Pollen segmentation and feature evaluation for automatic classification in bright-field microscopy

14 págs.; 10 figs.; 7 tabs.; 1 app.© 2014 Elsevier B.V. Besides the well-established healthy properties of pollen, palynology and apiculture are of extreme importance to avoid hard and fast unbalances in our ecosystems. To support such disciplines computer vision comes to alleviate tedious recognition tasks. In this paper we present an applied study of the state of the art in pattern recognition techniques to describe, analyze, and classify pollen grains in an extensive dataset specifically collected (15 types, 120 samples/type). We also propose a novel contour-inner segmentation of grains, improving 50% of accuracy. In addition to published morphological, statistical, and textural descriptors, we introduce a new descriptor to measure the grain's contour profile and a logGabor implementation not tested before for this purpose. We found a significant improvement for certain combinations of descriptors, providing an overall accuracy above 99%. Finally, some palynological features that are still difficult to be integrated in computer systems are discussed.This work has been supported by the European project APIFRESH FP7-SME-2008-2 ‘‘Developing European standards for bee pollen and royal jelly: quality, safety and authenticity’’ and we would like to thank to Mr. Walter Haefeker, President of the European Professional Beekeepers Association (EPBA). J. Victor Marcos is a ‘‘Juan de la Cierva’’ research fellow funded by the Spanish Ministry of Economy and Competitiveness. Rodrigo Nava thanks Consejo Nacional de Ciencia y Tecnología (CONACYT) and PAPIIT Grant IG100814.Peer Reviewe

Hardware and software integration and testing for the automation of bright-field microscopy for tuberculosis detection

Automated microscopy for the detection of tuberculosis (TB) in sputum smears would reduce the load on technicians, especially in countries with a high TB burden. This dissertation reports on the development and testing of an automated system built around a conventional microscope for the detection of TB in Ziehl-Neelsen (ZN) stained sputum smears. Microscope auto-focusing, image analysis and stage movement were integrated. Images were captured at 40x magnification

On Invariance, Equivariance, Correlation and Convolution of Spherical Harmonic Representations for Scalar and Vectorial Data

The mathematical representations of data in the Spherical Harmonic (SH) domain has recently regained increasing interest in the machine learning community. This technical report gives an in-depth introduction to the theoretical foundation and practical implementation of SH representations, summarizing works on rotation invariant and equivariant features, as well as convolutions and exact correlations of signals on spheres. In extension, these methods are then generalized from scalar SH representations to Vectorial Harmonics (VH), providing the same capabilities for 3d vector fields on spheresComment: 106 pages, tech repor

Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data

Image matching techniques are proven to be necessary in various fields of science and engineering, with many new methods and applications introduced over the years. In this PhD thesis, several computational image matching methods are introduced and investigated for improving the analysis of various biomedical image data. These improvements include the use of matching techniques for enhancing visualization of cross-sectional imaging modalities such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), denoising of retinal Optical Coherence Tomography (OCT), and high quality 3D reconstruction of surfaces from Scanning Electron Microscope (SEM) images. This work greatly improves the process of data interpretation of image data with far reaching consequences for basic sciences research. The thesis starts with a general notion of the problem of image matching followed by an overview of the topics covered in the thesis. This is followed by introduction and investigation of several applications of image matching/registration in biomdecial image processing: a) registration-based slice interpolation, b) fast mesh-based deformable image registration and c) use of simultaneous rigid registration and Robust Principal Component Analysis (RPCA) for speckle noise reduction of retinal OCT images. Moving towards a different notion of image matching/correspondence, the problem of view synthesis and 3D reconstruction, with a focus on 3D reconstruction of microscopic samples from 2D images captured by SEM, is considered next. Starting from sparse feature-based matching techniques, an extensive analysis is provided for using several well-known feature detector/descriptor techniques, namely ORB, BRIEF, SURF and SIFT, for the problem of multi-view 3D reconstruction. This chapter contains qualitative and quantitative comparisons in order to reveal the shortcomings of the sparse feature-based techniques. This is followed by introduction of a novel framework using sparse-dense matching/correspondence for high quality 3D reconstruction of SEM images. As will be shown, the proposed framework results in better reconstructions when compared with state-of-the-art sparse-feature based techniques. Even though the proposed framework produces satisfactory results, there is room for improvements. These improvements become more necessary when dealing with higher complexity microscopic samples imaged by SEM as well as in cases with large displacements between corresponding points in micrographs. Therefore, based on the proposed framework, a new approach is proposed for high quality 3D reconstruction of microscopic samples. While in case of having simpler microscopic samples the performance of the two proposed techniques are comparable, the new technique results in more truthful reconstruction of highly complex samples. The thesis is concluded with an overview of the thesis and also pointers regarding future directions of the research using both multi-view and photometric techniques for 3D reconstruction of SEM images

Addressing subjectivity in the classification of palaeoenvironmental remains with supervised deep learning convolutional neural networks

Archaeological object identifications have been traditionally undertaken through a comparative methodology where each artefact is identified through a subjective, interpretative act by a professional. Regarding palaeoenvironmental remains, this comparative methodology is given boundaries by using reference materials and codified sets of rules, but subjectivity is nevertheless present. The problem with this traditional archaeological methodology is that higher level of subjectivity in the identification of artefacts leads to inaccuracies, which then increases the potential for Type I and Type II errors in the testing of hypotheses. Reducing the subjectivity of archaeological identifications would improve the statistical power of archaeological analyses, which would subsequently lead to more impactful research. In this thesis, it is shown that the level of subjectivity in palaeoenvironmental research can be reduced by applying deep learning convolutional neural networks within an image recognition framework. The primary aim of the presented research is therefore to further the on-going paradigm shift in archaeology towards model-based object identifications, particularly within the realm of palaeoenvironmental remains. Although this thesis focuses on the identification of pollen grains and animal bones, with the latter being restricted to the astragalus of sheep and goats, there are wider implications for archaeology as these methods can easily be extended beyond pollen and animal remains. The previously published POLEN23E dataset is used as the pilot study of applying deep learning in pollen grain classification. In contrast, an image dataset of modern bones was compiled for the classification of sheep and goat astragali due to a complete lack of available bone image datasets and a double blind study with inexperienced and experienced zooarchaeologists was performed to have a benchmark to which image recognition models can be compared. In both classification tasks, the presented models outperform all previous formal modelling methods and only the best human analysts match the performance of the deep learning model in the sheep and goat astragalus separation task. Throughout the thesis, there is a specific focus on increasing trust in the models through the visualization of the models’ decision making and avenues of improvements to Grad-CAM are explored. This thesis makes an explicit case for the phasing out of the comparative methods in favour of a formal modelling framework within archaeology, especially in palaeoenvironmental object identification

Improved Multi-resolution Analysis of the Motion Patterns in Video for Human Action Classification

The automatic recognition of human actions in video is of great interest in many applications such as automated surveillance, content-based video summarization, video search, and indexing. The problem is challenging due to a wide range of variations among the motion pattern of a given action such as walking across different subjects and the low variations among similar motions such as running and jogging. This thesis has three contributions in a discriminative bottom-up framework to improve the multi-resolution analysis of the motion patterns in video for better recognition of human actions. The first contribution of this thesis is the introduction of a novel approach for a robust local motion feature detection in video. To this end, four different multi-resolution temporally causal and asymmetric filters of log Gaussian, scale-derivative Gaussian, Poisson, and asymmetric sinc are introduced. The performance of these filters is compared with the widely used multi-resolution Gabor filter in a common framework for detection of local salient motions. The features obtained from the asymmetric filtering are more precise and more robust under geometric deformations such as view change or affine transformations. Moreover, they provide higher classification accuracy when they are used with a standard bag-of-words representation of actions and a single discriminative classifier. The experimental results show that the asymmetric sinc performs the best. The Poisson and the scale-derivative Gaussian perform better than log Gaussian and that better than the symmetric temporal Gabor filter. The second contribution of this thesis is the introduction of an efficient action representation. The observation is that the salient features at different spatial and temporal scales characterize different motion information. A multi-resolution analysis of the motion characteristic should be representative of different actions. A multi-resolution action signature provides a more discriminative video representation. The third contribution of this thesis is on the classification of different human actions. To this end, an ensemble of classifiers in a multiple classifier systems (MCS) framework with a parallel topology is utilized. This framework can fully benefit from the multi-resolution characteristics of the motion patterns in the human actions. The classification combination concept of the MCS has been then extended to address two problems in the configuration setting of a recognition framework, namely the choice of distance metric for comparing the action representations and the size of the codebook by which an action is represented. This implication of MCS at multiple stages of the recognition pipeline provides a multi-stage MCS framework which outperforms the existing methods which use a single classifier. Based on the experimental results of the local feature detection and the action classification, the multi-stage MCS framework, which uses the multi-scale features obtained from the temporal asymmetric sinc filtering, is recommended for the task of human action recognition in video.1 yea

Biological image analysis

In biological research images are extensively used to monitor growth, dynamics and changes in biological specimen, such as cells or plants. Many of these images are used solely for observation or are manually annotated by an expert. In this dissertation we discuss several methods to automate the annotating and analysis of bio-images. Two large clusters of methods have been investigated and developed. A first set of methods focuses on the automatic delineation of relevant objects in bio-images, such as individual cells in microscopic images. Since these methods should be useful for many different applications, e.g. to detect and delineate different objects (cells, plants, leafs, ...) in different types of images (different types of microscopes, regular colour photographs, ...), the methods should be easy to adjust. Therefore we developed a methodology relying on probability theory, where all required parameters can easily be estimated by a biologist, without requiring any knowledge on the techniques used in the actual software. A second cluster of investigated techniques focuses on the analysis of shapes. By defining new features that describe shapes, we are able to automatically classify shapes, retrieve similar shapes from a database and even analyse how an object deforms through time

Investigations on chemometric approaches for diagnostic applications utilizing various combinations of spectral and image data types

In the presented work, several data fusion and machine learning approaches were explored within the frame of the data combination for various measurement techniques in biomedical applications. For each of the measurement techniques used in this work, the data was ana-lyzed by means of machine learning. Prior to applying these machine learning algorithms, a specific preprocessing pipeline for each type of data had to be established. These pipelines made it possible to standardize the data and to decrease sample-to-sample variations which originate from the instability of devices or small deviations in the sample preparation or measurement routine. The preprocessed data sets were used for various analyses of biological samples. Separate data analyses were performed for microscopic images, Raman spectra, and SERS data. However, this work mainly focused on the application of data fusion methods for the analy-sis of biological tissues and cells. To do so, different data fusion pipelines were constructed for each task, depending on the data structure. Both low-level (centralized) and high-level (distributed) data fusion approaches were tested and investigated within in this work. To demonstrate centralized and distributed data fusion, two examples were implemented for tissue investigation. In both examples, a combination of Raman spectroscopic and MALDI spectrometric data were analyzed. One example demonstrated centralized data fusion for the analysis of the chemical composition of a mouse brain section, and the other example employed distributed data fusion for liver cancer detection. Other data fusion examples were demonstrated for cell-based analysis. It was demonstrated that leukocyte cell subtype identification can be improved by a centralized data fusion of Raman spectroscopic data and morphological features obtained from microscopic images of stained cells. The last example presented in this work demonstrated a sepsis diagnostic pipeline based on the combination of Raman spectroscopic data and biomarkers. Besides the measured values, the demographic information of the patient was included in the analysis process for considering non-disease-related variations. During the construction of data fusion pipelines, such issues as unbalanced data contribu-tion, missing values, and variations that are not related to the investigated responses were faced. To resolve these issues, data weighting, missing data imputation, and the introduc-tion of additional responses were employed. For further improvement of analysis reliability, the data fusion pipelines and data processing routine were adjusted for each study in this work. As a result, the most suitable data fusion approach was found for every example, and a combination of the machine learning methods with data fusion approaches was demon-strated as a powerful tool for data analysis in biomedical applications

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp