Micro-Anatomical Quantitative Imaging Towards Enabling Automated Diagnosis of Thick Tissues at the Point of Care

Histopathology is the clinical standard for tissue diagnosis. However, histopathology has several limitations including that it requires tissue processing, which can take 30 minutes or more, and requires a highly trained pathologist to diagnose the tissue. Additionally, the diagnosis is qualitative, and the lack of quantitation leads to possible observer-specific diagnosis. Taken together, it is difficult to diagnose tissue at the point of care using histopathology.

Several clinical situations could benefit from more rapid and automated histological processing, which could reduce the time and the number of steps required between obtaining a fresh tissue specimen and rendering a diagnosis. For example, there is need for rapid detection of residual cancer on the surface of tumor resection specimens during excisional surgeries, which is known as intraoperative tumor margin assessment. Additionally, rapid assessment of biopsy specimens at the point-of-care could enable clinicians to confirm that a suspicious lesion is successfully sampled, thus preventing an unnecessary repeat biopsy procedure. Rapid and low cost histological processing could also be potentially useful in settings lacking the human resources and equipment necessary to perform standard histologic assessment. Lastly, automated interpretation of tissue samples could potentially reduce inter-observer error, particularly in the diagnosis of borderline lesions.

To address these needs, high quality microscopic images of the tissue must be obtained in rapid timeframes, in order for a pathologic assessment to be useful for guiding the intervention. Optical microscopy is a powerful technique to obtain high-resolution images of tissue morphology in real-time at the point of care, without the need for tissue processing. In particular, a number of groups have combined fluorescence microscopy with vital fluorescent stains to visualize micro-anatomical features of thick (i.e. unsectioned or unprocessed) tissue. However, robust methods for segmentation and quantitative analysis of heterogeneous images are essential to enable automated diagnosis. Thus, the goal of this work was to obtain high resolution imaging of tissue morphology through employing fluorescence microscopy and vital fluorescent stains and to develop a quantitative strategy to segment and quantify tissue features in heterogeneous images, such as nuclei and the surrounding stroma, which will enable automated diagnosis of thick tissues.

To achieve these goals, three specific aims were proposed. The first aim was to develop an image processing method that can differentiate nuclei from background tissue heterogeneity and enable automated diagnosis of thick tissue at the point of care. A computational technique called sparse component analysis (SCA) was adapted to isolate features of interest, such as nuclei, from the background. SCA has been used previously in the image processing community for image compression, enhancement, and restoration, but has never been applied to separate distinct tissue types in a heterogeneous image. In combination with a high resolution fluorescence microendoscope (HRME) and a contrast agent acriflavine, the utility of this technique was demonstrated through imaging preclinical sarcoma tumor margins. Acriflavine localizes to the nuclei of cells where it reversibly associates with RNA and DNA. Additionally, acriflavine shows some affinity for collagen and muscle. SCA was adapted to isolate acriflavine positive features or APFs (which correspond to RNA and DNA) from background tissue heterogeneity. The circle transform (CT) was applied to the SCA output to quantify the size and density of overlapping APFs. The sensitivity of the SCA+CT approach to variations in APF size, density and background heterogeneity was demonstrated through simulations. Specifically, SCA+CT achieved the lowest errors for higher contrast ratios and larger APF sizes. When applied to tissue images of excised sarcoma margins, SCA+CT correctly isolated APFs and showed consistently increased density in tumor and tumor + muscle images compared to images containing muscle. Next, variables were quantified from images of resected primary sarcomas and used to optimize a multivariate model. The sensitivity and specificity for differentiating positive from negative ex vivo resected tumor margins was 82% and 75%. The utility of this approach was further tested by imaging the in vivo tumor cavities from 34 mice after resection of a sarcoma with local recurrence as a bench mark. When applied prospectively to images from the tumor cavity, the sensitivity and specificity for differentiating local recurrence was 78% and 82%. The results indicate that SCA+CT can accurately delineate APFs in heterogeneous tissue, which is essential to enable automated and rapid surveillance of tissue pathology.

Two primary challenges were identified in the work in aim 1. First, while SCA can be used to isolate features, such as APFs, from heterogeneous images, its performance is limited by the contrast between APFs and the background. Second, while it is feasible to create mosaics by scanning a sarcoma tumor bed in a mouse, which is on the order of 3-7 mm in any one dimension, it is not feasible to evaluate an entire human surgical margin. Thus, improvements to the microscopic imaging system were made to (1) improve image contrast through rejecting out-of-focus background fluorescence and to (2) increase the field of view (FOV) while maintaining the sub-cellular resolution needed for delineation of nuclei. To address these challenges, a technique called structured illumination microscopy (SIM) was employed in which the entire FOV is illuminated with a defined spatial pattern rather than scanning a focal spot, such as in confocal microscopy.

Thus, the second aim was to improve image contrast and increase the FOV through employing wide-field, non-contact structured illumination microscopy and optimize the segmentation algorithm for new imaging modality. Both image contrast and FOV were increased through the development of a wide-field fluorescence SIM system. Clear improvement in image contrast was seen in structured illumination images compared to uniform illumination images. Additionally, the FOV is over 13X larger than the fluorescence microendoscope used in aim 1. Initial segmentation results of SIM images revealed that SCA is unable to segment large numbers of APFs in the tumor images. Because the FOV of the SIM system is over 13X larger than the FOV of the fluorescence microendoscope, dense collections of APFs commonly seen in tumor images could no longer be sparsely represented, and the fundamental sparsity assumption associated with SCA was no longer met. Thus, an algorithm called maximally stable extremal regions (MSER) was investigated as an alternative approach for APF segmentation in SIM images. MSER was able to accurately segment large numbers of APFs in SIM images of tumor tissue. In addition to optimizing MSER for SIM image segmentation, an optimal frequency of the illumination pattern used in SIM was carefully selected because the image signal to noise ratio (SNR) is dependent on the grid frequency. A grid frequency of 31.7 mm-1 led to the highest SNR and lowest percent error associated with MSER segmentation.

Once MSER was optimized for SIM image segmentation and the optimal grid frequency was selected, a quantitative model was developed to diagnose mouse sarcoma tumor margins that were imaged ex vivo with SIM. Tumor margins were stained with acridine orange (AO) in aim 2 because AO was found to stain the sarcoma tissue more brightly than acriflavine. Both acriflavine and AO are intravital dyes, which have been shown to stain nuclei, skeletal muscle, and collagenous stroma. A tissue-type classification model was developed to differentiate localized regions (75x75 µm) of tumor from skeletal muscle and adipose tissue based on the MSER segmentation output. Specifically, a logistic regression model was used to classify each localized region. The logistic regression model yielded an output in terms of probability (0-100%) that tumor was located within each 75x75 µm region. The model performance was tested using a receiver operator characteristic (ROC) curve analysis that revealed 77% sensitivity and 81% specificity. For margin classification, the whole margin image was divided into localized regions and this tissue-type classification model was applied. In a subset of 6 margins (3 negative, 3 positive), it was shown that with a tumor probability threshold of 50%, 8% of all regions from negative margins exceeded this threshold, while over 17% of all regions exceeded the threshold in the positive margins. Thus, 8% of regions in negative margins were considered false positives. These false positive regions are likely due to the high density of APFs present in normal tissues, which clearly demonstrates a challenge in implementing this automatic algorithm based on AO staining alone.

Thus, the third aim was to improve the specificity of the diagnostic model through leveraging other sources of contrast. Modifications were made to the SIM system to enable fluorescence imaging at a variety of wavelengths. Specifically, the SIM system was modified to enabling imaging of red fluorescent protein (RFP) expressing sarcomas, which were used to delineate the location of tumor cells within each image. Initial analysis of AO stained panels confirmed that there was room for improvement in tumor detection, particularly in regards to false positive regions that were negative for RFP. One approach for improving the specificity of the diagnostic model was to investigate using a fluorophore that was more specific to staining tumor. Specifically, tetracycline was selected because it appeared to specifically stain freshly excised tumor tissue in a matter of minutes, and was non-toxic and stable in solution. Results indicated that tetracycline staining has promise for increasing the specificity of tumor detection in SIM images of a preclinical sarcoma model and further investigation is warranted.

In conclusion, this work presents the development of a combination of tools that is capable of automated segmentation and quantification of micro-anatomical images of thick tissue. When compared to the fluorescence microendoscope, wide-field multispectral fluorescence SIM imaging provided improved image contrast, a larger FOV with comparable resolution, and the ability to image a variety of fluorophores. MSER was an appropriate and rapid approach to segment dense collections of APFs from wide-field SIM images. Variables that reflect the morphology of the tissue, such as the density, size, and shape of nuclei and nucleoli, can be used to automatically diagnose SIM images. The clinical utility of SIM imaging and MSER segmentation to detect microscopic residual disease has been demonstrated by imaging excised preclinical sarcoma margins. Ultimately, this work demonstrates that fluorescence imaging of tissue micro-anatomy combined with a specialized algorithm for delineation and quantification of features is a means for rapid, non-destructive and automated detection of microscopic disease, which could improve cancer management in a variety of clinical scenarios.

Morphology and compression behaviour of biodegradable scaffolds produced by the sintering process

Porous poly(L-lactic acid) (PLA) scaffolds of 85 per cent and 90 per cent porosity are prepared using polymer sintering and porogen leaching method. Different weight fractions of 10 per cent, 30 per cent, and 50 per cent of hydroxyapatite (HA) are added to the PLA to control the acidity and degradation rate. The three-dimensional (3D) morphology and surface porosity are tested using micro-computer tomography (micro-CT), optical microscopy, and scanning electron microscopy (SEM). Results indicate that the surface porosity does not change on the addition of HA. The micro-CT examinations show a slight decrease in the pore size and increase in the wall thickness accompanied by reduced anisotropy for the scaffolds containing HA. Scanning electron micrographs show detectable interconnected pores for the scaffold with pure PLA. Addition of the HA results in agglomeration of the HA particles and reduced leaching of the porogen. Compression tests of the scaffold identify three stages in the stress-strain curve. The addition of HA results in a reduction in the modulus of the scaffold at the first stage of elastic bending of the wall, but this is reversed for the second and third stages of collapse of the wall and densification in the compression tests. In the scaffolds with 85 per cent porosity, the addition of a high percentage of HA could result in 70 per cent decrease in stiffness in the first stage, 200 per cent increase in stiffness in the second stage, and 20 per cent increase in stiffness in the third stage. The results of these tests are compared with the Gibson cellular material model that is proposed for prediction of the behaviour of cellular material under compression. The pH and molecular weight changes are tracked for the scaffolds within a period of 35 days. The addition of HA keeps the pH in the alkaline region, which results in higher rate of degradation at an early period of observation, followed by a reduced rate of degradation later in the process. The final molecular weight is higher for the scaffolds with HA than for scaffolds of pure PLA. The manufactured scaffolds offer acceptable properties in terms of the pore size range and interconnectivity of the pores and porosity for non-load-bearing bone graft substitute; however, improvement to the mixing of the phases of PLA and HA is required to achieve better integrity of the composite scaffolds. © 2008 IMechE.

Strain gradients in Cu-Fe thin films and multilayers during micropillar compression

Plastic strain gradients can influence the work-hardening behaviour of metals due to the accumulation of geometrically necessary discolations at the micron/submicron scale. A finite element model based on the conventional theory of mechanism-based strain-gradient plasticity has been developed to simulate the micropillar compression of Cu–Fe thin films and multilayers. The modelling results show that the geometric constraints lead to inhomogeneous deformation in the Cu layers, which agrees well with the bulging of Cu layers observed experimentally. Plastic strain gradients develop inside the individual layers, leading to extra work-hardening due to the accumulation of geometrically necessary dislocations. In the multilayer specimens, the Cu layers deform more severely than the Fe layers, resulting in the development of tensile stresses in the Fe layers. It is proposed that these tensile stresses are responsible for the development of micro-cracks in the Fe layers.

CHARACTERIZATION OF THE MICRO-SITE CONDITIONS FROM RESTORED AREAS WITH DIFFERENT AGES

Regeneration microsites are characterized by diverse combinations of attributes which assure the best conditions for seed germination and seedling establishment. By understanding these attributes, we can contribute to determining better management methodologies for reestablishing ecological process in sites under restoration. Thus, we sought to characterize and differentiate the micro-site conditions of restoration plantings to indentify likely physical-chemical limitations for the establishment of native tree species in the forest understory. This study was carried out in reforestation plantings with different ages (10, 22 and 55 years). The physical-chemical characterization of the micro-site of regeneration of the study areas was carried out by evaluating the soil compression level, porosity, humidity, organic matter and nutrients content and granulometry, as well as litter dry mass and canopy cover. An increase on the canopy cover and soil porosity, humidity, clay and organic matter content were observed in the oldest restored areas, as well as a decrease in soil compression. Thus, these findings demonstrated that the evaluated microsite properties are in process of restoration. Therefore, microsite conditions for seedling establishment become even more similar to reference ecosystems as restoration planting evolve.

Study of an anisotropic polymeric cellular material under compression loading

This paper emphasizes the influence of micro mechanisms of failure of a cellular material on its phenomenological response. Most of the applications of cellular materials comprise a compression loading. Thus, the study focuses on the influence of the anisotropy in the mechanical behavior of cellular material under cyclic compression loadings. For this study, a Digital Image Correlation (DIC) technique (named Correli) was applied, as well as SEM (Scanning Electron Microscopy) images were analyzed. The experimental results are discussed in detail for a closed-cell rigid poly (vinyl chloride) (PVC) foam, showing stress-strain curves in different directions and why the material can be assumed as transversely isotropic. Besides, the present paper shows elastic and plastic Poisson's ratios measured in different planes, explaining why the plastic Poisson's ratios approach to zero. Yield fronts created by the compression loadings in different directions and the influence of spring-back phenomenon on hardening curves are commented, also.

High resolution study of local stress inside alumina - micro mechanical analysis using laser scanning confocal microscope

The aim of this work is to measure the stress inside a hard micro object under extreme compression. To measure the internal stress, we compressed ruby spheres (a-Al2O3: Cr3+, 150 µm diameter) between two sapphire plates. Ruby fluorescence spectrum shifts to longer wavelengths under compression and can be related to the internal stress by a conversion coefficient. A confocal laser scanning microscope was used to excite and collect fluorescence at desired local spots inside the ruby sphere with spatial resolution of about 1 µm3. Under static external loads, the stress distribution within the center plane of the ruby sphere was measured directly for the first time. The result agreed to Hertz’s law. The stress across the contact area showed a hemispherical profile. The measured contact radius was in accord with the calculation by Hertz’s equation. Stress-load curves showed spike-like decrease after entering non-elastic phase, indicating the formation and coalescence of microcracks, which led to relaxing of stress. In the vicinity of the contact area luminescence spectra with multiple peaks were observed. This indicated the presence of domains of different stress, which were mechanically decoupled. Repeated loading cycles were applied to study the fatigue of ruby at the contact region. Progressive fatigue was observed when the load exceeded 1 N. As long as the load did not exceed 2 N stress-load curves were still continuous and could be described by Hertz’s law with a reduced Young’s modulus. Once the load exceeded 2 N, periodical spike-like decreases of the stress could be observed, implying a “memory effect” under repeated loading cycles. Vibration loading with higher frequencies was applied by a piezo. Redistributions of intensity on the fluorescence spectra were observed and it was attributed to the repopulation of the micro domains of different elasticity. Two stages of under vibration loading were suggested. In the first stage continuous damage carried on until certain limit, by which the second stage, e.g. breakage, followed in a discontinuous manner.

In vitro biomechanical testing of a micro external skeletal fixator

OBJECTIVE To biomechanically test the properties of three different Universal Micro External Fixator (UMEX™) configurations with regard to their use in very small animals (<5kg) and compare the UMEX system to the widely used IMEX External Skeletal Fixation (SK™) system in terms of stiffness, space needed for pin placement and weight. METHODS Three different UMEX configurations (type Ia, type Ib, and type II modified) and one SK configuration type Ia were used to stabilize Delrin plastic rods in a 1 cm fracture gap model. These constructs were tested in axial compression, craniocaudal bending, mediolateral bending, and torsion. Testing was conducted within the elastic range and mean stiffness in each mode was determined from the slope of the linear portion of the load-deformation curve. A Kruskal Wallis one-way analysis of variance on ranks test was utilized to assess differences between constructs (p <0.05). RESULTS The UMEX type II modified configuration was significantly stiffer than the other UMEX configurations and the SK type Ia, except in craniocaudal bending, where the SK type Ia configuration was stiffer than all UMEX constructs. The UMEX type Ia configuration was significantly the weakest of those frames. The UMEX constructs were lighter and smaller than the SK, thus facilitating closer pin placement. CONCLUSIONS Results supported previous reports concerning the superiority of more complex constructs regarding stiffness. The UMEX system appears to be a valid alternative for the treatment of long-bone fractures in very small animals.

Yielding Behaviour of Electron Beam Lithography and Focused Ion Beam Made Nanocrystalline Micro/Nanopillars

Electron beam lithography (EBL) and focused ion beam (FIB) methods were developed in house to fabricate nanocrystalline nickel micro/nanopillars so to compare the effect of fabrication on plastic yielding. EBL was used to fabricate 3 μm and 5 μm thick poly-methyl methacrylate patterned substrates in which nickel pillars were grown by electroplating with height to diameter aspect ratios from 2:1 to 5:1. FIB milling was used to reduce larger grown pillars to sizes similar to EBL grown pillars. X-ray diffraction, electron back-scatter diffraction, scanning electron microscopy, and FIB imaging were used to characterize the nickel pillars. The measured grain size of the pillars was 91±23 nm, with strong <110> and weaker <111> and <110> crystallographic texture in the growth. Load-controlled compression tests were conducted using a MicroMaterials nano-indenter equipped with a 10 μm flat punch at constant rates from 0.0015 to 0.03 mN/s on EBL grown pillars, and 0.0015 and 0.015 mN/s on FIB-milled pillars. The measured Young’s modulus ranged from 55 to 350 GPa for all pillars, agreeing with values in the literature. EBL grown pillars exhibited stochastic strain-bursts at slow loading rates, attributed to local micro yield events, followed by work hardening. Sharp yield points were also observed and attributed to the gold seed layer de-bonding between the nickel pillar and substrate due to the shear stress associated with end effects that arise from the substrate constraint. The onset of yield ranged from 108 to 1800 MPa, which is greater than bulk nickel, but within values given in the literature. FIB-milled pillars demonstrated stochastic yield behaviour at all loading rates tested, yielding between 320 and 625 MPa. Deformation was apparent at FIB-milled pillar tops, where the smallest cross-sectional area was measured, but still exhibited superior yield strength to bulk nickel. The gallium damage at the outer surface of the pillars likely aids in dislocation nucleation and plasticity, leading to lower yield strengths than for the EBL pillars. Thermal drift, substrate effects, and noise due to vibrations within the indenter system contributed to variance and inconsistency in the data.

3D Porous Architecture of Stacks of β-TCP Granules Compared with That of Trabecular Bone: A microCT, Vector Analysis, and Compression Study

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Implementation of soft processor based SOC for JPEG compression on FPGA

With the advent of semiconductor process and EDA tools technology, IC designers can integrate more functions. However, to reduce the demand of time-to-market and tackle the increasing complexity of SoC, the need of fast prototyping and testing is growing. Taking advantage of deep submicron technology, modern FPGAs provide a fast and low-cost prototyping with large logic resources and high performance. So the hardware is mapped onto an emulation platform based on FPGA that mimics the behaviour of SOC. In this paper we use FPGA as a system on chip which is then used for image compression by 2-D DCT respectively and proposed SoC for image compression using soft core Microblaze. The JPEG standard defines compression techniques for image data. As a consequence, it allows to store and transfer image data with considerably reduced demand for storage space and bandwidth. From the four processes provided in the JPEG standard, only one, the baseline process is widely used. Proposed SoC for JPEG compression has been implemented on FPGA Spartan-6 SP605 evaluation board using Xilinx platform studio, because field programmable gate array have reconfigurable hardware architecture. Hence the JPEG image with high speed and reduced size can be obtained at low risk and low power consumption of about 0.699W. The proposed SoC for image compression is evaluated at 83.33MHz on Xilinx Spartan-6 FPGA.