Development of Techniques for the Automatic Extraction and Grade Detection of Glioma Tumors from Conventional Brain Magnetic Resonant Images

Cerebral glioma is the most prevalent primary brain tumor, which are classified broadly into low and high grades according to the degree of malignancy. High grade gliomas are highly malignant which possess a poor prognosis, and the patients survive less than eighteen months after diagnosis. Low grade gliomas are slow growing, least malignant and has better response to therapy. To date, histological grading is used as the standard technique for diagnosis, treatment planning and survival prediction. The main objective of this thesis is to propose novel methods for automatic extraction of low and high grade glioma and other brain tissues, grade detection techniques for glioma using conventional magnetic resonance imaging (MRI) modalities and 3D modelling of glioma from segmented tumor slices in order to assess the growth rate of tumors. Two new methods are developed for extracting tumor regions, of which the second method, named as Adaptive Gray level Algebraic set Segmentation Algorithm (AGASA) can also extract white matter and grey matter from T1 FLAIR an T2 weighted images. The methods were validated with manual Ground truth images, which showed promising results. The developed methods were compared with widely used Fuzzy c-means clustering technique and the robustness of the algorithm with respect to noise is also checked for different noise levels. Image texture can provide significant information on the (ab)normality of tissue, and this thesis expands this idea to tumour texture grading and detection. Based on the thresholds of discriminant first order and gray level cooccurrence matrix based second order statistical features three feature sets were formulated and a decision system was developed for grade detection of glioma from conventional T2 weighted MRI modality.The quantitative performance analysis using ROC curve showed 99.03% accuracy for distinguishing between advanced (aggressive) and early stage (non-aggressive) malignant glioma. The developed brain texture analysis techniques can improve the physician’s ability to detect and analyse pathologies leading to a more reliable diagnosis and treatment of disease. The segmented tumors were also used for volumetric modelling of tumors which can provide an idea of the growth rate of tumor; this can be used for assessing response to therapy and patient prognosis.

Statistical evaluation of texture analysis from the biocrystallization method

The consumers are becoming more concerned about food quality, especially regarding how, when and where the foods are produced (Haglund et al., 1999; Kahl et al., 2004; Alföldi, et al., 2006). Therefore, during recent years there has been a growing interest in the methods for food quality assessment, especially in the picture-development methods as a complement to traditional chemical analysis of single compounds (Kahl et al., 2006). The biocrystallization as one of the picture-developing method is based on the crystallographic phenomenon that when crystallizing aqueous solutions of dihydrate CuCl2 with adding of organic solutions, originating, e.g., from crop samples, biocrystallograms are generated with reproducible crystal patterns (Kleber & Steinike-Hartung, 1959). Its output is a crystal pattern on glass plates from which different variables (numbers) can be calculated by using image analysis. However, there is a lack of a standardized evaluation method to quantify the morphological features of the biocrystallogram image. Therefore, the main sakes of this research are (1) to optimize an existing statistical model in order to describe all the effects that contribute to the experiment, (2) to investigate the effect of image parameters on the texture analysis of the biocrystallogram images, i.e., region of interest (ROI), color transformation and histogram matching on samples from the project 020E170/F financed by the Federal Ministry of Food, Agriculture and Consumer Protection(BMELV).The samples are wheat and carrots from controlled field and farm trials, (3) to consider the strongest effect of texture parameter with the visual evaluation criteria that have been developed by a group of researcher (University of Kassel, Germany; Louis Bolk Institute (LBI), Netherlands and Biodynamic Research Association Denmark (BRAD), Denmark) in order to clarify how the relation of the texture parameter and visual characteristics on an image is. The refined statistical model was accomplished by using a lme model with repeated measurements via crossed effects, programmed in R (version 2.1.0). The validity of the F and P values is checked against the SAS program. While getting from the ANOVA the same F values, the P values are bigger in R because of the more conservative approach. The refined model is calculating more significant P values. The optimization of the image analysis is dealing with the following parameters: ROI(Region of Interest which is the area around the geometrical center), color transformation (calculation of the 1 dimensional gray level value out of the three dimensional color information of the scanned picture, which is necessary for the texture analysis), histogram matching (normalization of the histogram of the picture to enhance the contrast and to minimize the errors from lighting conditions). The samples were wheat from DOC trial with 4 field replicates for the years 2003 and 2005, “market samples”(organic and conventional neighbors with the same variety) for 2004 and 2005, carrot where the samples were obtained from the University of Kassel (2 varieties, 2 nitrogen treatments) for the years 2004, 2005, 2006 and “market samples” of carrot for the years 2004 and 2005. The criterion for the optimization was repeatability of the differentiation of the samples over the different harvest(years). For different samples different ROIs were found, which reflect the different pictures. The best color transformation that shows efficiently differentiation is relied on gray scale, i.e., equal color transformation. The second dimension of the color transformation only appeared in some years for the effect of color wavelength(hue) for carrot treated with different nitrate fertilizer levels. The best histogram matching is the Gaussian distribution. The approach was to find a connection between the variables from textural image analysis with the different visual criteria. The relation between the texture parameters and visual evaluation criteria was limited to the carrot samples, especially, as it could be well differentiated by the texture analysis. It was possible to connect groups of variables of the texture analysis with groups of criteria from the visual evaluation. These selected variables were able to differentiate the samples but not able to classify the samples according to the treatment. Contrarily, in case of visual criteria which describe the picture as a whole there is a classification in 80% of the sample cases possible. Herewith, it clearly can find the limits of the single variable approach of the image analysis (texture analysis).

Development of a method fon non-destructive testing of fruits using scanning laser vibrometry (SLV)

Quality control on fruits requires reliable methods, able to assess with reasonable accuracy and possibly in a non-destructive way their physical and chemical characteristics. More specifically, a decreased firmness indicates the presence of damage or defects in the fruit or else that the fruit has exceeded its “best before date”, becoming unsuitable for consumption. In high-value exotic fruits, such as mangoes, where firmness cannot be easily measured from a simple observation of texture, colour changes and unevenness of fruits surface, the use of non-destructive techniques is highly recommendable. In particular, the application of Laser vibrometry, based on the Doppler effect, a non-contact technique sensitive to differences in displacements inferior to the nanometre, appears ideal for a possible on-line control on food. Previous results indicated that a phase shift can be in a repeatable way associated with the presence of damage on the fruit, whilst a decreased firmness results in significant differences in the displacement of the fruits under the same excitation signal. In this work, frequency ranges for quality control via the application of a sound chirp are suggested, based on the measurement of the signal coherence. The variations of the average vibration spectrum of a grid of points, or of point-by-point signal velocity allows the go-no go recognition of “firm” and “over-ripe” fruits, with notable success in the particular case of mangoes. The future exploitation of this work will include the application of this method to allow on-line control during conveyor belt distribution of fruits.

A SEPALLATA gene is involved in the development and ripening of strawberry (Fragaria X ananassa Duch.) fruit, a non-climacteric tissue

Climacteric and non-climacteric fruits have traditionally been viewed as representing two distinct programmes of ripening associated with differential respiration and ethylene hormone effects. In climacteric fruits, such as tomato and banana, the ripening process is marked by increased respiration and is induced and co-ordinated by ethylene, while in non-climacteric fruits, such as strawberry and grape, it is controlled by an ethylene-independent process with little change in respiration rate. The two contrasting mechanisms, however, both lead to texture, colour, and flavour changes that probably reflect some common programmes of regulatory control. It has been shown that a SEPALLATA(SEP)4-like gene is necessary for normal ripening in tomato. It has been demonstrated here that silencing a fruit-related SEP1/2-like (FaMADS9) gene in strawberry leads to the inhibition of normal development and ripening in the petal, achene, and receptacle tissues. In addition, analysis of transcriptome profiles reveals pleiotropic effects of FaMADS9 on fruit development and ripening-related gene expression. It is concluded that SEP genes play a central role in the developmental regulation of ripening in both climacteric and non-climacteric fruits. These findings provide important information to extend the molecular control of ripening in a non-climacteric fruit beyond the limited genetic and cultural options currently available.

Texture analysis using graphs generated by deterministic partially self-avoiding walks

Texture is one of the most important visual attributes for image analysis. It has been widely used in image analysis and pattern recognition. A partially self-avoiding deterministic walk has recently been proposed as an approach for texture analysis with promising results. This approach uses walkers (called tourists) to exploit the gray scale image contexts in several levels. Here, we present an approach to generate graphs out of the trajectories produced by the tourist walks. The generated graphs embody important characteristics related to tourist transitivity in the image. Computed from these graphs, the statistical position (degree mean) and dispersion (entropy of two vertices with the same degree) measures are used as texture descriptors. A comparison with traditional texture analysis methods is performed to illustrate the high performance of this novel approach. (C) 2011 Elsevier Ltd. All rights reserved.

Properties of ectin isolated from Lawulu (Crysophylum roxbergi G Don) and development of jam and fruit leather using Lawulu and pineapple

Lawulu fruit (Crysophylum roxberghi GDon) possess nutritional, medicinal and functional properties. However, it is less consumed due to its  characteristic off flavour. The present study was carried out to investigate the potential of utilizing lawulu fruit for isolation of pectin and to develop jam and fruit leather. Products were evaluated based on physico-chemical and sensory properties.

Pectin isolated fromf irm ripe lawuluf ruit using 0.1 M hydrochloric acid  followed by 96% ethanol precipitation yielded 7. 3% pectin on wet weight basis and 26.1% on dry weight basis. The isolated pectin contained 0.74% ash, 0.02% acetyl content and 7.85% methoxyl content with equivalent weight 993.5. These values were comparable with commercial high methoxyl pectin. In addition, Iawulu pectin at 1.5% concentration formed a gel within 12-14 min in the presence of 68% sucrose and 0.5% citric acid.

Jam was prepared by using Iawulu-pineapple ratio as 1:2, 1:1 and 2:1 respectively. The gel strength of jam (65⁰ Brix and pH 3.1) at 0.35% commercial high methoxyl pectin was comparable with commercial mixed fruit jam. Sensory evaluation indicated a significant preference (p<.05) for jam containing lawulu-pineapple ratio of 1:2 and 1.1 respectively overthe ratio of 2:1. With increased lawulu percentage both yellowness and lightness of jam increased significantly (p<0.05).

Fruit leather was prepared by changing lawulu-pineapple ratio as 1:2, 1:1 and 2:1 respectively with 20% sucrose, 0.3% citric acid, 0.05% pectin and 100 ppm potassium metabisulphite followed by drying at 65±1⁰C for 12-14 h. Sensory evaluation data revealed that changes in lawulu-pineapple ratio had no significant effect on taste, texture and overall quality of fruit leather.   However, significant preference (p<0.05) for colour was observed with increasing lawulu percentage. Both yellowness (b' value) and lightness (L'value) of fruit leather were sign[icantly increased (p<0.05) with increasing lawulu percentage.

Identification of cashmere and superfine merino wool with wavelet texture analysis

This paper presents the use of the wavelet transform to extract fibre surface texture features for classifying cashmere and superfine merino wool fibres. To extract features from brightness variations caused by the cuticular scale height, shape and interval provides an effective way for characterising different animal fibres and subsequently classifying them. This may enable the development of a completely automated and objective system for animal fibre
identification.

Identification of animal fibers with wavelet texture analysis

This paper presents the use of the wavelet transform to extract fiber surface texture features for classifying cashmere and superfine merino wool fibers. Extracting features from brightness variations caused by the cuticular scale height, shape and interval provides an effective way for characterizing different animal fibers and subsequently classifying them. This may enable the development of a completely automated and objective system for animal fiber identification.

On the characteristics of substructure development through dynamic recrystallization

Substructure development in an austenitic Ni-30%Fe model alloy was investigated within a dynamic recrystallization (DRX) regime. The substructure characteristics of the deformed matrix and DRX grains were markedly different regardless of the grain size and orientation. The former largely displayed 'organized', banded subgrain arrangements with alternating misorientations, resulting from a limited number of active slip systems. In contrast, the substructure of DRX grains was generally more 'random' and exhibited complex subgrain/cell arrangements characterized by local accumulation of misorientations, suggesting multiple slip. The proposed mechanism of the unique substructure development within DRX grains suggests that the DRX nuclei, forming along pre-existing grain boundaries and triple points, essentially represent grain boundary regions, which experience multiple slip to preserve the compatibility with neighbouring deformed grains. This results in the formation of a complex cell/subgrain structure, which progressively extends as the grain boundary regions expand outwards during DRX growth.

Substructure development through dynamic recrystallisation in an austenitic Ni–30%Fe alloy

This data looks at the effect of grain boundary movement on the characteristics of substructure development within the DRX regime. Different thermo-mechanical processing routes were employed to produce a range of DRX grain sizes at a given deformation temperature. The development of dislocation substructure was investigated using electron back-scattered diffraction (EBSD) in conjunction with transmission electron microscopy (TEM).

On the characteristics of substructure development through dynamic recrystallization

This body of data is the result of an investigation into the effect of grain boundary movement on the characteristics of substructure development in an austenitic Ni-30%Fe model alloy within the DRX regime. Different thermo-mechanical processing routes were employed to produce a range of DRX grain sizes at a given deformation temperature. The development of dislocation substructure was investigated using electron back-scattered diffraction (EBSD) in conjunction with transmission electron microscopy (TEM).

Development of asymmetric rolling for the better control over structure and mechanical properties in IF steel

In the present study, the effects of kinematic and geometric asymmetries in rolling during multi-pass processing of IF steel are examined. The theoretical investigation by final element simulations and experimental investigations by means of electron-backscatter diffraction analysis and tensile tests suggest that asymmetric rolling increases the total imposed strain compared to symmetric rolling, and largely re-distributes the strain components due to additional shear. This enhances the intensity of grain refinement, strengthens and tilts crystallographic orientations, and increases mechanical strength. The effect is highest in the asymmetric rolling with differential roll diameters.

Effective grain orientation on the substructure development of 304 stainless steel and NA-30% fe

This data is the result of an investigation into the effect of grain orientation on the substructure development of 304 stainless steel and a Ni-30wt.%Fe alloy. Both alloys have been used as model alloys to study the high temperature deformation of austenite. The development of the dislocation substructure as a function of strain, temperature and grain orientation was investigated using a combination of electron backscatterd diffraction (EBSD) and transmission electron microscopy (TEM).

Substructure and texture characteristics of the deformed matrix and dynamically recrystallized grains in a Ni-30%Fe austenitic alloy

The substructure and crystallographic texture characteristics of both the deformed matrix and dynamically recrystallized (DRX) grains were investigated in a Ni-30%Fe austenitic model alloy subjected to hot torsion. Deformation was performed at a temperature of 1000°C using strain rates of 1, 0.1 and 0.01 s-1, which produced a range of DRX grain sizes. Electron back-scattered diffraction and transmission electron microscopy were employed in the investigation. Both the deformed matrix and DRX grains revealed the texture components expected for simple shear deformation by crystallographic slip. The texture of DRX grains was dominated by low Taylor factor components as a result of their lower consumption rate during growth of these grains. There was a marked difference in the substructure characteristics between the deformed matrix and DRX grains regardless of the grain size and orientation. The deformed matrix substructure was largely characterized by organized, banded subgrain arrangements with alternating misorientations. By contrast, the substructure of DRX grains was generally more random in character and displayed complex, more equiaxed subgrain/cell arrangements characterized by local accumulation of misorientations. Based on the experimental observations, a mechanism of the distinct substructure development within DRX grains has been proposed.

Development of boundary misorientations during grain growth in silicon steels

Changes in grain size, texture and misorientation distributions have been monitored during extensive normal grain growth in 3%Si steels. The boundary misorientation distributions deviate significantly from the Mackenzie relationship. Comparisons of correlated and uncorrelated distributions show large excesses of low angle boundaries. However, these are not a result of low energy boundaries being favoured during grain growth since the deviation diminishes as growth proceeds. The effect originates in the nucleation of grains in colonies of similar orientation during primary recrystallisation. A slight tendency for promotion of 60º boundaries may indicate some preference for the retention of lower energy twin boundaries during grain growth in silicon steel.