scholarly journals Quantification of spatial tumor heterogeneity in immunohistochemistry staining images

2020 ◽  
Author(s):  
Inna Chervoneva ◽  
Amy R Peck ◽  
Misung Yi ◽  
Boris Freydin ◽  
Hallgeir Rui
Keyword(s):  
Point Process ◽  
Signal Intensity ◽  
Tumor Heterogeneity ◽  
Marked Point ◽  
Supplementary Information ◽  
Marked Point Process ◽  
Cancer Tissue ◽  
Subcellular Compartment ◽  
Spatial Indices ◽  
Protein Expressions

Abstract Motivation Quantitative Immunofluorescence (QIF) is often used for immunohistochemistry (IHC) quantification of proteins that serve as cancer biomarkers. Advanced image analysis systems for pathology allow capturing expression levels in each individual cell or subcellular compartment. However, only the Mean Signal Intensity (MSI) within the cancer tissue region of interest is usually considered as biomarker completely ignoring the issue of tumor heterogeneity. Results We propose using IHC image-derived information on the spatial distribution of cellular signal intensity (CSI) of protein expression within the cancer cell population to quantify both mean expression level and tumor heterogeneity of CSI levels. We view CSI levels as marks in a marked point process of cancer cells in the tissue and define spatial indices based on conditional mean and conditional variance of the marked point process. The proposed methodology provides objective metrics of cell-to-cell heterogeneity in protein expressions that allow discriminating between different patterns of heterogeneity. The prognostic utility of new spatial indices is investigated and compared to the standard MSI biomarkers using the protein expressions in tissue microarrays (TMAs) incorporating tumor tissues from1000+ breast cancer patients. Supplementary information Supplementary data are available at Bioinformatics online.

Connected-Tube MPP Model for Unsupervised 3D Fiber Detection

2020 ◽  
Vol 2020 (14) ◽  
pp. 305-1-305-6
Author(s):  
Tianyu Li ◽  
Camilo G. Aguilar ◽  
Ronald F. Agyei ◽  
Imad A. Hanhan ◽  
Michael D. Sangid ◽  
...  
Keyword(s):  
Composite Material ◽  
Point Process ◽  
Marked Point ◽  
Experimental Results ◽  
Marked Point Process ◽  
Fiber Reinforced Composite ◽  
Reinforced Composite ◽  
Proposed Model ◽  
Cylinder Model ◽  
Reinforced Composite Material

In this paper, we extend our previous 2D connected-tube marked point process (MPP) model to a 3D connected-tube MPP model for fiber detection. In the 3D case, a tube is represented by a cylinder model with two spherical areas at its ends. The spherical area is used to define connection priors that encourage connection of tubes that belong to the same fiber. Since each long fiber can be fitted by a series of connected short tubes, the proposed model is capable of detecting curved long tubes. We present experimental results on fiber-reinforced composite material images to show the performance of our method.

Marked point processes as limits of Markovian arrival streams

1993 ◽  
Vol 30 (02) ◽  
pp. 365-372 ◽  
Author(s):  
Søren Asmussen ◽  
Ger Koole
Keyword(s):  
Point Process ◽  
Point Processes ◽  
Marked Point ◽  
The State ◽  
Marked Point Processes ◽  
Marked Point Process ◽  
State Transitions ◽  
Poisson Arrival ◽  
Convergence Of Moments ◽  
Environmental Process

A Markovian arrival stream is a marked point process generated by the state transitions of a given Markovian environmental process and Poisson arrival rates depending on the environment. It is shown that to a given marked point process there is a sequence of such Markovian arrival streams with the property that as m →∞. Various related corollaries (involving stationarity, convergence of moments and ergodicity) and counterexamples are discussed as well.

State aggregation and discrete-state Markov chains embedded in a class of point processes

1995 ◽  
Vol 32 (01) ◽  
pp. 39-51
Author(s):  
Xi-Ren Cao
Keyword(s):  
Markov Chains ◽  
Poisson Process ◽  
Point Process ◽  
Point Processes ◽  
Marked Point ◽  
Practical Importance ◽  
Marked Point Process ◽  
Interarrival Time ◽  
Discrete State ◽  
State Aggregation

One result that is of both theoretical and practical importance regarding point processes is the method of thinning. The basic idea of this method is that under some conditions, there exists an embedded Poisson process in any point process such that all its arrival points form a sub-sequence of the Poisson process. We extend this result by showing that on the embedded Poisson process of a uni- or multi-variable marked point process in which interarrival time distributions may depend on the marks, one can define a Markov chain with a discrete state that characterizes the stage of the interarrival times. This implies that one can construct embedded Markov chains with countable state spaces for the state processes of many practical systems that can be modeled by such point processes.

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