Segmenting images with gradient-based edge detection using Membrane Computing

In this paper, we present a parallel implementation of a new algorithm for segmenting images with gradient-based edge detection by using techniques from Natural Computing. This bio-inspired parallel algorithm has been implemented in a novel device architecture called CUDA™(Compute Unified Device Architecture). The implementation has been designed via tissue P systems on the framework of Membrane Computing. Some examples and experimental results are also presented.Ministerio de Ciencia e Innovación TIN2008-04487-EMinisterio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08–TIC-04200Junta de Andalucía P06-TIC-02268Ministerio de Educación y Ciencia MTM2009-12716Universidad del Pais Vasco EHU09/0

Tissue-like P system for Segmentation of 2D Hexagonal Images

Membrane computing, which is a new computational model inspired by the structure and functioning of biological cells and by the way the cells are organized in tissues. MC has been adopted in many real world applications including image segmentation. In contrast to the traditional square grid for representing and sampling digital images, hexagonal grid is an alternative efficient mechanism which can better represents and visualizes the curved objects. In this paper, a tissue-like P system with region-based and edge-based segmentation is used to segment two dimensional hexagonal images, wherein P-Lingua programming language is used to implement and validate the proposed system. The achieved experimental results clearly demonstrated the effectiveness of using hexagonal connectivity to segment two dimensional images in a less number of rules and computational steps. Moreover, the results reveal that this approach has the potential of segmenting large images in few number of steps

Membrane Computing for Real Medical Image Segmentation

In this paper, membrane-based computing image segmentation, both region-based and edge-based, is proposed for medical images that involve two types of neighborhood relations between pixels. These neighborhood relations—namely, 4-adjacency and 8-adjacency of a membrane computing approach—construct a family of tissue-like P systems for segmenting actual 2D medical images in a constant number of steps; the two types of adjacency were compared using different hardware platforms. The process involves the generation of membrane-based segmentation rules for 2D medical images. The rules are written in the P-Lingua format and appended to the input image for visualization. The findings show that the neighborhood relations between pixels of 8-adjacency give better results compared with the 4-adjacency neighborhood relations, because the 8-adjacency considers the eight pixels around the center pixel, which reduces the required communication rules to obtain the final segmentation results. The experimental results proved that the proposed approach has superior results in terms of the number of computational steps and processing time. To the best of our knowledge, this is the first time an evaluation procedure is conducted to evaluate the efficiency of real image segmentations using membrane computing

Doctor of Philosophy

dissertationNeuroscientists are developing new imaging techniques and generating large volumes of data in an effort to understand the complex structure of the nervous system. The complexity and size of this data makes human interpretation a labor intensive task. To aid in the analysis, new segmentation techniques for identifying neurons in these feature rich datasets are required. However, the extremely anisotropic resolution of the data makes segmentation and tracking across slices difficult. Furthermore, the thickness of the slices can make the membranes of the neurons hard to identify. Similarly, structures can change significantly from one section to the next due to slice thickness which makes tracking difficult. This thesis presents a complete method for segmenting many neurons at once in two-dimensional (2D) electron microscopy images and reconstructing and visualizing them in three-dimensions (3D). First, we present an advanced method for identifying neuron membranes in 2D, necessary for whole neuron segmentation, using a machine learning approach. The method described uses a series of artificial neural networks (ANNs) in a framework combined with a feature vector that is composed of image and context; intensities sampled over a stencil neighborhood. Several ANNs are applied in series allowing each ANN to use the classification context; provided by the previous network to improve detection accuracy. To improve the membrane detection, we use information from a nonlinear alignment of sequential learned membrane images in a final ANN that improves membrane detection in each section. The final output, the detected membranes, are used to obtain 2D segmentations of all the neurons in an image. We also present a method that constructs 3D neuron representations by formulating the problem of finding paths through sets of sections as an optimal path computation, which applies a cost function to the identification of a cell from one section to the next and solves this optimization problem using Dijkstras algorithm. This basic formulation accounts for variability or inconsistencies between sections and prioritizes cells based on the evidence of their connectivity. Finally, we present a tool that combines these techniques with a visual user interface that enables users to quickly segment whole neurons in large volumes

Automatic 2d image segmentation using tissue-like p system

This paper uses P-Lingua, a standard programming language that is designed specifically for P systems, to automatically simulate the region-based segmentation of 2D images. P-Lingua, which is based on membrane computing, links to Java Netbeans using the PLinguaCore4 Java library to automatically codify the pixels of the input image as long as automatically draw the output segmented image. Many methods have been suggested previously and used for artificial image segmentation, but to the best of our knowledge, none of those techniques were automatic, where the image was codified manually and the visualization of the output image was done manually in the tissue simulator which takes time and effort, especially when dealing with large images in the system. Two types of pixel adjacency have been utilized in this paper, namely; 4-adjacency and 8-adjacency. The jacquard index method has been used to measure the accuracy of the segmentation. The results of the proposed method demonstrated that beside its ability to automatically segmenting 2D images with arbitrary sizes, it is more efficient and faster than the tissue simulator tool, since the latter needs the input image to be codified manually pixel by pixel which makes it impractical for real-world applications

Learning to segment clustered amoeboid cells from brightfield microscopy via multi-task learning with adaptive weight selection

Detecting and segmenting individual cells from microscopy images is critical to various life science applications. Traditional cell segmentation tools are often ill-suited for applications in brightfield microscopy due to poor contrast and intensity heterogeneity, and only a small subset are applicable to segment cells in a cluster. In this regard, we introduce a novel supervised technique for cell segmentation in a multi-task learning paradigm. A combination of a multi-task loss, based on the region and cell boundary detection, is employed for an improved prediction efficiency of the network. The learning problem is posed in a novel min-max framework which enables adaptive estimation of the hyper-parameters in an automatic fashion. The region and cell boundary predictions are combined via morphological operations and active contour model to segment individual cells. The proposed methodology is particularly suited to segment touching cells from brightfield microscopy images without manual interventions. Quantitatively, we observe an overall Dice score of 0.93 on the validation set, which is an improvement of over 15.9% on a recent unsupervised method, and outperforms the popular supervised U-net algorithm by at least $5.8\%$ on average

Active mesh and neural network pipeline for cell aggregate segmentation

Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction

A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.Comment: Accepted by Journal of Structural Biolog

Achieving the Way for Automated Segmentation of Nuclei in Cancer Tissue Images through Morphology-Based Approach: a Quantitative Evaluation

In this paper we address the problem of nuclear segmentation in cancer tissue images, that is critical for specific protein activity quantification and for cancer diagnosis and therapy. We present a fully automated morphology-based technique able to perform accurate nuclear segmentations in images with heterogeneous staining and multiple tissue layers and we compare it with an alternate semi-automated method based on a well established segmentation approach, namely active contours. We discuss active contours’ limitations in the segmentation of immunohistochemical images and we demonstrate and motivate through extensive experiments the better accuracy of our fully automated approach compared to various active contours implementations