Image segmentation is important with applications to several problems in biology and medicine. While extensively researched, generally, current segmentation methods perform adequately in the applications for which they were designed, but often require extensive modifications or calibrations before used in a different application. We describe a system that, with few modifications, can be used in a variety of image segmentation problems. The system is based on a supervised learning strategy that utilizes intensity neighborhoods to assign each pixel in a test image its correct class based on training data. In summary, we have several innovations: (1) A general framework for such a system is proposed, where rotations and variations of intensity neighborhoods in scales are modeled, and a multi-scale classification framework is utilized to segment unknown images; (2) A fast algorithm for training data selection and pixel classification is presented, where a majority voting based criterion is proposed for selecting a small subset from raw training set. When combined with 1-nearest neighbor (1-NN) classifier, such an algorithm is able to provide descent classification accuracy within reasonable computational complexity. (3) A general deformable model for optimization of segmented regions is proposed, which takes the decision values from previous pixel classification process as input, and optimize the segmented regions in a partial differential equation (PDE) framework. We show that the performance of this system in several different biomedical applications, such as tissue segmentation tasks in magnetic resonance and histopathology microscopy images, as well as nuclei segmentation from fluorescence microscopy images, is similar or better than several algorithms specifically designed for each of these applications. In addition, we describe another general segmentation system for biomedical applications where a strong prior on shape is available (e.g. cells, nuclei). The idea is based on template matching and supervised learning, and we show the examples of segmenting cells and nuclei from microscopy images. The method uses examples selected by a user for building a statistical model which captures the texture and shape variations of the nuclear structures from a given data set to be segmented. Segmentation of subsequent, unlabeled, images is then performed by finding the model instance that best matches (in the normalized cross correlation sense) local neighborhood in the input image. We demonstrate the application of our method to segmenting cells and nuclei from a variety of imaging modalities, and quantitatively compare our results to several other methods. Quantitative results using both simulated and real image data show that, while certain methods may work well for certain imaging modalities, our software is able to obtain high accuracy across several imaging modalities studied. Results also demonstrate that, relative to several existing methods, the template based method we propose presents increased robustness in the sense of better handling variations in illumination, variations in texture from different imaging modalities, providing more smooth and accurate segmentation borders, as well as handling better cluttered cells and nuclei.

Geospatial analysis involves application of statistical methods, algorithms and information retrieval techniques to geospatial data. It incorporates time into spatial databases and facilitates investigation of land cover (LC) dynamics through data, model, and analytics. LC dynamics induced by human and natural processes play a major role in global as well as regional scale patterns, which in turn influence weather and climate. Hence, understanding LC dynamics at the local / regional as well as at global levels is essential to evolve appropriate management strategies to mitigate the impacts of LC changes. This can be captured through the multi-resolution remote sensing (RS) data. However, with the advancements in sensor technologies, suitable algorithms and techniques are required for optimal integration of information from multi-resolution sensors which are cost effective while overcoming the possible data and methodological constraints. In this work, several per-pixel traditional and advanced classification techniques have been evaluated with the multi-resolution data along with the role of ancillary geographical data on the performance of classifiers. Techniques for linear and non-linear un-mixing, endmember variability and determination of spatial distribution of class components within a pixel have been applied and validated on multi-resolution data. Endmember estimation method is proposed and its performance is compared with manual, semi-automatic and fully automatic methods of endmember extraction. A novel technique - Hybrid Bayesian Classifier is developed for per pixel classification where the class prior probabilities are determined by un-mixing a low spatial-high spectral resolution multi-spectral data while posterior probabilities are determined from the training data obtained from ground, that are assigned to every pixel in a high spatial-low spectral resolution multi-spectral data in Bayesian classification. These techniques have been validated with multi-resolution data for various landscapes with varying altitudes. As a case study, spatial metrics and cellular automata based models applied for rapidly urbanising landscape with moderate altitude has been carried out.

The aim of this study was to propose a non-destructive method for measuring Pinus sylvestris seedlings, to determine whether water stress would be evident in laboratory spectra of pines, to compare whether the response of pines would differ by ecotype, and to investigate whether two ecotypes of Pinus sylvestris could be distinguished using laboratory and image spectroscopy. For these purposes, hyperspectral images of seed orchards from August 2020 were processed and a three-month laboratory experiment was conducted, in which stress from water deficit was induced in two-year-old pine seedlings from the upland and hilly ecotypes. Spectral data were analysed using mixed statistical models, analysis of variance, principal component analysis, training of supervised pixel classifiers, vegetation indices, and linear regression. Based on the analyses, it was found that water stress can be detected in severely stressed Pinus sylvestris seedlings. The most sensitive spectral bands to water content were observed in the region between 1000-2500 nm. The initial response to water stress did not differ by ecotype, but a faster recovery was observed at the upland ecotype after the period of draught. The two Pinus sylvestris ecotypes were distinguished with high accuracy from both laboratory and image spectral...