Multimodal microscopy for automated histologic analysis of prostate cancer

<p>Abstract</p> <p>Background</p> <p>Prostate cancer is the single most prevalent cancer in US men whose gold standard of diagnosis is histologic assessment of biopsies. Manual assessment of stained tissue of all biopsies limits speed and accuracy in clinical practice and research of prostate cancer diagnosis. We sought to develop a fully-automated multimodal microscopy method to distinguish cancerous from non-cancerous tissue samples.</p> <p>Methods</p> <p>We recorded chemical data from an unstained tissue microarray (TMA) using Fourier transform infrared (FT-IR) spectroscopic imaging. Using pattern recognition, we identified epithelial cells without user input. We fused the cell type information with the corresponding stained images commonly used in clinical practice. Extracted morphological features, optimized by two-stage feature selection method using a minimum-redundancy-maximal-relevance (mRMR) criterion and sequential floating forward selection (SFFS), were applied to classify tissue samples as cancer or non-cancer.</p> <p>Results</p> <p>We achieved high accuracy (area under ROC curve (AUC) >0.97) in cross-validations on each of two data sets that were stained under different conditions. When the classifier was trained on one data set and tested on the other data set, an AUC value of ~0.95 was observed. In the absence of IR data, the performance of the same classification system dropped for both data sets and between data sets.</p> <p>Conclusions</p> <p>We were able to achieve very effective fusion of the information from two different images that provide very different types of data with different characteristics. The method is entirely transparent to a user and does not involve any adjustment or decision-making based on spectral data. By combining the IR and optical data, we achieved high accurate classification.</p

The Burning Bush: Linking LiDAR-derived Shrub Architecture to Flammability

Light detection and ranging (LiDAR) and terrestrial laser scanning (TLS) sensors are powerful tools for characterizing vegetation structure and for constructing three-dimensional (3D) models of trees, also known as quantitative structural models (QSM). 3D models and structural traits derived from them provide valuable information for biodiversity conservation, forest management, and fire behavior modeling. However, vegetation studies and 3D modeling methodologies often only focus on the forest canopy, with little attention given to understory vegetation. In particular, 3D structural information of shrubs is limited or not included in fire behavior models. Yet, understory vegetation is an important component of forested ecosystems, and has an essential role in determining fire behavior. In this dissertation, I explored the use of TLS data and quantitative structure models to model shrub architecture in three related studies. In the first study, I present a semi-automated methodology for reconstructing architecturally different shrubs from TLS LiDAR. By investigating shrubs with different architectures and point cloud densities, I showed that occlusion, shrub complexity, and shape greatly affect the accuracy of shrub models. In my second study, I assessed the 3D architectural drivers of understory flammability by evaluating the use of architectural metrics derived from the TLS point cloud and 3D reconstructions of the shrubs. I focused on eight species common in the understory of the fire-prone longleaf pine forest ecosystem of the state of Florida, USA. I found a general tendency for each species to be associated with a unique combination of flammability and architectural traits. Novel shrub architectural traits were found to be complementary to the direct use of TLS data and improved flammability predictions. The inherent complexity of shrub architecture and uncertainty in the TLS point cloud make scaling up from an individual shrub to a plot level a challenging task. Therefore, in my third study, I explored the effects of lidar uncertainty on vegetation parameter prediction accuracy. I developed a practical workflow to create synthetic forest stands with varying densities, which were subsequently scanned with simulated terrestrial lidar. This provided data sets quantitatively similar to those created by real-world LiDAR measurements, but with the advantage of exact knowledge of the forest plot parameters, The results showed that the lidar scan location had a large effect on prediction accuracy. Furthermore, occlusion is strongly related to the sampling density and plot complexity. The results of this study illustrate the potential of non-destructive lidar approaches for quantifying shrub architectural traits. TLS, empirical quantitative structural models, and synthetic models provide valuable insights into shrub structure and fire behavior

Investigating the use of Raman spectroscopy as a histopathological tool to identify metastatic brain tumours and their sites of origin

It is reported that 13,000 people in the UK are diagnosed with tumours in the brain every year, of which 60% are metastatic. Current methods for diagnosing the disease can be subjective, invasive and have long diagnostic windows. Raman spectroscopy provides a non-destructive, non-invasive, rapid and economical method for diagnosis. The aim of this study was to assess the use of Raman and immersion Raman spectroscopy for diagnosing metastatic brain and glioblastoma multiforme tumours and identifying primary sites of origin, and investigate the substrate effect on sample preparation and resultant spectra. The tissue specimens used in this study were formalin fixed-paraffin preserved and were supported on spectroscopic substrates for analysis. Samples were dewaxed prior to analysis to reduce/eliminate the paraffin contributions in the Raman spectra. The substrate was shown to have a significant influence on this dewaxing procedure and thus resulting spectra. It was also observed that specimens on CaF2 and Spectrosil quartz retained paraffin after dewaxing, whereas specimens on Low-E substrates did not. Through data examination, the 721 cm-1 and 782 cm-1 peaks were identified as being the most distinct peaks for discriminating between glioblastoma multiforme, metastatic and normal brain tissue spectra. A ratio score plot of these peaks determined classification sensitivities and specificities as 100% and 94.44% for glioblastoma multiforme, 96.55% and 100% for metastatic brain, and 85.71% and 100% for normal brain tissue respectively. Cancerous tissue was observed to retain more wax than normal tissue. This difference in dewaxing efficiency was attributed to alterations in tissue density between the histological types. Principle component-discriminant function analysis revealed separation between metastatic sites: breast, lung, melanoma, colon/rectum and oesophagus and stomach, showing the potential of Raman spectroscopy to identify primary sites of origin from metastatic brain tissue. Overall, this study demonstrated the diagnostic ability of Raman spectroscopy and the importance of substrate influence on tissue preparation and the quality of spectra

Detection, identification, and quantification of fungal diseases of sugar beet leaves using imaging and non-imaging hyperspectral techniques

Plant diseases influence the optical properties of plants in different ways. Depending on the host pathogen system and disease specific symptoms, different regions of the reflectance spectrum are affected, resulting in specific spectral signatures of diseased plants. The aim of this study was to examine the potential of hyperspectral imaging and non-imaging sensor systems for the detection, differentiation, and quantification of plant diseases. Reflectance spectra of sugar beet leaves infected with the fungal pathogens Cercospora beticola, Erysiphe betae, and Uromyces betae causing Cercospora leaf spot, powdery mildew, and sugar beet rust, respectively, were recorded repeatedly during pathogenesis. Hyperspectral data were analyzed using various methods of data and image analysis and were compared to ground truth data. Several approaches with different sensors on the measuring scales leaf, canopy, and field have been tested and compared. Much attention was paid on the effect of spectral, spatial, and temporal resolution of hyperspectral sensors on disease recording. Another focus of this study was the description of spectral characteristics of disease specific symptoms. Therefore, different data analysis methods have been applied to gain a maximum of information from spectral signatures. Spectral reflectance of sugar beet was affected by each disease in a characteristic way, resulting in disease specific signatures. Reflectance differences, sensitivity, and best correlating spectral bands differed depending on the disease and the developmental stage of the diseases. Compared to non-imaging sensors, the hyperspectral imaging sensor gave extra information related to spatial resolution. The preciseness in detecting pixel-wise spatial and temporal differences was on a high level. Besides characterization of diseased leaves also the assessment of pure disease endmembers as well as of different regions of typical symptoms was realized. Spectral vegetation indices (SVIs) related to physiological parameters were calculated and correlated to the severity of diseases. The SVIs differed in their sensitivity to the different diseases. Combining the information from multiple SVIs in an automatic classification method with Support Vector Machines, high sensitivity and specificity for the detection and differentiation of diseased leaves was reached in an early stage. In addition to the detection and identification, the quantification of diseases was possible with high accuracy by SVIs and Spectral Angle Mapper classification, calculated from hyperspectral images. Knowledge from measurements under controlled condition was carried over to the field scale. Early detection and monitoring of Cercospora leaf spot and powdery mildew was facilitated. The results of this study contribute to a better understanding of plant optical properties during disease development. Methods will further be applicable in precision crop protection, to realize the detection, differentiation, and quantification of plant diseases in early stages.Nachweis, Identifizierung und Quantifizierung pilzlicher Blattkrankheiten der Zuckerrübe mit abbildenden und nicht-abbildenden hyperspektralen Sensoren Pflanzenkrankheiten wirken sich auf die optischen Eigenschaften von Pflanzen in unterschiedlicher Weise aus. Verschiedene Bereiche des Reflektionsspektrums werden in Abhängigkeit von Wirt-Pathogen System und krankheitsspezifischen Symptomen beeinflusst. Hyperspektrale, nicht-invasive Sensoren bieten die Möglichkeit, optische Veränderungen zu einem frühen Zeitpunkt der Krankheitsentwicklung zu detektieren. Ziel dieser Arbeit war es, das Potential hyperspektraler abbildender und nicht abbildender Sensoren für die Erkennung, Identifizierung und Quantifizierung von Pflanzenkrankheiten zu beurteilen. Zuckerrübenblätter wurden mit den pilzlichen Erregern Cercospora beticola, Erysiphe betae bzw. Uromyces betae inokuliert und die Auswirkungen der Entwicklung von Cercospora Blattflecken, Echtem Mehltau bzw. Rübenrost auf die Reflektionseigenschaften erfasst und mit optischen Bonituren verglichen. Auf den Skalenebenen Blatt, Bestand und Feld wurden Messansätze mit unterschiedlichen Sensoren verglichen. Besonders berücksichtigt wurden hierbei Anforderungen an die spektrale, räumliche und zeitliche Auflösung der Sensoren. Ein weiterer Schwerpunkt lag auf der Beschreibung der spektralen Eigenschaften von charakteristischen Symptomen. Verschiedene Auswerteverfahren wurden mit dem Ziel angewendet, einen maximalen Informationsgehalt aus spektralen Signaturen zu gewinnen. Jede Krankheit beeinflusste die spektrale Reflektion von Zuckerrübenblättern auf charakteristische Weise. Differenz der Reflektion, Sensitivität sowie Korrelation der spektralen Bänder zur Befallsstärke variierten in Abhängigkeit von den Krankheiten. Eine höhere Präzision durch die pixelweise Erfassung räumlicher und zeitlicher Unterschiede von befallenem und gesundem Gewebe konnte durch abbildende Sensoren erreicht werden. Spektrale Vegetationsindizes (SVIs), mit Bezug zu pflanzenphysiologischen Parametern wurden aus den Hyperspektraldaten errechnet und mit der Befallsstärke korreliert. Die SVIs unterschieden sich in ihrer Sensitivität gegenüber den drei Krankheiten. Durch den Einsatz von maschinellem Lernen wurde die kombinierte Information der errechneten Vegetationsindizes für eine automatische Klassifizierung genutzt. Eine hohe Sensitivität sowie eine hohe Spezifität bezüglich der Erkennung und Differenzierung von Krankheiten wurden erreicht. Eine Quantifizierung der Krankheiten war neben der Detektion und Identifizierung mittels SVIs bzw. Klassifizierung mit Spektral Angle Mapper an hyperspektralen Bilddaten möglich. Die Ergebnisse dieser Arbeit tragen zu einem besseren Verständnis der optischen Eigenschaften von Pflanzen unter Pathogeneinfluss bei. Die untersuchten Methoden bieten die Möglichkeit in Anwendungen des Präzisionspflanzenschutzes implementiert zu werden, um eine frühzeitige Erkennung, Differenzierung und Quantifizierung von Pflanzenkrankheiten zu ermöglichen

Natural variations in the biofilm-associated protein BslA from the genus <i>Bacillus</i>

AbstractBslA is a protein secreted by Bacillus subtilis which forms a hydrophobic film that coats the biofilm surface and renders it water-repellent. We have characterised three orthologues of BslA from Bacillus amyloliquefaciens, Bacillus licheniformis and Bacillus pumilus as well as a paralogue from B. subtilis called YweA. We find that the three orthologous proteins can substitute for BslA in B. subtilis and confer a degree of protection, whereas YweA cannot. The degree to which the proteins functionally substitute for native BslA correlates with their in vitro biophysical properties. Our results demonstrate the use of naturally-evolved variants to provide a framework for teasing out the molecular basis of interfacial self-assembly.</jats:p