Automated segmentation of tissue images for computerized IHC analysis

This paper presents two automated methods for the segmentation ofimmunohistochemical tissue images that overcome the limitations of themanual approach aswell as of the existing computerized techniques. The first independent method, based on unsupervised color clustering, recognizes automatically the target cancerous areas in the specimen and disregards the stroma; the second method, based on colors separation and morphological processing, exploits automated segmentation of the nuclear membranes of the cancerous cells. Extensive experimental results on real tissue images demonstrate the accuracy of our techniques compared to manual segmentations; additional experiments show that our techniques are more effective in immunohistochemical images than popular approaches based on supervised learning or active contours. The proposed procedure can be exploited for any applications that require tissues and cells exploration and to perform reliable and standardized measures of the activity of specific proteins involved in multi-factorial genetic pathologie

Machine Learning for Instance Segmentation

Volumetric Electron Microscopy images can be used for connectomics, the study of brain connectivity at the cellular level. A prerequisite for this inquiry is the automatic identification of neural cells, which requires machine learning algorithms and in particular efficient image segmentation algorithms. In this thesis, we develop new algorithms for this task. In the first part we provide, for the first time in this field, a method for training a neural network to predict optimal input data for a watershed algorithm. We demonstrate its superior performance compared to other segmentation methods of its category. In the second part, we develop an efficient watershed-based algorithm for weighted graph partitioning, the \emph{Mutex Watershed}, which uses negative edge-weights for the first time. We show that it is intimately related to the multicut and has a cutting edge performance on a connectomics challenge. Our algorithm is currently used by the leaders of two connectomics challenges. Finally, motivated by inpainting neural networks, we create a method to learn the graph weights without any supervision

A curvature-enhanced random walker segmentation method for detailed capture of 3D cell surface Membranes

High-resolution 3D microscopy is a fast advancing field and requires new techniques in image analysis to handle these new datasets. In this work, we focus on detailed 3D segmentation of Dictyostelium cells undergoing macropinocytosis captured on an iSPIM microscope. We propose a novel random walker-based method with a curvature-based enhancement term, with the aim of capturing fine protrusions, such as filopodia and deep invaginations, such as macropinocytotic cups, on the cell surface. We tested our method on both real and synthetic 3D image volumes, demonstrating that the inclusion of the curvature enhancement term can improve the segmentation of the aforementioned features. We show that our method performs better than other state of the art segmentation methods in 3D images of Dictyostelium cells, and performs competitively against CNN-based methods in two Cell Tracking Challenge datasets, demonstrating the ability to obtain accurate segmentations without the requirement of large training datasets. We also present an automated seeding method for microscopy data, which, combined with the curvature-enhanced random walker method, enables the segmentation of large time series with minimal input from the experimenter

Automated segmentation, tracking and evaluation of bacteria in microscopy images

Dissertação para obtenção do Grau de Mestre em Engenharia BiomédicaMost of the investigation in microbiology relies on microscope imaging and needs to be complemented with reliable methods of computer assisted image processing, in order to avoid manual analysis. In this work, a method to assist the study of the in vivo kinetics of protein expression from Escherichia coli cells was developed. Confocal fluorescence microscopy (CFM) and Differential Interference Contrast (DIC) microscopy images were acquired and processed using the developed method. This method comprises two steps: the first one is focused on the cells detection using DIC images. The latter aligns both DIC and CFM images and computes the fluorescence level emitted by each cell. For the first step, the Gradient Path Labelling (GPL) algorithm was used which produces a moderate over-segmented DIC image. The proposed algorithm, based on decision trees generated by the Classification and Regression Trees (CART) algorithm, discards the backgrounds regions and merges the regions belonging to the same cell. To align DIC/fluorescence images an exhaustive search of the relative position and scale parameters that maximizes the fluorescence inside the cells is made. After the cells have been located on the CFM images, the fluorescence emitted by each cell is evaluated. The discard classifier performed with an error rate of 1:81% 0:98% and the merge classifier with 3:25% 1:37%. The segmentation algorithm detected 93:71% 2:06% of the cells in the tested images. The tracking algorithm correctly followed 64:52% 16:02% of cells and the alignment method successfully aligned all the tested images

High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticles

<p>Abstract</p> <p>Background</p> <p>High content screening (HCS)-based image analysis is becoming an important and widely used research tool. Capitalizing this technology, ample cellular information can be extracted from the high content cellular images. In this study, an automated, reliable and quantitative cellular image analysis system developed in house has been employed to quantify the toxic responses of human H4 neuroglioma cells exposed to metal oxide nanoparticles. This system has been proved to be an essential tool in our study.</p> <p>Results</p> <p>The cellular images of H4 neuroglioma cells exposed to different concentrations of CuO nanoparticles were sampled using IN Cell Analyzer 1000. A fully automated cellular image analysis system has been developed to perform the image analysis for cell viability. A multiple adaptive thresholding method was used to classify the pixels of the nuclei image into three classes: bright nuclei, dark nuclei, and background. During the development of our image analysis methodology, we have achieved the followings: (1) The Gaussian filtering with proper scale has been applied to the cellular images for generation of a local intensity maximum inside each nucleus; (2) a novel local intensity maxima detection method based on the gradient vector field has been established; and (3) a statistical model based splitting method was proposed to overcome the under segmentation problem. Computational results indicate that 95.9% nuclei can be detected and segmented correctly by the proposed image analysis system.</p> <p>Conclusion</p> <p>The proposed automated image analysis system can effectively segment the images of human H4 neuroglioma cells exposed to CuO nanoparticles. The computational results confirmed our biological finding that human H4 neuroglioma cells had a dose-dependent toxic response to the insult of CuO nanoparticles.</p

Computer-aided acute leukemia blast cells segmentation in peripheral blood images

Computer-aided diagnosis system of leukemic cells is vital tool, which can assist domain experts in the diagnosis and evaluation procedure. Accurate blast cells segmentation is the initial stage in building a successful computer-aided diagnosis system. Blast cells segmentation is still an open research topic due to several problems such as variation of blats cells in terms of color, shape and texture, touching and overlapping of cells, inconsistent image quality, etc. Although numerous blast cells segmentation methods have been developed, only few studies attempted to address these problems simultaneously. This paper presents a new image segmentation method to extract acute leukemia blast cells in peripheral blood. The first aim is to segment the leukemic cells by mean of color transformation and mathematical morphology. The method also introduces an approach to split overlapping cells using the marker-controlled watershed algorithm based on a new marker selection scheme. Furthermore, the paper presents a powerful approach to separate the nucleus region and the cytoplasm region based on the seeded region growing algorithm powered by histogram equalization and arithmetic addition to handle the issue of non-homogenous nuclear chromatin pattern. The robustness of the proposed method is tested on two datasets comprise of 1024 peripheral blood images acquired from two different medical centers. The quantitative evaluation reveals that the proposed method obtain a better segmentation performance compared with its counterparts and achieves remarkable segmentation results of approximately 96 % in blast cell extraction and 94 % in nucleus/cytoplasm separation

Phase contrast cell detection using multilevel classification

In this paper, we propose a fully automated learning based approach for detecting cells in time-lapse phase contrast images. The proposed system combines two machine learning approaches to achieve bottom-up image segmentation