged is covered by overlapping cylinders, each corresponding to the reconstructed volume of one mosaic tomogram. The number of rings per cylinder and the total number of cylinders can be tuned to the specimen at hand. We demonstrate this approach for a 2cm-wide section of a human brain stem, imaged at the Anatomix beamline of Synchrotron Soleil, France with 0.65µm voxel size, resulting in reconstructed slices 29,650 voxels wide. For mosaic reconstruction we used our team’s existing pipeline. For stitching of volumes, image registration was performed in the overlap regions. As pairwise displacements between cylinders are not independent, we modified the registration approach to force a consistent solution. The results of the hybrid acquisition in seven tiles with four rings were compared to a pure projection tiling approach with eight rings and to local regions representing reconstruction tiling. In conclusion, we propose an extended field of view acquisition scheme building on the speed and dose efficiency of mosaic acquisition, but relaxing the requirements for mechanical and beam stability.
Noise-induced hearing loss can be caused by sudden or prolonged exposure to loud noise. Noise exposure is known to contribute to the degeneration of sensory cells, disrupting the conversion of mechanical sound waves into electrical impulses and further their transmission to the brain. To determine the pathophysiological condition of the inner ear cells in animal models, the measurement of the animals' hearing is essential. The follow-up examination of the cochlea is particularly important as it provides information on the cellular morphology changes. Our aim was therefore to investigate the hair cell survival in the inner ear of mice exposed to two high noise levels using synchrotron radiation-based microtomography. Its spatial resolution allows for the reconstruction of three-dimensional images of unstained cochlea at the cellular level. We segmented the basilar membrane via automatic cell segmentation and fast manual cell removal, and determined its length using a one-dimensional Isomap embedding. After extracting its middle region and image slices aligned with it, surviving inner and outer hair cell locations were semi-automatically determined and then manually corrected using the ImageJ plugin PointPicker. These results were compared with the confocal microscopy data. The data collected provides meaningful information about healthy and damaged hair cells in the adult cochlea.
Joint tissues consist of trabecular and cortical bone as well as calcified and hyaline cartilage, which presents a challenge for hard X-ray-based visualization on the sub-cellular level due to the wide range of local X-ray absorption values. The density of the calcified tissues requires rather high photon energy, which often leads to insufficient contrast within the cartilage and impedes the visualization of individual biological cells. Decalcification of the tissues reduces the total and local X-ray absorption values and allows for selecting a lower photon energy. Further contrast enhancement can be achieved by ethanol fixation and paraffin tissue embedding. In this study, we (i) searched for an appropriate visualization method to investigate lesions generated by a laser osteotome and (ii) visualized a decalcified porcine joint after ethanol fixation and subsequent paraffin embedding using laboratory- and synchrotron radiation-based microtomography. The experiments at the ANATOMIX beamline of Synchrotron SOLEIL were performed in off-axis scan mode with a pixel size of 1.3 µm. Individual cells in all layers of the joint could be made visible and the effect of ethanol fixation and paraffin embedding demonstrated.
The famous Swiss mummy, the "Lady of the Franciscan Church", is located in Basel. Subsequent to discovery in 1975, many investigations on her origin were performed without success. Four decades later, however, the mummy’s origin has been identified: Anna Catharina Gernler-Bischoff (1719-1787), who was a direct ancestor of Boris Johnson, the former Prime Minister of the United Kingdom. Further details about her life have been collected. For this purpose, teeth were removed and physically sliced for imaging using optical microscopy. One single tooth remained and became available for this cementochronology study. We have applied microtomography to visualize the annual deposits in tooth cementum, termed incremental layers, without the need of physical slicing. The applicability of synchrotron radiation-based tomography to cementochronology has previously been investigated and showed promise. It is, however, unclear how far tomography will work for the mummy tooth. Laboratory-based microtomography enabled us to discriminate between enamel, dentin, and cementum, but the annual layers remained invisible. The improved density and spatial resolution of the tomography setup at the beamline ANATOMIX, Synchrotron SOLEIL, France, however, brought the incremental layers to light. We have counted 30 layers on average. Their thickness corresponds to (4.6 ± 1.4) µm. The available tomography data of the entire tooth should be further analyzed to correlate the life history of Anna Catharina Gernler-Bischoff with thickness and contrast of the incremental layers. The pipeline developed and the gained knowledge will be beneficial for cementochronology of humans dead and alive.
Caries is detected visually, often supported by palpation and conventional radiographs, and is characterized by reduced Xray absorption. The fringe regions of carious lesions, however, are hardly distinguished. Therefore, the treatment is usually suboptimal, because either a substantial part of healthy crown is removed or the carious lesion is still partially present. This in vitro study applied conventional micro computed tomography to quantify remaining carious tissue after treatment with respect to the volume of tissue mechanically removed. For this purpose, 16 teeth with 23 lesions were treated by an experienced dentist. The teeth were imaged before and after caries removal using a SKYSCAN 1275 system, Bruker, Belgium. Pre- and post-treatment datasets were rigidly registered. Manual segmentation gave rise to the volume of the remaining carious tissue. Twenty of the 23 lesions had a residual carious lesion that amounted to less than 3% of the mechanically erased tissue. Still, residual caries with volumes between 0.8 and 3.4 mm3 was found in three cases. Thus, more detailed microtomography studies are to be performed to give the desired feedback for caries therapy to clinicians.
Dental restorations should match the color of the surrounding enamel. Carefully selecting the appropriate shade for the filling material is a challenge for dentists. Moreover, tooth color can change over time due to habits such as smoking or drinking coffee. In the last few years, single-shade dental composites have come to the market. They rely on a chameleon effect to provide acceptable to good color matching regardless of the tooth color. The chameleon effect refers to a dental filling’s ability to guide light in such a way that its color blends in with that of the tooth. Structural color is a contributing factor to the chameleon effect and an active area of research where structures at the submicron scale play a critical role. We investigated the size, shape, and three-dimensional spatial arrangement of filler particles in single-shade dental resin composites. Cylindrical samples of dental composites were prepared and imaged with the transmission X-ray microscope at the ANATOMIX beamline, Synchrotron SOLEIL, France. The centers of the filler particles were determined from the tomography data. Combined with shape information from scanning electron microscopy, a Monte Carlo approach was used to model the transmittance for light at wavelengths from the visible to the ultraviolet. The results were compared to optical transmission measurements. The combination of nanotomography and simulation can thus help to understand the influence of the size and distribution of filler particles on the chameleon effect.
The quantification of appearance and geometrical changes between structures captured across several images relies on the determination of correspondences between these image structures. Automatic methods for establishing sparse and dense spatial correspondences are feature tracking and image registration, respectively. Main registration challenges are weak image features, complex appearance change, large shape changes, and huge images. These challenges can make the problem intractable. We present approaches to overcome these challenges for registration tasks including microtomography images. Applications include assessing tissue changes due to embedding material, comparison of microtomography with optical microscopy images, and optimization of process parameters for materials.
Mammalian brains are extremely complex: a mouse brain contains one hundred million neurons. Mapping an entire brain’s three-dimensional cytoarchitecture from the nano- to centimeter-scale is a monumental challenge. For standard microtomography with sub-µm pixel size, reconstructed volume is limited to about a few mm3 . For full brain mapping, even for the mouse brain with volume of 450 mm3 , the field-of-view must be significantly increased in all three dimensions. We demonstrate mosaic tiling to extend imaged volume by 400× and a dedicated pipeline to process these tera-voxel sized datasets. Here, an entire mouse brain was imaged with 0.65 µm-wide voxels. The datasets, which are 6 TB in size at 16-bit depth, contain a wealth of microanatomical information but present challenges for registration and segmentation.
Cementum deposits on mammalian teeth contain layered microstructures associated with the chronological age of an animal and other details of their life history. Hard X-ray tomography data captured this record contained within the cementum deposits from whole teeth without sectioning. We investigated three teeth of African bovids, namely gemsbok (Oryx gazella), eland (Taurotragus oryx), and African or Cape buffalo (Syncerus caffer) using the laboratorybased system nanotom m for measuring each complete tooth to identify relevant regions, which were scanned at the ANATOMIX beamline of Synchrotron SOLEIL, France. Using microtomography in archaeological materials such as teeth, eliminates the need for tooth sectioning, making it a desirable alternative for archaeologists and museum curators. Synchrotron measurements enabled the application of pixel sizes as low as 0.65µm, which generated around 40 TB of data. The three adult bovids investigated here, have a known day of death and season of death, and come from regions with distinct seasonal patterns in temperature and/or rainfall. They also have an estimated age at death based on occlusal wear. The known information serves as a control to determine the applicability of microtomography on whole teeth of large bovids. Preliminary results show that microtomography can successfully replace the need of sectioning in cementum dental analysis. Our future goal is to develop a protocol to standardize procedures of tooth cementum analysis in bovids using microtomography.
Purpose: The morphology of a polymer aligner, designed according to an orthodontic treatment plan, determines clinical outcomes. A fundamental element of orthodontic tooth movement with aligner treatment is the fit of the aligner’s surface to the individual teeth. Gaps between the aligner and teeth do occur because current aligner fabrication is not capable of completely reproducing the complex anatomy of the individual denture. Our study aims at a quantitative three-dimensional assessment of the fit between optically transparent aligners placed on a polymeric model of the upper dental arch for two thermofoil thicknesses at preselected thermoforming temperatures.
Approach: Using an intraoral scan of a subject’s upper dental arch, eight models were printed using a stereolithographic system. A series of eight NaturAligners® was manufactured with a pressure molding process, using thermofoils with thicknesses of 550 and 750 μm and preselected process temperatures between 110°C and 210°C. These aligners placed on the corresponding models were imaged by an advanced micro computed tomography system. The aligners and the models were segmented to extract the gaps and aligners’ local thicknesses as a function of the processing temperature for the two foil thicknesses.
Results: The results indicate that the aligners show a better fit when the foils are processed at higher temperatures. Nevertheless, processing temperatures can be kept below 150°C, as the gain becomes negligible. Thermal processing reduces the average thickness of the aligners to 60% with respect to the planar starting foil. These thickness distributions demonstrate that the aligners are generally thicker on the occlusal surfaces of molars and premolars but thinner around the incisors and buccal as well as on oral surfaces.
Conclusions: Hard x-ray tomography with micrometer resolution is a powerful technique employed to localize the gaps between aligners and teeth, and it also enables film thickness measurements after thermoforming. The thicker film on the occlusal surfaces is most welcome because of aligner abrasion during wear. The NaturAligner® surfaces consist of a 25-μm-thin cellulose layer, and thus the microplastics released via abrasion of less than this thickness are expected to be substantially less critical than for other commercially available, optically transparent aligners.
Comparable to annual rings present in a tree trunk, human tooth cementum contains yearly deposited incremental layers often termed incremental lines, which are generally visualized from tooth slides with optical microscopy in two dimensions. These micrometer-thin incremental lines are used to decode age-at-death and stress periods over the lifetime of an individuum. One can also visualize these layers without physical slicing by means of hard X rays because of density modulations. Within this project, two optically almost transparent tooth slides were used to record optical data in two dimensions with submicron pixel sizes. These data were registered with projections of available synchrotron radiation-based tomography data of the slides. Such data were also acquired for an entire tooth to determine thickness variations in each layer, the intra-layer thickness, and variations between the layers, the inter-layer thickness, automatically.
Purpose: Synchrotron radiation-based tomography yields microanatomical features in human and animal tissues without physical slicing. Recent advances in instrumentation have made laboratory-based phase tomography feasible. We compared the performance of three cutting-edge laboratory systems benchmarked by synchrotron radiation-based tomography for three specimens. As an additional criterion, the user-friendliness of the three microtomography systems was considered.
Approach: The three tomography systems—SkyScan 2214 (Bruker-microCT, Kontich, Belgium), Exciscope prototype (Stockholm, Sweden), and Xradia 620 Versa (Zeiss, Oberkochen, Germany)—were given 36 h to measure three medically relevant specimens, namely, zebrafish larva, archaeological human tooth, and porcine nerve. The obtained datasets were registered to the benchmark synchrotron radiation-based tomography from the same specimens and selected ones to the SkyScan 1275 and phoenix nanotom m® laboratory systems to characterize development over the last decade.
Results: Next-generation laboratory-based microtomography almost reached the quality achieved by synchrotron-radiation facilities with respect to spatial and density resolution, as indicated by the visualization of the medically relevant microanatomical features. The SkyScan 2214 system and the Exciscope prototype demonstrated the complementarity of phase information by imaging the eyes of the zebrafish larva. The 3-μm thin annual layers in the tooth cementum were identified using Xradia 620 Versa.
Conclusions: SkyScan 2214 was the simplest system and was well-suited to visualizing the wealth of anatomical features in the zebrafish larva. Data from the Exciscope prototype with the high photon flux from the liquid metal source showed the spiral nature of the myelin sheaths in the porcine nerve. Xradia 620 Versa, with detector optics as typically installed for synchrotron tomography beamlines, enabled the three-dimensional visualization of the zebrafish larva with comparable quality to the synchrotron data and the annual layers in the tooth cementum.
Physical and mechanical properties of aligners determine the clinical success of orthodontic treatments. A main element of the successful orthodontic tooth movements is the fitting of the aligner’s surface to the backside of the related teeth. The complex human tooth anatomy and the aligner’s production make gaps inevitable. The aim of the tomography study is the morphological assessment of the recently introduced NaturAligner (Bottmedical AG, Basel, Switzerland). Using the advanced micro-CT system (nanotom m, phoenix|xray, Waygate Technologies, Wunstorf, Germany), a series of eight different aligners, placed on the 3D-printed model of the upper jaw, were visualized. Based on these 3D datasets, the gaps between model and aligner were automatically segmented and the thickness distribution of the aligners automatically determined. This quantification, validated by manual inspection, clearly indicated that aligners fitted better the model, when higher process temperatures were applied.
Tooth cementum annulation (TCA) is used for determining age-at-death and stress periods based on yearly deposited lines in the root cementum of human teeth. Traditionally, TCA analysis employs optical microscopy, which requires cutting sections of the root and provides only sparse sampling in the third dimension. Ancient teeth are unique specimens that should not be sliced. In this imaging study, we show that extended field of view synchrotron radiation-based tomography provides true micrometer resolution and coverage for non-destructively surveying for incremental lines. To rapidly review the root cementum layer of four teeth from early 19th century cemetery with historical records of life events, we employed machine learning for semi-automatic detection and analysis of incremental lines. Surveying large regions of the root cementum enables detection of incremental lines and hence improves TCA analysis as an alternative to slicing of the unique teeth.
Inline phase tomography using synchrotron radiation with sub-micrometer voxel sizes is nowadays the gold standard for investigation of soft and hard tissues with micron resolution. Recent developments on detectors and X-ray sources allow the transfer of the technique into laboratory environment. For the comparison of three manufacturers, we performed microtomography with advanced laboratory microtomography devices with micron resolution on a porcine nerve, a zebrafish embryo and a historic human tooth. These data sets were also compared with data acquired at the ANATOMIX beamline at Synchrotron Soleil and the TOMCAT beamline at SLS. For the lab-based experiments following scanners were chosen: Skyscan 2214 (Bruker-microCT, Kontich, Belgium), Xradia 620 Versa (Zeiss, Oberkochen, Germany) and a prototype with a MetalJet X-ray source from Exillum from the company Exciscope (Stockholm, Sweden). All devices contained detectors including X-ray optics.
Formalin fixation and paraffin embedding of post mortem tissue specimens is widely used for high-resolution neuroimaging with both conventional and X-ray virtual histology. Exchange of embedding solutions generates non-uniform brain shrinkage and changes relative tissue densities. We used synchrotron radiation-based X-ray micro computed tomography to visualize the embedding process for a single mouse brain. Non-rigid registration was employed to determine the volumetric strain fields and to track the X-ray absorption changes of corresponding features. This allows for a correction of the observed microanatomy to improve the anatomical context. Through embedding, the entire brain shrinks to around 40% of its volume in formalin. Shrinkage is non-uniform and varies over anatomical regions and the distance to external surfaces.
X rays have been used for medical imaging since RÖNTGEN's fascinating discovery 125 years ago. The first radiographs of human hands were made public less than a month after his famous paper. The conventional X-ray sources integrated into the CT-machines of today’s hospitals still rely on the same physical principles. X-ray imaging has traditionally offered high spatial resolution and low contrast for soft tissues such as the brain. Magnetic resonance imaging is therefore the method of choice for brain imaging in a clinical setting, although for cellular resolution studies it suffers from limited spatial resolution. The gold standard in post mortem brain imaging is histology, which involves fixation, embedding, physical sectioning, staining, and optical microscopy. Currently, section thickness limits isotropic voxel sizes to 20 μm. Advanced X-ray sources including synchrotron radiation facilities offer complementary modalities such as phase-contrast imaging and spatially resolved small-angle X-ray scattering. We showed that X-ray phase contrast of the human cerebellum with micrometer resolution yields complementary three-dimensional images to magnetic resonance microscopy with even better contrast and spatial resolution. Grating interferometry enabled us to visualize individual Purkinje cells in the nonstained cerebellum. Taking advantage of well-established paraffin embedding, Purkinje cells were visualized within the human cerebellum even with conventional instrumentation. Hard X-ray nano-holotomography allowed for label-free, three-dimensional neuroimaging beyond the optical limit with a spatial resolution below 100 nm. Spatially resolved smallangle X-ray scattering permitted the localization of periodic nanostructures such as myelin sheaths on square-inch brain slices and included the orientational information on the axons. These developments have contributed to the establishment of virtual histology and extended the conventional histology to the third dimension. Further advances are required to image the entire human brain with an isotropic micrometer resolution and to suitably handle the petabyte datasets.
Hard X-ray micro computed tomography can be used for three-dimensional histological phenotyping of zebrafish embryos down to 1 µm or below without the need for staining or physical slicing. Current advances in ze- brafish embryo imaging, however, mostly rely on synchrotron radiation sources or highly advanced laboratory sources, which despite their evident strengths with regard to their beam properties and the implementation of phase contrast imaging techniques, lack accessibility. Therefore, we evaluated the performance of a conventional SkyScan 1275 laboratory µCT scanner in absorption contrast mode for the visualization of anatomical features in ethanol- and paraffin-embedded zebrafish embryos. We compare our results to readily available synchrotron data where 35 anatomical structures were identified. Despite having a more than ten times larger voxel length, approximately two thirds of the features could also be determined with laboratory microtomography. This could allow to monitor morphological changes during development or disease progression on large sample numbers, enabling the performance of preclinical studies in a local laboratory.
Biological matter may change shape via water absorption or loss. For example, brain tissue shows non-uniform shrinkage during formalin fixation and paraffin embedding, which is the most common tissue preparation for conventional histological analysis. Local deformations can be analyzed with non-rigid registration of non-destructive three-dimensional imaging datasets. We utilized synchrotron radiation microtomography at the ANATOMIX beamline of Synchrotron SOLEIL to image a mouse brain with 3 micron voxel length after formalin fixation, immersion in ascending alcohol series and xylene, and after paraffin embedding. We created a pipeline for non- rigid registration to align the volumes and extract volumetric strain fields. In this way, we could visualize the swelling/shrinkage of anatomical features. This method avoids time-consuming segmentation of brain regions, however it is sensitive to the registration parameters. In this proceedings paper, we discuss the selection of registration parameters in order to generate plausible volumetric strain fields. This protocol can be deployed to any type of shape change of biological matter and allows for the quantification of the related processes.
Successful tomographic imaging of soft tissues with micrometer resolution includes preparation, acquisition, re- construction, and data evaluation. Tissue preparation is essential for hard X-ray microtomography, because staining- and embedding materials can substantially alter the biological tissue post mortem. We performed to- mographic imaging of zebrafish embryos in alcohol and after paraffin embedding with a conventional X-ray source and at a synchrotron radiation facility. The resulting multi-modal, three-dimensional data were registered for direct comparison. Single-cell precision was reached for the synchrotron radiation-based approach, which allows for segmentation of full organs such as the embryonic kidneys. While this approach offers an order of magnitude higher spatial resolution, many of the anatomical features can be readily recognized with the more accessible laboratory system. Propagation-based data acquisition enabled us to demonstrate the complementary nature of the edge-enhanced absorption contrast- and the phase contrast-based modality for visualizing multiple microanatomical features. While ethanol and paraffin embeddings allowed for identification of the same anatomical structures, paraffin-embedding, however, led to more artefacts and shrinkage. The presented multi-modal imaging approaches can be further extended to visualize three to four orders of magnitude larger volumes such as adult zebrafish or complete organs of larger animals such as mouse brains. Going towards even larger volumes, such as the human brain, presents further challenges related to paraffin embedding, data acquisition and handling of the peta-byte scale data volumes. This study provided a multi-modal imaging strategy by the combination of X-ray sources and sample embeddings which can play a role in addressing these challenges.
KEYWORDS: Lung, Motion models, Data modeling, Principal component analysis, Tumors, Data acquisition, 3D modeling, Image registration, Image segmentation, Prototyping
Treatment of tumor sites affected by respiratory motion requires knowledge of the position and the shape of
the tumor and the surrounding organs during breathing. As not all structures of interest can be observed in
real-time, their position needs to be predicted from partial information (so-called surrogates) like motion of
diaphragm, internal markers or patients surface. Here, we present an approach to model respiratory lung motion
and predict the position and shape of the lungs from surrogates. 4D-MRI lung data of 10 healthy subjects was
acquired and used to create a model based on Principal Component Analysis (PCA). The mean RMS motion
ranged from 1.88 mm to 9.66 mm. Prediction was done using a Bayesian approach and an average RMSE of
1.44 mm was achieved.
This work applies fractional differentiation (differentiation to non-integer order) to the gradients determined
from image intensities for enhanced image registration. The technique is used to correct known simulated
deformations of volumetric breast MR data using two algorithms: direct registration of gradient magnitude
images and an extension of a previously published method that incorporates both image intensity and image
gradient information to enhance registration performance. Better recovery of known deformations are seen
when using non-integer order derivatives: half-derivative breast images are better registered when these
methods are incorporated into a standard diffusion-based registration algorithm.
KEYWORDS: Breast, Optical spheres, Digital breast tomosynthesis, Nipple, Tissues, Computer aided diagnosis and therapy, Mammography, Mathematical modeling, Data modeling
To improve cancer detection in mammography, breast exams usually consist of two views per breast. To combine
information from both views, radiologists and multiview computer-aided detection (CAD) systems need to match
corresponding regions in the two views. In digital breast tomosynthesis (DBT), finding corresponding regions
in ipsilateral volumes may be a difficult and time-consuming task for radiologists, because many slices have to
be inspected individually. In this study we developed a method to quickly estimate corresponding locations in
ipsilateral tomosynthesis views by applying a mathematical transformation. First a compressed breast model is
matched to the tomosynthesis view containing a point of interest. Then we decompress, rotate and compress
again to estimate the location of the corresponding point in the ipsilateral view. In this study we use a simple
elastically deformable sphere model to obtain an analytical solution for the transformation in a given DBT
case. The model is matched to the volume by using automatic segmentation of the pectoral muscle, breast
tissue and nipple. For validation we annotated 181 landmarks in both views and applied our method to each
location. Results show a median 3D distance between the actual location and estimated location of 1.5 cm; a
good starting point for a feature based local search method to link lesions for a multiview CAD system. Half of
the estimated locations were at most 1 slice away from the actual location, making our method useful as a tool
in mammographic workstations to interactively find corresponding locations in ipsilateral tomosynthesis views.
This paper describes the development of a cylindrical affine transformation model for image registration. The
usefulness of the model for initial alignment was demonstrated for the application of registering prone and
supine 3D MR images of the breast. Final registration results visually improved when using the cylindrical affine
transformation model instead of none or a Cartesian affine transformation model before non-rigid registration.
Stable features under simulated mammographic compressions, which will become candidate landmarks for a temporal
mammographic feature-based registration algorithm, are discussed in this paper. Using these simulated mammograms,
we explore the extraction of features based on standard intensity projection images and local phase projection images.
One approach to establishing corresponding features is by template matching using a similarity measure. Simulated
mammographic projections from deformed MR volumes are employed, as the mean projected 3D displacements are
computed and therefore validation of the technique is possible. Tracking is done by template matching using normalized
cross correlation as the similarity measure. The performance of standard projection images and local phase projection
images is compared. The preliminary results reveal that although the majority of the points within the breast are difficult
to track, a small number may be successfully tracked, which is indicative of their stability and thus their suitability as
candidate landmarks. Whilst matching using the standard projection images achieves an overall error of 14.46mm, this
error increases to 22.7mm when computing local phase of the projection images. These results suggest that using local
phase alone does not improve template matching. For the identification of stable landmarks for feature-based
mammogram registration, we conclude that intensity based template matching using normalized correlation is a feasible
approach for identifying stable features.
This paper presents a novel approach to X-ray mammography - MRI registration. The proposed method uses
an intensity-based technique and an affine transformation matrix to approximate the 3D deformation of the
breast resulting from the compression applied during mammogram acquisition. The registration is driven by a
similarity measure that is calculated at each iteration of the algorithm between the target X-ray mammogram and
a simulated X-ray image, created from the MR volume. Although the similarity measure is calculated in 2D, we
compute a 3D transformation that is updated at each iteration. We have performed two types of experiments.
In the first set, we used simulated X-ray target data, for which the ground truth deformation of the volume
was known and thus the results could be validated. For this case, we examined the performance of 4 different
similarity measures and we show that Normalized Cross Correlation and Gradient Difference perform best. The
calculated mean reprojection error was for both similarity measures 4mm, for an initial misregistration of 14mm.
In the second set of experiments, we present the initial results of registering real X-ray mammograms with MR
volumes. The results indicate that the breast boundaries were registered well and the volume was deformed in
3D in a similar way to the deformation of the breast during X-ray mammogram acquisition. The experiments
were carried out on five patients.
This paper describes a novel method for registering multimodal breast images. The method is based on guiding
initial alignment by a 3D statistical deformation model (SDM) followed by a standard non-rigid registration
method for fine alignment. The method was applied to the problem of compensating for large breast compressions,
namely registering magnetic resonance (MR) images to tomosynthesis images and X-ray mammograms. The
SDM was based on simulating plausible breast compressions for a population of 20 subjects via finite element
models created from segmented 3D MR breast images. Leave-one-out tests on simulated data showed that using
SDM guided registration rather than affine registration for the initial alignment led on average to lower mean
registration errors, namely 3.2 mm versus 4.2 mm for MR to tomosynthesis images (17.1 mm initially) and
5.0 mm versus 6.2 mm for MR to X-ray mammograms (15.0 mm initially).
We have previously proposed a system for image-guided breast surgery that compensates for the deformation of the
breast during patient set-up. Since breast surgery is performed with the patient positioned supine, but MR imaging is
performed with the patient positioned prone, a large soft tissue deformation must be accounted for. A biomechanical
model can help to constrain the associated registrations. However the necessary material properties for breast tissue
under such strains are not available in the literature. This paper describes a method to determine these properties. We
first show that the stress-free or 'reference' state of an object can be approximated by submerging it in liquid of a similar
density. MR images of the breast submerged in water and in a pendulous prone position are acquired. An intensity-based
non-rigid image registration algorithm is used to establish point-by-point correspondence between these images. A finite
element model of the breast is then constructed from the submerged images and the deformation to free-pendulous is
simulated. The material properties for which the model deformation best fits the observed deformation are determined.
Assuming neo-Hookean material properties, the initial shear moduli of fibroglandular and adipose tissue are found to be
0.4 kPa and 0.3 kPa respectively.
Image registration is a very important procedure in medical imaging analysis. However, the intensive computations involved in image registration have to some extent made it impractical for interactive use as well as limiting its general availability. This paper presents our current Grid project to facilitate image registration tasks. We have set up an image registration Grid by combining the attractive features of both Globus and Condor distributed computing environments. In order to make it more convenient to use, we have also developed a web interface for potential clients to specify and submit their image registration jobs to the Grid. The initial experiments in 3D breast MR images have shown encouraging results and demonstrated the suitability of Grid technology to this type of computationally intensive applications. The image registration Grid makes it much more straightforward for different institutes to use the identical registration program and protocols to register images consistently, quickly and efficiently. This can greatly improve data sharing and comparative studies in multi-centre trials. The Grid presented here could be an important step for clinical applications of image registration. Future work will focus on refining the Grid with the aim of upgrading it to a Grid Service and testing the system more extensively with medical imaging dataset.
We present initial results from evaluating the accuracy with which biomechanical breast models based on finite element methods can predict the displacements of tissue within the breast. We investigate the influence of different tissue elasticity values, Poisson's ratios, boundary conditions, finite element solvers and mesh resolutions on one data set. MR images were acquired before and after compressing a volunteer's breast gently. These images were aligned using a 3D non-rigid registration algorithm. The boundary conditions were derived from the result of the non-rigid registration or by assuming no patient motion at the deep or medial side. Three linear and two non-linear elastic material models were tested. The accuracy of the BBMs was assessed by the Euclidean distance of twelve corresponding anatomical landmarks. Overall, none of the tested material models was obviously superior to another regarding the set of investigated values. A major average error increase was noted for partially inaccurate boundary conditions at high Poisson's ratios due to introduced volume change. Maximal errors remained, however, high for low Poisson's ratio due to the landmarks closeness to the inaccurate boundary conditions. The choice of finite element solver or mesh resolution had almost no effect on the performance outcome.
This work presents a validation study for non-rigid registration of 3D contrast enhanced magnetic resonance mammography images. We are using our previously developed methodology for simulating physically plausible, biomechanical tissue deformations using finite element methods to compare two non-rigid registration algorithms based on single-level and multi-level free-form deformations using B-splines and normalized mutual information. We have constructed four patient-specific finite element models and applied the solutions to the original post-contrast scans of the patients, simulating tissue deformation between image acquisitions. The original image pairs were registered to the FEM-deformed post-contrast images using different free-form deformation mesh resolutions. The target registration error was computed for each experiment with respect to the simulated gold standard on a voxel basis. Registration error and single-level free-form deformation resolution were found to be intrinsically related: the smaller the spacing, the higher localized errors, indicating local registration failure. For multi-level free-form deformations, the registration errors improved for increasing mesh resolution. This study forms an important milestone in making our non-rigid registration framework applicable for clinical routine use.
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