Imaging Informatics

High-throughput Prediction of Nephrotoxicity in Humans

The Lush Science Prize 2016 was awarded to Daniele Zink and Lit-Hsin Loo for the interdisciplinary
and collaborative work between their research groups in developing alternative methods for the
prediction of nephrotoxicity in humans. The collaboration has led to the establishment of a series of pioneering alternative methods for nephrotoxicity prediction, which includes: predictive gene expression
markers based on pro-inflammatory responses; predictive in vitro cellular models based on pluripotent

type: 
Journal Paper
journal: 
ATLA 45, Pg 241-252, 5 Nov 2017
Url: 
http://www.atla.org.uk/high-throughput-prediction-of-nephrotoxicity-in-humans/
Impact Factor: 
1.021

Transduction on Directed Graphs via Absorbing Random Walks

In this paper we consider the problem of graph-based transductive classification, and we are particularly interested in the directed graph scenario which is a natural form for many real world applications.Different from existing research efforts that either only deal with undirected graphs or circumvent directionality by means of symmetrization, we propose a novel random walk approach on directed graphs using absorbing Markov chains, which can be regarded as maximizing the accumulated expected number of visits from the unlabeled transient states.

type: 
Journal Paper
journal: 
IEEE Transactions on Pattern Analysis and Machine Intelligence, Issue 99, 2017, doi:10.1109/TPAMI.2017.2730871
pubmed: 
28809671
Url: 
http://ieeexplore.ieee.org/document/8008851/
Impact Factor: 
8.329

Semi-automated quantitative Drosophila wings measurements

BACKGROUND:
Drosophila melanogaster is an important organism used in many fields of biological research such as genetics and developmental biology. Drosophila wings have been widely used to study the genetics of development, morphometrics and evolution. Therefore there is much interest in quantifying wing structures of Drosophila. Advancement in technology has increased the ease in which images of Drosophila can be acquired. However such studies have been limited by the slow and tedious process of acquiring phenotypic data.

RESULTS:

type: 
Journal Paper
journal: 
BMC Bioinformatics 2017 Jun 28;18(1):319. doi: 10.1186/s12859-017-1720-y
pubmed: 
28659123
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28659123
Impact Factor: 
2.435
Date of acceptance: 
2017-06-09

Quantitative 3D analysis of complex single border cell behaviors in coordinated collective cell migration

Understanding the mechanisms of collective cell migration is crucial for cancer metastasis, wound healing and many developmental processes. Imaging a migrating cluster in vivo is feasible, but the quantification of individual cell behaviours remains challenging. We have developed an image analysis toolkit, CCMToolKit, to quantify the Drosophila border cell system. In addition to chaotic motion, previous studies reported that the migrating cells are able to migrate in a highly coordinated pattern.

type: 
Journal Paper
journal: 
Nature Communications, 2017 Apr 4;8:14905. doi: 10.1038/ncomms14905
pubmed: 
28374738
Url: 
https://www.nature.com/articles/ncomms14905
Impact Factor: 
12.124
Date of acceptance: 
2017-02-10

Early spatiotemporal-specific changes in intermediate signals are predictive of cytotoxic sensitivity to TNFα and co-treatments

Signaling pathways can generate different cellular responses to the same cytotoxic agents. Current quantitative models for predicting these differential responses are usually based on large numbers of intracellular gene products or signals at different levels of signaling cascades. Here, we report a study to predict cellular sensitivity to tumor necrosis factor alpha (TNFα) using high-throughput cellular imaging and machine-learning methods.

type: 
Journal Paper
journal: 
Scientific Reports 7, Article 43541 (2017), doi:10.1038/srep43541
Url: 
http://www.nature.com/articles/srep43541
Impact Factor: 
5.228
Date of acceptance: 
2017-01-27

Fusion of Magnetic and Visual Sensors for Indoor Localization: Infrastructure-free and More Effective

Accurate and infrastructure-free indoor positioning can be very useful in a variety of applications. However, most

type: 
Journal Paper
journal: 
IEEE Transactions on Medical Imaging, Issue 99, 2016, doi: 10.1109/TMI.2016.2623357
Impact Factor: 
3.756

Automated Classification for Pathological Prostate Images using AdaBoost-based

We present an AdaBoost-based Ensemble Learning for supporting automated Gleason grading of prostate adenocarcinoma (PRCA). The method is able to differentiate Gleason patterns 4–5 from patterns 1–3 as the patterns 4-5 are correlated to more aggressive disease while patterns 1-3 tend to reflect more favorable patient outcome. This method is based on various feature descriptors and classifiers for multiple color channels, including color channels of red, green and blue, as well as the optical intensity of hematoxylin and eosin stainings.

type: 
Conference Paper/Poster
journal: 
2016 IEEE Sympsosium Series on Computational Intelligence (IEEE SSCI 2016) Dec 6 to 9, Athens, Greece,

Action Recognition in Still Images With Minimum Annotation Efforts

We focus on the problem of still image-based human action recognition, which essentially involves making prediction by analyzing human poses and their interaction with objects in the scene. Besides image-level action labels (e.g., riding, phoning), during both training and testing stages, existing works usually require additional input of human bounding boxes to facilitate the characterization of the underlying human–object interactions. We argue that this additional input requirement might severely discourage potential applications and is not very necessary.

type: 
Journal Paper
journal: 
IEEE Transactions on Image Processing, Vol. 25, Issue 11, Nov 2016, Pg 5479-5490, doi: 10.1109/TIP.2016.2605305
Url: 
http://ieeexplore.ieee.org/document/7558119/
Impact Factor: 
3.735

Weibel-Palade body size modulates the adhesive activity of its von Willebrand Factor cargo in cultured endothelial cells

Changes in the size of cellular organelles are often linked to modifications in their function. Endothelial cells store von Willebrand Factor (vWF), a glycoprotein essential to haemostasis in Weibel-Palade bodies (WPBs), cigar-shaped secretory granules that are generated in a wide range of sizes. We recently showed that forcing changes in the size of WPBs modifies the activity of this cargo. We now find that endothelial cells treated with statins produce shorter WPBs and that the vWF they release at exocytosis displays a reduced capability to recruit platelets to the endothelial cell surface.

type: 
Journal Paper
journal: 
Scientific Reports 6, Article no. 32473 (2016), doi:10.1038/srep32473
Url: 
http://www.nature.com/articles/srep32473
Impact Factor: 
5.228
Date of acceptance: 
2016-08-09

Large-scale image-based screening and profiling of cellular phenotypes

Cellular phenotypes are observable characteristics of cells resulting from the interactions of intrinsic and extrinsic chemical or biochemical factors. Image-based phenotypic screens under large numbers of basal or perturbed conditions can be used to study the influences of these factors on cellular phenotypes. Hundreds to thousands of phenotypic descriptors can also be quantified from the images of cells under each of these experimental conditions. Therefore, huge amounts of data can be generated, and the analysis of these data has become a major bottleneck in large-scale phenotypic screens.

type: 
Journal Paper
journal: 
Cytometry Part A, 2016, doi: 10.1002/cyto.a.22909
Url: 
http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22909/abstract
Impact Factor: 
3.18
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