42,017 research outputs found
Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis
The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions
Deep Cytometry: Deep learning with Real-time Inference in Cell Sorting and Flow Cytometry
Deep learning has achieved spectacular performance in image and speech
recognition and synthesis. It outperforms other machine learning algorithms in
problems where large amounts of data are available. In the area of measurement
technology, instruments based on the photonic time stretch have established
record real-time measurement throughput in spectroscopy, optical coherence
tomography, and imaging flow cytometry. These extreme-throughput instruments
generate approximately 1 Tbit/s of continuous measurement data and have led to
the discovery of rare phenomena in nonlinear and complex systems as well as new
types of biomedical instruments. Owing to the abundance of data they generate,
time-stretch instruments are a natural fit to deep learning classification.
Previously we had shown that high-throughput label-free cell classification
with high accuracy can be achieved through a combination of time-stretch
microscopy, image processing and feature extraction, followed by deep learning
for finding cancer cells in the blood. Such a technology holds promise for
early detection of primary cancer or metastasis. Here we describe a new deep
learning pipeline, which entirely avoids the slow and computationally costly
signal processing and feature extraction steps by a convolutional neural
network that directly operates on the measured signals. The improvement in
computational efficiency enables low-latency inference and makes this pipeline
suitable for cell sorting via deep learning. Our neural network takes less than
a few milliseconds to classify the cells, fast enough to provide a decision to
a cell sorter for real-time separation of individual target cells. We
demonstrate the applicability of our new method in the classification of OT-II
white blood cells and SW-480 epithelial cancer cells with more than 95%
accuracy in a label-free fashion
How to understand the cell by breaking it: network analysis of gene perturbation screens
Modern high-throughput gene perturbation screens are key technologies at the
forefront of genetic research. Combined with rich phenotypic descriptors they
enable researchers to observe detailed cellular reactions to experimental
perturbations on a genome-wide scale. This review surveys the current
state-of-the-art in analyzing perturbation screens from a network point of
view. We describe approaches to make the step from the parts list to the wiring
diagram by using phenotypes for network inference and integrating them with
complementary data sources. The first part of the review describes methods to
analyze one- or low-dimensional phenotypes like viability or reporter activity;
the second part concentrates on high-dimensional phenotypes showing global
changes in cell morphology, transcriptome or proteome.Comment: Review based on ISMB 2009 tutorial; after two rounds of revisio
Updates in metabolomics tools and resources: 2014-2015
Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table
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