6 research outputs found

    Robust normalization protocols for multiplexed fluorescence bioimage analysis

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    study of mapping and interaction of co-localized proteins at a sub-cellular level is important for understanding complex biological phenomena. One of the recent techniques to map co-localized proteins is to use the standard immuno-fluorescence microscopy in a cyclic manner (Nat Biotechnol 24:1270–8, 2006; Proc Natl Acad Sci 110:11982–7, 2013). Unfortunately, these techniques suffer from variability in intensity and positioning of signals from protein markers within a run and across different runs. Therefore, it is necessary to standardize protocols for preprocessing of the multiplexed bioimaging (MBI) data from multiple runs to a comparable scale before any further analysis can be performed on the data. In this paper, we compare various normalization protocols and propose on the basis of the obtained results, a robust normalization technique that produces consistent results on the MBI data collected from different runs using the Toponome Imaging System (TIS). Normalization results produced by the proposed method on a sample TIS data set for colorectal cancer patients were ranked favorably by two pathologists and two biologists. We show that the proposed method produces higher between class Kullback-Leibler (KL) divergence and lower within class KL divergence on a distribution of cell phenotypes from colorectal cancer and histologically normal samples

    Robust normalization protocols for multiplexed fluorescence bioimage analysis

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    Ahmed Raza SE, Langenkämper D, Sirinukunwattana K, Epstein D, Nattkemper TW, Rajpoot NM. Robust normalization protocols for multiplexed fluorescence bioimage analysis. BioData Mining. 2016;9(1): 11

    BioIMAX : a Web2.0 approach to visual data mining in bioimage data

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    Loyek C. BioIMAX : a Web2.0 approach to visual data mining in bioimage data. Bielefeld: Universität Bielefeld; 2012

    Paving the Way:Contributions of Big Data to Apicomplexan and Kinetoplastid Research

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    In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated

    Preprocessing algorithms for the digital histology of colorectal cancer

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    Pre-processing techniques were developed for cell identification algorithms. These algorithms which locate and classify cells in digital microscopy images are important in digital pathology. The pre-processing methods included image sampling and colour normalisation for standard Haemotoxilyn and Eosin (H&E) images and co-localisation algorithms for multiplexed images. Data studied in the thesis came from patients with colorectal cancer. Patient histology images came from `The Cancer Genome Atlas' (TCGA), a repository with contributions from many different institutional sites. The multiplexed images were created by TIS, the Toponome Imaging System. Experiments with image sampling were applied to TCGA diagnostic images. The effect of sample size and sampling policy were evaluated. TCGA images were also used in experiments with colour normalisation algorithms. For TIS multiplexed images, probabilistic graphical models were developed as well as clustering applications. NW-BHC, an extension to Bayesian Hierarchical Clustering, was developed and, for TIS antibodies, applied to TCGA expression data. Using image sampling with a sample size of 100 tiles gave accurate prediction results while being seven to nine times faster than processing the entire image. The two most accurate colour normalisation methods were that of Macenko and a `Nave' algorithm. Accuracy varied by TCGA site, indicating that researchers should use several independent data sets when evaluating colour normalisation algorithms. Probabilistic graphical models, applied to multiplexed images, calculated links between pairs of antibodies. The application of clustering to cell nuclei resulted in two main groups, one associated with epithelial cells and the second associated with the stromal environment. For TCGA expression data and for several clustering metrics, NW-BHC improved on the standard EM algorithm

    Cell phenotyping in multi-tag fluorescent bioimages

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    Multi-tag bioimaging systems have recently emerged as powerful tools which provide spatiotemporal localization of several different proteins in the same tissue specimen. The analysis of such multivariate bioimages requires sophisticated analytical methods that extract a molecular signature of various types of cells and assist in analyzing interaction behaviors of functional protein complexes. Previous studies were mainly focused on pixel-level analysis which essentially ignore cellular structures as units which can be crucial when analyzing cancerous cells. In this paper, we present a framework in order to overcome these limitations by incorporating cell-level analysis. We use this framework to identify cell phenotypes based on their high-dimensional co-expression profiles contained within the images generated by the robotically controlled TIS microscope installed at Warwick. The proposed paradigm employs a refined cell segmentation algorithm followed by a locality preserving nonlinear embedding algorithm which is shown to produce significantly better cell classification and phenotype distribution results as compared to its linear counterpart
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