Marios is a post-doctoral researcher in Michael Zeineh's group, where he studies brain microstructure alterations in Alzheimer's disease, primarily using X-ray scattering and (diffusion) MRI.
He is a mechanical engineer by training (School of Mechanical Engineering, National Technical University of Athens, Greece). His thesis "Closed-loop force control of a haptic surgical simulator", was performed in the Control Systems Lab of Prof. Evangelos Papadopoulos.
In 2011 he obtained his MSc in Biomedical Engineering from ETH Zurich (Swiss Federal Institute of Technology). He performed his thesis in IBM Research on "Advanced pathology using the Microfluidic Probe", under Emmanuel Delamarche and Govind Kaigala, and was awarded the ETH medal for this work.
He completed his PhD in Bone Biomechanics in the lab of Prof. Ralph Muller in ETH Zurich, where he developed X-ray scattering-based methods to investigate bone microstructure in 3D, research that earned him the 2nd Student Award from the European Society for Biomechanics in 2015.
In 2016 he started using imaging methods to study brain microstructure, in the lab of Prof. Markus Rudin, in the Institute for Biomedical Engineering of ETH Zurich. There, he combined X-ray scattering with DTI, histology and CLARITY for studying rodent brain.
In 2017 he joined the MRI Biophysics group of Profs. Els Fieremans and Dmitry Novikov in New York University School of Medicine, to study human and mouse brain microstructure using X-ray scattering and diffusion MRI.
His research concerning brain imaging using X-ray scattering has been and is being supported by the Swiss National Science Foundation.
Doctor of Philosophy, Eidgenossische Technische Hochschule (ETH Zurich) (2016)
Master of Science, Eidgenossische Technische Hochschule (ETH Zurich) (2011)
Diploma, National Technical University of Athens (2010)
Michael Zeineh, Postdoctoral Faculty Sponsor
Validation study of small-angle X-ray scattering tensor tomography
JOURNAL OF SYNCHROTRON RADIATION
2020; 27: 779–87
Small-angle scattering tensor tomography (SASTT) is a recently developed technique able to tomographically reconstruct the 3D reciprocal space from voxels within a bulk volume. SASTT extends the concept of X-ray computed tomography, which typically reconstructs scalar values, by reconstructing a tensor per voxel, which represents the local nanostructure 3D organization. In this study, the nanostructure orientation in a human trabecular-bone sample obtained by SASTT was validated by sectioning the sample and using 3D scanning small-angle X-ray scattering (3D sSAXS) to measure and analyze the orientation from single voxels within each thin section. Besides the presence of cutting artefacts from the slicing process, the nanostructure orientations obtained with the two independent methods were in good agreement, as quantified with the absolute value of the dot product calculated between the nanostructure main orientations obtained in each voxel. The average dot product per voxel over the full sample containing over 10 000 voxels was 0.84, and in six slices, in which fewer cutting artefacts were observed, the dot product increased to 0.91. In addition, SAXS tensor tomography not only yields orientation information but can also reconstruct the full 3D reciprocal-space map. It is shown that the measured anisotropic scattering for individual voxels was reproduced from the SASTT reconstruction in each voxel of the 3D sample. The scattering curves along different 3D directions are validated with data from single voxels, demonstrating SASTT's potential for a separate analysis of nanostructure orientation and structural information from the angle-dependent intensity distribution.
View details for DOI 10.1107/S1600577520003860
View details for Web of Science ID 000531472900027
View details for PubMedID 32381781
View details for PubMedCentralID PMC7206543
Retrieving neuronal orientations using 3D scanning SAXS and comparison with diffusion MRI.
While diffusion MRI (dMRI) is currently the method of choice to non-invasively probe tissue microstructure and study structural connectivity in the brain, its spatial resolution is limited and its results need structural validation. Current ex vivo methods employed to provide 3D fiber orientations have limitations, including tissue-distorting sample preparation, small field of view or inability to quantify 3D fiber orientation distributions. 3D fiber orientation in tissue sections can be obtained from 3D scanning small-angle X-ray scattering (3D sSAXS) by analyzing the anisotropy of scattering signals. Here we adapt the 3D sSAXS method for use in brain tissue, exploiting the high sensitivity of the SAXS signal to the ordered molecular structure of myelin. We extend the characterization of anisotropy from vectors to tensors, employ the Funk-Radon-Transform for converting scattering information to real space fiber orientations, and demonstrate the feasibility of the method in thin sections of mouse brain with minimal sample preparation. We obtain a second rank tensor representing the fiber orientation distribution function (fODF) for every voxel, thereby generating fODF maps. Finally, we illustrate the potential of 3D sSAXS by comparing the result with diffusion MRI fiber orientations in the same mouse brain. We show a remarkably good correspondence, considering the orthogonality of the two methods, i.e. the different physical processes underlying the two signals. 3D sSAXS can serve as validation method for microstructural MRI, and can provide novel microstructural insights for the nervous system, given the method's orthogonality to dMRI, high sensitivity to myelin sheath's orientation and abundance, and the possibility to extract myelin-specific signal and to perform micrometer-resolution scanning.
View details for DOI 10.1016/j.neuroimage.2019.116214
View details for PubMedID 31568873
High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
2019; 75: 223–38
The recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), 527, 349-352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction.
View details for DOI 10.1107/S2053273318017394
View details for Web of Science ID 000460056400003
View details for PubMedID 30821257
View details for PubMedCentralID PMC6396401
Small-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirements
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
2018; 74: 12–24
Small-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349-352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.
View details for DOI 10.1107/S205327331701614X
View details for Web of Science ID 000418592200002
View details for PubMedID 29269594
View details for PubMedCentralID PMC5740453
Ultrastructure Organization of Human Trabeculae Assessed by 3D sSAXS and Relation to Bone Microarchitecture
2016; 11 (8): e0159838
Although the organization of bone ultrastructure, i.e. the orientation and arrangement of the mineralized collagen fibrils, has been in the focus of research for many years for cortical bone, and many models on the osteonal arrangement have been proposed, limited attention has been paid to trabecular bone ultrastructure. This is surprising because trabeculae play a crucial role for the mechanical strength of several bone sites, including the vertebrae and the femoral head. On this account, we first validated a recently developed method (3D sSAXS or 3D scanning small-angle X-ray scattering) for investigating bone ultrastructure in a quantitative and spatially resolved way, using conventional linearly polarized light microscopy as a gold standard. While both methods are used to analyze thin tissue sections, in contrast to polarized light microscopy, 3D sSAXS has the important advantage that it provides 3D information on the orientation and arrangement of bone ultrastructure. In this first study of its kind, we used 3D sSAXS to investigate the ultrastructural organization of 22 vertebral trabeculae of different alignment, types and sizes, obtained from 4 subjects of different ages. Maps of ultrastructure orientation and arrangement of the trabeculae were retrieved by stacking information from consecutive 20-μm-thick bone sections. The organization of the ultrastructure was analyzed in relation to trabecular microarchitecture obtained from computed tomography and to relevant parameters such as distance to trabecular surface, local curvature or local bone mineralization. We found that (i) ultrastructure organization is similar for all investigated trabeculae independent of their particular characteristics, (ii) bone ultrastructure exhibiting a high degree of orientation was arranged in domains, (iii) highly oriented ultrastructural areas were located closer to the bone surface, (iv) the ultrastructure of the human trabecular bone specimens followed the microarchitecture, being oriented mostly parallel to bone surface, and (v) local surface curvature seems to have an effect on the ultrastructure organization. Further studies that investigate bone ultrastructure orientation and arrangement are needed in order to understand its organization and consequently its relation to bone biology and mechanics.
View details for DOI 10.1371/journal.pone.0159838
View details for Web of Science ID 000381768400009
View details for PubMedID 27547973
View details for PubMedCentralID PMC4993496
Techniques to assess bone ultrastructure organization: orientation and arrangement of mineralized collagen fibrils
JOURNAL OF THE ROYAL SOCIETY INTERFACE
2016; 13 (119)
Bone's remarkable mechanical properties are a result of its hierarchical structure. The mineralized collagen fibrils, made up of collagen fibrils and crystal platelets, are bone's building blocks at an ultrastructural level. The organization of bone's ultrastructure with respect to the orientation and arrangement of mineralized collagen fibrils has been the matter of numerous studies based on a variety of imaging techniques in the past decades. These techniques either exploit physical principles, such as polarization, diffraction or scattering to examine bone ultrastructure orientation and arrangement, or directly image the fibrils at the sub-micrometre scale. They make use of diverse probes such as visible light, X-rays and electrons at different scales, from centimetres down to nanometres. They allow imaging of bone sections or surfaces in two dimensions or investigating bone tissue truly in three dimensions, in vivo or ex vivo, and sometimes in combination with in situ mechanical experiments. The purpose of this review is to summarize and discuss this broad range of imaging techniques and the different modalities of their use, in order to discuss their advantages and limitations for the assessment of bone ultrastructure organization with respect to the orientation and arrangement of mineralized collagen fibrils.
View details for DOI 10.1098/rsif.2016.0088
View details for Web of Science ID 000386722200005
View details for PubMedID 27335222
View details for PubMedCentralID PMC4938080
Nanostructure surveys of macroscopic specimens by small-angle scattering tensor tomography
2015; 527 (7578): 349-+
The mechanical properties of many materials are based on the macroscopic arrangement and orientation of their nanostructure. This nanostructure can be ordered over a range of length scales. In biology, the principle of hierarchical ordering is often used to maximize functionality, such as strength and robustness of the material, while minimizing weight and energy cost. Methods for nanoscale imaging provide direct visual access to the ultrastructure (nanoscale structure that is too small to be imaged using light microscopy), but the field of view is limited and does not easily allow a full correlative study of changes in the ultrastructure over a macroscopic sample. Other methods of probing ultrastructure ordering, such as small-angle scattering of X-rays or neutrons, can be applied to macroscopic samples; however, these scattering methods remain constrained to two-dimensional specimens or to isotropically oriented ultrastructures. These constraints limit the use of these methods for studying nanostructures with more complex orientation patterns, which are abundant in nature and materials science. Here, we introduce an imaging method that combines small-angle scattering with tensor tomography to probe nanoscale structures in three-dimensional macroscopic samples in a non-destructive way. We demonstrate the method by measuring the main orientation and the degree of orientation of nanoscale mineralized collagen fibrils in a human trabecula bone sample with a spatial resolution of 25 micrometres. Symmetries within the sample, such as the cylindrical symmetry commonly observed for mineralized collagen fibrils in bone, allow for tractable sampling requirements and numerical efficiency. Small-angle scattering tensor tomography is applicable to both biological and materials science specimens, and may be useful for understanding and characterizing smart or bio-inspired materials. Moreover, because the method is non-destructive, it is appropriate for in situ measurements and allows, for example, the role of ultrastructure in the mechanical response of a biological tissue or manufactured material to be studied.
View details for DOI 10.1038/nature16056
View details for Web of Science ID 000365356800050
View details for PubMedID 26581291
3D scanning SAXS: A novel method for the assessment of bone ultrastructure orientation
2015; 71: 42–52
The arrangement and orientation of the ultrastructure plays an important role for the mechanical properties of inhomogeneous and anisotropic materials, such as polymers, wood, or bone. However, there is a lack of techniques to spatially resolve and quantify the material's ultrastructure orientation in a macroscopic context. In this study, a new method is presented, which allows deriving the ultrastructural 3D orientation in a quantitative and spatially resolved manner. The proposed 3D scanning small-angle X-ray scattering (3D sSAXS) method was demonstrated on a thin trabecular bone specimen of a human vertebra. A micro-focus X-ray beam from a synchrotron radiation source was used to raster scan the sample for different rotation angles. Furthermore, a mathematical framework was developed, validated and employed to describe the relation between the SAXS data for the different rotation angles and the local 3D orientation and degree of orientation (DO) of the bone ultrastructure. The resulting local 3D orientation was visualized by a 3D orientation map using vector fields. Finally, by applying the proposed 3D scanning SAXS method on consecutive bone sections, a 3D map of the local orientation of a complete trabecular element could be reconstructed for the first time. The obtained 3D orientation map provided information on the bone ultrastructure organization and revealed links between trabecular bone microarchitecture and local bone ultrastructure. More specifically, we observed that trabecular bone ultrastructure is organized in orientation domains of tens of micrometers in size. In addition, it was observed that domains with a high DO were more likely to be found near the surface of the trabecular structure, and domains with lower DO (or transition zones) were located in-between the domains with high DO. The method reproducibility was validated by comparing the results obtained when scanning the sample under different sample tilt angles. 3D orientation maps such as the ones created using 3D scanning SAXS will help to quantify and understand structure-function relationships between bone ultrastructure and bone mechanics. Beyond that, the proposed method can also be used in other research fields such as material sciences, with the aim to locally determine the 3D orientation of material components.
View details for DOI 10.1016/j.bone.2014.10.002
View details for Web of Science ID 000347770000006
View details for PubMedID 25306893
Advanced glycation end-products diminish tendon collagen fiber sliding
2013; 32 (3-4): 169–77
Connective tissue aging and diabetes related comorbidity are associated with compromised tissue function, increased susceptibility to injury, and reduced healing capacity. This has been partly attributed to collagen cross-linking by advanced glycation end-products (AGEs) that accumulate with both age and disease. While such cross-links are believed to alter the physical properties of collagen structures and tissue behavior, existing data relating AGEs to tendon mechanics is contradictory. In this study, we utilized a rat tail tendon model to quantify the micro-mechanical repercussion of AGEs at the collagen fiber-level. Individual tendon fascicles were incubated with methylglyoxal (MGO), a naturally occurring metabolite known to form AGEs. After incubation in MGO solution or buffer only, tendons were stretched on the stage of a multiphoton confocal microscope and individual collagen fiber stretch and relative fiber sliding were quantified. Treatment by MGO yielded increased fluorescence and elevated denaturation temperatures as found in normally aged tissue, confirming formation of AGEs and related cross-links. No apparent ultrastructural changes were noted in transmission electron micrographs of cross-linked fibrils. MGO treatment strongly reduced tissue stress relaxation (p<0.01), with concomitantly increased tissue yield stress (p<0.01) and ultimate failure stress (p=0.036). MGO did not affect tangential modulus in the linear part of the stress-strain curve (p=0.46). Microscopic analysis of collagen fiber kinematics yielded striking results, with MGO treatment drastically reducing fiber-sliding (p<0.01) with a compensatory increase in fiber-stretch (p<0.01). We thus conclude that the main mechanical effect of AGEs is a loss of tissue viscoelasticity driven by matrix-level loss of fiber-fiber sliding. This has potentially important implications to tissue damage accumulation, mechanically regulated cell signaling, and matrix remodeling. It further highlights the importance of assessing viscoelasticity - not only elastic response - when considering age-related changes in the tendon matrix and connective tissue in general.
View details for DOI 10.1016/j.matbio.2013.01.003
View details for Web of Science ID 000319533800004
View details for PubMedID 23348249
Micro-immunohistochemistry using a microfluidic probe
LAB ON A CHIP
2012; 12 (6): 1040–43
A flexible method to extract more high-quality information from tissue sections is critically needed for both drug discovery and clinical pathology. Here, we present micro-immunohistochemistry (μIHC), a method for staining tissue sections at the micrometre scale. Nanolitres of antibody solutions are confined over micrometre-sized areas of tissue sections using a vertical microfluidic probe (vMFP) for their incubation with primary antibodies, the key step in conventional IHC. The vMFP operates several micrometres above the tissue section, can be interactively positioned on it, and even enables the staining of individual cores of tissue microarrays with multiple antigens. μIHC using such a microfluidic probe is preservative of tissue samples and reagents, alleviates antibody cross-reactivity issues, and allows a wide range of staining conditions to be applied on a single tissue section. This method may therefore find broad use in tissue-based diagnostics and in research.
View details for DOI 10.1039/c2lc21016a
View details for Web of Science ID 000300511500004
View details for PubMedID 22237742