Tag: analysis

Mother machine image analysis with MM3

The mother machine is a microfluidic device for high-throughput time-lapse imaging of microbes. Here, we present MM3, a complete and modular image analysis pipeline. MM3 turns raw mother machine images, both phase contrast and fluorescence, into a data structure containing cells with their measured features. MM3 employs machine learning and non-learning algorithms, and is implemented…
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Predictive Metagenomic Analysis of Autoimmune Disease Identifies Robust Autoimmunity and Disease Specific Signatures

Within the last decade, numerous studies have demonstrated changes in the gut microbiome associated with specific autoimmune diseases. Due to differences in study design, data quality control, analysis and statistical methods, the results of these studies are inconsistent and incomparable. To better understand the relationship between the intestinal microbiome and autoimmunity, we have completed a…
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Machine Learning Analysis of Motor Evoked Potential Time Series to Predict Disability Progression in Multiple Sclerosis

Background: Evoked potentials (EPs) are a measure of the conductivity of the central nervous system. They are used to monitor disease progression of multiple sclerosis patients. Previous studies only extracted a few variables from the EPs, which are often further condensed into a single variable: the EP score. We perform a machine learning analysis of…
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Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data

Facetto is a scalable visual analytics application that is used to discover single-cell phenotypes in high-dimensional multi-channel microscopy images of human tumors and tissues. Such images represent the cutting edge of digital histology and promise to revolutionize how diseases such as cancer are studied, diagnosed, and treated. Highly multiplexed tissue images are complex, comprising 10^9…
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