Daniel Truhn

Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping

Root phenotyping is a challenging task, mainly because of the hidden nature of this organ. Only recently, imaging technologies have become available that allow us to elucidate the dynamic establishment of root structure and function in the soil. In root tips, optical analysis of the relative elemental growth rates in root expansion zones of hydroponically-grown plants revealed that it is the maximum intensity of cellular growth processes rather than the length of the root growth zone that control the acclimation to dynamic changes in temperature. Acclimation of entire root systems was studied at high throughput in agar-filled Petri dishes. In the present study, optical analysis of root system architecture showed that low temperature induced smaller branching angles between primary and lateral roots, which caused a reduction in the volume that roots access at lower temperature. Simulation of temperature gradients similar to natural soil conditions led to differential responses in basal and apical parts of the root system, and significantly affected the entire root system. These results were supported by first data on the response of root structure and carbon transport to different root zone temperatures. These data were acquired by combined magnetic resonance imaging (MRI) and positron emission tomography (PET). They indicate acclimation of root structure and geometry to temperature and preferential accumulation of carbon near the root tip at low root zone temperatures. Overall, this study demonstrated the value of combining different phenotyping technologies that analyse processes at different spatial and temporal scales. Only such an integrated approach allows us to connect differences between genotypes obtained in artificial high throughput conditions with specific characteristics relevant for field performance. Thus, novel routes may be opened up for improved plant breeding as well as for mechanistic understanding of root structure and function.

Gradient transparent RF housing for simultaneous PET/MRI using carbon fiber composites

The construction of a simultaneous PET/MRI scanner affords careful design to avoid disadvantageous interference between both imaging modalities. In this work we focus on the housing of the PET detector. The primary function of the housing is to encapsulate and shield the detector electronics and it should provide a reliable mechanical support. High conductive materials, e.g. copper, show excellent radio frequency (RF) shielding properties, but have negative impact on the MRI image quality due to induced eddy currents. Carbon fiber composites are less conductive for low frequencies and thus minimize MRI gradient induced eddy currents. Nevertheless they show good RF shielding properties for higher frequencies. Furthermore, carbon fibers have excellent mechanical properties and are highly gamma transparent, which make them a very interesting material for the construction of MRI compatible housings for PET detectors. We developed a housing based on a thin carbon fiber laminate shell, which encloses the PET electronics and combines electrical and mechanical properties as well. First prototypes have shown excellent eddy current performance, good RF shielding properties and superior mechanical robustness. Our method allows to produce custom shaped housings which can be easily replaced to evaluate different material compositions. The presented housing is used to build up the Hyperion lID scanner, a preclinical simultaneous PET/MRI insert based on digital SiPM technology for rodent studies.

Functional MR Imaging Mapping of Human Articular Cartilage Response to Loading

Purpose To determine if multiparametric magnetic resonance (MR) imaging mapping can be used to quantify the response to loading of histologically intact human knee cartilage. Materials and Methods Institutional review board approval and written informed consent were obtained. Twenty macroscopically intact cartilage-bone samples were obtained from the central lateral femoral condyles in 11 patients undergoing total knee replacement. A clinical 3.0-T MR imaging system was used to generate T1, T1ρ, T2, and T2* maps with inversion recovery, spin-lock multiple gradient-echo, multiple spin-echo, and multiple gradient-echo sequences. Serial mapping was performed at three defined strain levels (strain 0 [δ0], 0%; strain 1 [δ1/2], 19.8% ± 4.6 [standard deviation]; strain 2 [δ1], 39.5% ± 9.3) by using displacement-controlled static indentation loading. The entire sample and specific cartilage zones (superficial zone [SZ], transitional zone [TZ], and deep zone [DZ]) and regions (subpistonal area [SPA] and peripistonal area [PPA]) were defined as regions of interest. Upon log transformation, repeated measures analysis of variance was used to detect groupwise regional and zonal differences. Load-induced relative changes were determined and analyzed by using paired Student t test and Spearman correlation. Biomechanical testing (unconfined compression) and histologic assessment (Mankin score) served as the reference standard. Results All samples were histologically intact. Strain-related decreases were found at the SZ and TZ for T1 and T2*; for T1ρ, increases were seen in all zones; and for T2, increases were seen at the SZ and PPA only. Significant parameter changes in the entire sample depth of SPA versus PPA were found for δ1/2 (T1ρ, 14% ± 12 vs 6% ± 9) and δ1 (T1, -4% ± 5 vs -1% ± 3; T1ρ, 13% ± 12 vs 7% ± 7; T2*, -9% ± 12 vs -2% ± 8). SPA versus PPA changes were significant at the SZ and TZ (T1), TZ and DZ (T1ρ), and SZ (T2*). No significant correlations were found between relative changes and biomechanical or histologic parameters. Conclusion Serial multiparametric MR imaging mapping can be used to evaluate cartilage beyond mere static analysis and may provide the basis for more refined graduation strategies of cartilage degeneration.

Measuring Plant Root Growth

Plants represent a significant part of our natural environment and their detailed study becomes more and more interesting (also economically) because of their importance for mankind as a source of food and/or energy. One of the most characteristic biological processes in plant life is their growth; it serves as a good indicator for the compatibility of a plant with varying environmental conditions. For the analysis of such influences, measuring the growth of plant roots is a widely used technique. Unfortunately, traditional schemes of measuring roots with a ruler or scanner are extremely time-consuming, hardly reproducible, and do not allow to follow growth over time. Image analysis can provide a solution. In this paper, we describe a complete image analysis system, from imaging issues to the extraction of various biological features for a subsequent statistical analysis. This opens a variety of new possibilities for biologists, including many economical applications in the study of agricultural crops.

CAMERA CALIBRATION FOR FISH-EYE LENSES IN ENDOSCOPYWITH AN APPLICATION TO 3D RECONSTRUCTION

Image analysis tasks such as 3D reconstruction from endoscopic images require compensation of geometric distortions introduced by the lens system. Appropriate camera calibration is thus necessary. Commonly used calibration algorithms rely on the well-known pinhole camera model, extended by parametric terms for radial distortions. In this paper, we demonstrate that these models are not appropriate if very strong distortions occur as is the case for endoscopic fish-eye lenses. As an alternative, we analyze a generic calibration algorithm published recently by Kannala and Brandt, which is based on more general projection equations. We show qualitatively and quantitatively that this algorithm is well suited to deal with significant distortions especially in the images rim regions. Furthermore, we demonstrate how images of a colon phantom that were corrected in such a manner can be used to obtain a 3D reconstruction

Towards Optical Coherence Tomography-based elastographic evaluation of human cartilage.

Optical Coherence Tomography (OCT) is an imaging technique that allows the surface and subsurface evaluation of semitransparent tissues by generating microscopic cross-sectional images in real time, to millimetre depths and at micrometre resolutions. As the differentiation of cartilage degeneration remains diagnostically challenging to standard imaging modalities, an OCT- and MRI-compatible indentation device for the assessment of cartilage functional properties was developed and validated in the present study. After describing the system design and performing its comprehensive validation, macroscopically intact human cartilage samples (n=5) were indented under control of displacement (δ1=202µm; δ2=405µm; δ3=607µm; δ4=810µm) and simultaneous OCT imaging through a transparent indenter piston in direct contact with the sample; thus, 3-D OCT datasets from surface and subsurface areas were obtained. OCT-based evaluation of loading-induced changes included qualitative assessment of image morphology and signal characteristics. For inter-method cross referencing, the device׳s compatibility with MRI as well as qualitative morphology changes under analogous indentation loading conditions were evaluated by a series of T2 weighted gradient echo sequences. Cartilage thickness measurements were performed using the needle-probe technique prior to OCT and MRI imaging, and subsequently referenced to sample thickness as determined by MRI and histology. Dynamic indentation testing was performed to determine Young׳s modulus for biomechanical reference purposes. Distinct differences in sample thickness as well as corresponding strains were found; however, no significant differences in cartilage thickness were found between the used techniques. Qualitative assessment of OCT and MRI images revealed either distinct or absent sample-specific patterns of morphological changes in relation to indentation loading. For OCT, the tissue area underneath the indenter piston could be qualitatively assessed and displayed in multiple reconstructions, while for MRI, T2 signal characteristics indicated the presence of water and related tissue pressurisation within the sample. In conclusion, the present indentation device has been developed, constructed and validated for qualitative assessment of human cartilage and its response to loading by OCT and MRI. Thereby, it may provide the basis for future quantitative approaches that measure loading-induced deformations within the tissue to generate maps of local tissue properties as well as investigate their relation to degeneration.

T2 MR imaging vs. computational modeling of human articular cartilage tissue functionality

The detection of early stages of cartilage degeneration remains diagnostically challenging. One promising non-invasive approach is to functionally assess the tissue response to loading by serial magnetic resonance (MR) imaging in terms of T2 mapping under simultaneous mechanical loading. As yet, however, it is not clear which cartilage component contributes to the tissue functionality as assessed by quantitative T2 mapping. To this end, quantitative T2 maps of histologically intact cartilage samples (n=8) were generated using a clinical 3.0-T MR imaging system. Using displacement-controlled quasi-static indentation loading, serial T2 mapping was performed at three defined strain levels and loading-induced relative changes were determined in distinct regions-of-interest. Samples underwent conventional biomechanical testing (by unconfined compression) as well as histological assessment (by Mankin scoring) for reference purposes. Moreover, an anisotropic hyperelastic constitutive model of cartilage was implemented into a finite element (FE) code for cross-referencing. In efforts to simulate the evolution of compositional and structural intra-tissue changes under quasi-static loading, the indentation-induced changes in quantitative T2 maps were referenced to underlying changes in cartilage composition and structure. These changes were parameterized as cartilage fluid, proteoglycan and collagen content as well as collagen orientation. On a pixel-wise basis, each individual component correlation with T2 relaxation times was determined by Spearmans ρs and significant correlations were found between T2 relaxation times and all four tissue parameters for all indentation strain levels. Thus, the biological changes in functional MR Imaging parameters such as T2 can further be characterized to strengthen the scientific basis of functional MRI techniques with regards to their perspective clinical applications.

Ex vivo quantitative multiparametric MRI mapping of human meniscus degeneration.

ObjectivesTo evaluate the diagnostic performance of T1, T1ρ, T2, T2*, and UTE-T2* (ultrashort-echo time-enhanced T2*) mapping in the refined graduation of human meniscus degeneration with histology serving as standard-of-reference.Materials and methodsThis IRB-approved intra-individual comparative ex vivo study was performed on 24 lateral meniscus body samples obtained from 24 patients undergoing total knee replacement. Samples were assessed on a 3.0-T MRI scanner using inversion-recovery (T1), spin-lock multi-gradient-echo (T1ρ), multi-spin-echo (T2) and multi-gradient-echo (T2* and UTE-T2*) sequences to determine relaxation times of quantitative MRI (qMRI) parameters. Relaxation times were calculated on the respective maps, averaged to the entire meniscus and to its zones. Histologically, samples were analyzed on a four-point score according to Williams (0-III). QMRI results and Williams (sub)scores were correlated using Spearman’s ρ, while Williams grade-dependent differences were assessed using Kruskal–Wallis and Dunn’s tests. Sensitivities and specificities in the detection of intact (Williams grade [WG]-0) and severely degenerate meniscus (WG-II-III) were calculated.ResultsExcept for T2*, significant increases in qMRI parameters with increasing Williams grades were observed. T1, T1ρ, T2, and UTE-T2* exhibited high sensitivity and variable specificity rates. Significant marked-to-strong correlations were observed for these parameters with each other, with histological WGs and the subscores tissue integrity and cellularity.ConclusionsQMRI mapping holds promise in the objective evaluation of human meniscus. Although sufficient discriminatory power of T1, T1ρ, T2, and UTE-T2* was only demonstrated for the histological extremes, these data may aid in the future MRI-based parameterization and quantification of human meniscus degeneration.

Polarization-sensitive optical coherence tomography-based imaging, parameterization, and quantification of human cartilage degeneration

Abstract. Polarization-sensitive optical coherence tomography (PS-OCT) is a light-based, high-resolution, real-time, noninvasive, and nondestructive imaging modality yielding quasimicroscopic cross-sectional images of cartilage. As yet, comprehensive parameterization and quantification of birefringence and tissue properties have not been performed on human cartilage. PS-OCT and algorithm-based image analysis were used to objectively grade human cartilage degeneration in terms of surface irregularity, tissue homogeneity, signal attenuation, as well as birefringence coefficient and band width, height, depth, and number. Degeneration-dependent changes were noted for the former three parameters exclusively, thereby questioning the diagnostic value of PS-OCT in the assessment of human cartilage degeneration.

3D Human cartilage surface characterization by optical coherence tomography.

Early diagnosis and treatment of cartilage degeneration is of high clinical interest. Loss of surface integrity is considered one of the earliest and most reliable signs of degeneration, but cannot currently be evaluated objectively. Optical Coherence Tomography (OCT) is an arthroscopically available light-based non-destructive real-time imaging technology that allows imaging at micrometre resolutions to millimetre depths. As OCT-based surface evaluation standards remain to be defined, the present study investigated the diagnostic potential of 3D surface profile parameters in the comprehensive evaluation of cartilage degeneration. To this end, 45 cartilage samples of different degenerative grades were obtained from total knee replacements (2 males, 10 females; mean age 63.8 years), cut to standard size and imaged using a spectral-domain OCT device (Thorlabs, Germany). 3D OCT datasets of 8  ×  8, 4  ×  4 and 1  ×  1 mm (width  ×  length) were obtained and pre-processed (image adjustments, morphological filtering). Subsequent automated surface identification algorithms were used to obtain the 3D primary profiles, which were then filtered and processed using established algorithms employing ISO standards. The 3D surface profile thus obtained was used to calculate a set of 21 3D surface profile parameters, i.e. height (e.g. Sa), functional (e.g. Sk), hybrid (e.g. Sdq) and segmentation-related parameters (e.g. Spd). Samples underwent reference histological assessment according to the Degenerative Joint Disease classification. Statistical analyses included calculation of Spearmans rho and assessment of inter-group differences using the Kruskal Wallis test. Overall, the majority of 3D surface profile parameters revealed significant degeneration-dependent differences and correlations with the exception of severe end-stage degeneration and were of distinct diagnostic value in the assessment of surface integrity. None of the 3D surface profile parameters investigated were capable of reliably differentiating healthy from early-degenerative cartilage, while scan area sizes considerably affected parameter values. In conclusion, cartilage surface integrity may be adequately assessed by 3D surface profile parameters, which should be used in combination for the comprehensive and thorough evaluation and overall improved diagnostic performance. OCT- and image-based surface assessment could become a valuable adjunct tool to standard arthroscopy.