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Naked eye instant reversible sensing of Cu²⁺ and its in situ imaging in live brine shrimp Artemia

ANALYST 2015年第16期140卷 5464-5468页

作者： Nair, Ratish R. Raju, M. Patel, Neha P. Raval, Ishan H. Suresh, E. Haldar, Soumya Chatterjee, Pabitra B. CSIR CSMCRI Analyt Discipline & Centralized Instrumental Faci Bhavnagar 364002 Gujarat India CSIR CSMCRI Marine Biotechnol & Ecol Discipline Bhavnagar 364002 Gujarat India CSIR CSMCRI Acad Sci & Innovat Res Bhavnagar 364002 Gujarat India

A Cu2+-specific colorimetric reversible fluorescent receptor HL was designed and synthesized which showed a naked eye observable colour change from colourless to pink on addition of an aqueous buffer (pH 7.4) solution of 30 ppb Cu2+. Short response time (<= 5 s) and low detection limit (nearly 3 ppb) make HL suitable as a reliable "dip-in" open eye sensor for Cu2+. Bio-imaging application in live brine shrimp Artemia enabled HL to detect Cu2+ at as low as 10 ppb exposure.

关键词： Animals Artemia/metabolism Colorimetry/methods Coloring Agents/chemistry Copper/analysis Copper/chemistry Gastrointestinal Tract/metabolism image processing, computer-assisted/methods Limit of Detection Microscopy, Polarization Water/chemistry

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Microscopy-Based High-Content Screening

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CELL 2015年第6期163卷 1314-1325页

作者： Boutros, Michael Heigwer, Florian Laufer, Christina Heidelberg Univ German Canc Res Ctr DKFZ Div Signaling & Funct Genom D-69120 Heidelberg Germany Heidelberg Univ Dept Cell & Mol Biol D-69120 Heidelberg Germany German Canc Consortium DKTK D-69120 Heidelberg Germany

image-based screening is used to measure a variety of phenotypes in cells and whole organisms. Combined with perturbations such as RNA interference, small molecules, and mutations, such screens are a powerful method for gaining systematic insights into biological processes. Screens have been applied to study diverse processes, such as protein-localization changes, cancer cell vulnerabilities, and complex organismal phenotypes. Recently, advances in imaging and image-analysis methodologies have accelerated large-scale perturbation screens. Here, we describe the state of the art for image-based screening experiments and delineate experimental approaches and image-analysis approaches as well as discussing challenges and future directions, including leveraging CRISPR/Cas9-mediated genome engineering.

关键词： Cells/chemistry Cells/cytology CRISPR-Cas Systems High-Throughput Screening Assays image processing, computer-assisted/methods Microscopy Proteins/analysis RNA Interference

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Development of a Noninvasive Method to Diagnose Bladder Outlet Obstruction Based on Decorrelation of Sequential Ultrasound images

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UROLOGY 2015年第3期85卷 648-652页

作者： Arif, Muhammad Idzenga, Tim de Korte, Chris L. van Mastrigt, Ron Erasmus MC Sect Furore Dept Urol NL-3015 GE Rotterdam Netherlands Radboud Univ Nijmegen Med Ctr Med UltraSound Imaging Ctr MUSIC Dept Radiol NL-6525 ED Nijmegen Netherlands

OBJECTIVE To develop an ultrasound (US)-based method for noninvasive diagnosing of bladder outlet obstruction, and the relationship between decorrelation of sequential US images and the degree of obstruction in a urethra model was studied. MATERIALS AND methods A flexible model of a male urethra was constructed from 15% aqueous solution of polyvinyl alcohol cryogel. To create 4 different degrees of obstruction, polyvinyl alcohol rings representing the prostate were placed around the model. Each model was perfused at different flow rates (1-15 mL/s) with an aqueous solution containing scattering particles mimicking urine. At each flow rate, 10 sequential US images were acquired. The average correlation coefficients between the images were calculated and plotted as a function of the degree of obstruction and the flow rate. RESULTS The average correlation decreased approximately linearly with an increase in the degree of obstruction. This decrease in correlation (decorrelation) might be due to turbulence caused by the obstruction. A higher degree of obstruction creates more turbulence and results in a higher decorrelation between sequential US images. CONCLUSION Quantification of the decorrelation between sequential US images may provide us with a new approach to noninvasively diagnose bladder outlet obstruction. (C) 2015 Elsevier Inc.

关键词： Diagnostic Techniques, Urological Humans image processing, computer-assisted/methods image processing, computer-assisted/statistics & numerical data Male Models, Anatomic Urinary Bladder Neck Obstruction/ultrasonography

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The impact of gradient strength on in vivo diffusion MRI estimates of axon diameter

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NEUROimage 2015年 106卷 464-472页

作者： Huang, Susie Y. Nummenmaa, Aapo Witzel, Thomas Duval, Tanguy Cohen-Adad, Julien Wald, Lawrence L. McNab, Jennifer A. Harvard Univ Massachusetts Gen Hosp Sch Med Athinoula A Martinos Ctr Biomed ImagingDept Radi Boston MA 02138 USA Ecole Polytech Inst Biomed Engn Montreal PQ H3C 3A7 Canada MIT Harvard Mit Div Hlth Sci & Technol Cambridge MA 02139 USA Stanford Univ Dept Radiol Radiol Sci Lab Stanford CA 94305 USA

Diffusion magnetic resonance imaging (MRI) methods for axon diameter mapping benefit from higher maximum gradient strengths than are currently available on commercial human scanners. Using a dedicated high-gradient 3 T human MRI scanner with a maximum gradient strength of 300 mT/m, we systematically studied the effect of gradient strength on in vivo axon diameter and density estimates in the human corpus callosum. Pulsed gradient spin echo experiments were performed in a single scan session lasting approximately 2 h on each of three human subjects. The data were then divided into subsets with maximum gradient strengths of 77, 145, 212, and 293 mT/m and diffusion times encompassing short (16 and 25 ms) and long (60 and 94 ms) diffusion time regimes. A three-compartment model of intra-axonal diffusion, extra-axonal diffusion, and free diffusion in cerebrospinal fluid was fitted to the data using a Markov chain Monte Carlo approach. For the acquisition parameters, model, and fitting routine used in our study, it was found that higher maximum gradient strengths decreased the mean axon diameter estimates by two to three fold and decreased the uncertainty in axon diameter estimates by more than half across the corpus callosum. The exclusive use of longer diffusion times resulted in axon diameter estimates that were up to two times larger than those obtained with shorter diffusion times. Axon diameter and density maps appeared less noisy and showed improved contrast between different regions of the corpus callosum with higher maximum gradient strength. Known differences in axon diameter and density between the genu, body, and splenium of the corpus callosum were preserved and became more reproducible at higher maximum gradient strengths. Our results suggest that an optimal q-space sampling scheme for estimating in vivo axon diameters should incorporate the highest possible gradient strength. The improvement in axon diameter and density estimates that we demonstrate from in

关键词： Axons Corpus Callosum/anatomy & histology Diffusion Magnetic Resonance Imaging/methods Humans image processing, computer-assisted/methods Markov Chains Models, Statistical Monte Carlo Method

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NucleusJ: an imageJ plugin for quantifying 3D images of interphase nuclei

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BIOINFORMATICS 2015年第7期31卷 1144-1146页

作者： Poulet, Axel Arganda-Carreras, Ignacio Legland, David Probst, Aline V. Andrey, Philippe Tatout, Christophe Clermont Univ GRED INSERM U 1103UMR CNRS 6293 Aubiere France IJPB ERL CNRS 3559 UMR INRA AgroParisTech 1318 Versailles France Food Proc Engn & Microbiol UMR INRA AgroParisTech 782 Thiverval Grignon France Univ Paris 06 Sorbonne Univ UFR 927 Paris France

A Summary: NucleusJ is a simple and user-friendly imageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus. A step-by-step documentation is available for self-training, together with data sets of nuclei with different nuclear organization.

关键词： Algorithms Cell Nucleus/genetics Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Interphase/genetics

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Gradient-free MCMC methods for dynamic causal modelling

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NEUROimage 2015年 112卷 375-381页

作者： Sengupta, Biswa Friston, Karl J. Penny, Will D. UCL Wellcome Trust Ctr Neuroimaging Inst Neurol London WC1N 3BG England

In this technical note we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling;yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density-albeit at almost 1000% increase in computational time, in comparison to the most efficient algorithm (i.e., the adaptive MCMC sampler). (C) 2015 The Authors. Published by Elsevier Inc.

关键词： Algorithms Bayes Theorem Humans image processing, computer-assisted/methods image processing, computer-assisted/statistics & numerical data Markov Chains Models, Neurological Monte Carlo Method Software Walking/physiology Walking/physiology

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A Background Color Scheme for Piper Plots to Spatially Visualize Hydrochemical Patterns

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GROUNDWATER 2014年第1期52卷 2-6页

作者： Peeters, Luk CSIRO Land & Water Groundwater Hydrol Program Glen Osmond SA 5064 Australia

The combination of ternary diagrams of cations and anions with a central diamond graph make the Piper plot very useful in visualizing groundwater chemistry datasets. One of the major drawbacks is that it is hard to link spatial attributes of the dataset to the plot. In this study, we propose a background color scheme of the Piper plot so that spatial representations of these data can be colored according to their location in the Piper plot. The color scheme is chosen to have maximum resolution while still being perceptually uniform. The linking between Piper plot and maps through this color scheme allows the interpretation of the trends and processes deduced from the Piper plot in terms of the location in the aquifer, the geology, and the groundwater flow dynamics. The colored Piper plot is applied to a groundwater quality dataset of the Condamine Alluvium in Queensland, Australia.

关键词： Anions Cations Color Databases, Factual Environmental Monitoring/methods Groundwater image processing, computer-assisted/methods Maps as Topic Potassium/analysis Queensland Radium/analysis Thorium/analysis Water Quality

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Multi-atlas segmentation of the whole hippocampus and subfields using multiple automatically generated templates

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NEUROimage 2014年 101卷 494-512页

作者： Pipitone, Jon Park, Min Tae M. Winterburn, Julie Lett, Tristram A. Lerch, Jason P. Pruessner, Jens C. Lepage, Martin Voineskos, Aristotle N. Chakravarty, M. Mallar Ctr Addict & Mental Hlth Kimel Family Translat Imaging Genet Lab Toronto ON M5T 1R8 Canada Hosp Sick Children Neurosciences & Mental Hlth Lab Toronto ON M5G 1X8 Canada Univ Toronto Dept Med Biophys Toronto ON Canada Douglas Mental Hlth Univ Inst Verdun PQ Canada McGill Univ Dept Psychiat Montreal PQ Canada Univ Toronto Dept Psychiat Toronto ON Canada Univ Toronto Inst Biomat & Biomed Engn Toronto ON Canada Baycrest Rotman Res Inst Toronto ON Canada Univ Toronto Inst Med Sci Toronto ON Canada

Introduction: Advances in image segmentation of magnetic resonance images (MRI) have demonstrated that multi-atlas approaches improve segmentation over regular atlas-based approaches. These approaches often rely on a large number of manually segmented atlases (e.g. 30-80) that take significant time and expertise to produce. We present an algorithm, MAGeT-Brain (Multiple Automatically Generated Templates), for the automatic segmentation of the hippocampus that minimises the number of atlases needed whilst still achieving similar agreement to multi-atlas approaches. Thus, our method acts as a reliable multi-atlas approach when using special or hard-to-define atlases that are laborious to construct. Method: MAGeT-Brain works by propagating atlas segmentations to a template library, formed from a subset of target images, via transformations estimated by nonlinear image registration. The resulting segmentations are then propagated to each target image and fused using a label fusion method. We conduct two separate Monte Carlo cross-validation experiments comparing MAGeT-Brain and basic multi-atlas whole hippocampal segmentation using differing atlas and template library sizes, and registration and label fusion methods. The first experiment is a 10-fold validation (per parameter setting) over 60 subjects taken from the Alzheimer's Disease Neuroimaging Database (ADNI), and the second is a five-fold validation over 81 subjects having had a first episode of psychosis. In both cases, automated segmentations are compared with manual segmentations following the Pruessner-protocol. Using the best settings found from these experiments, we segment 246 images of the ADNI1: Complete 1Yr 1.5T dataset and compare these with segmentations from existing automated and semi-automated methods: FSL FIRST, FreeSurfer, MAPER, and SNT. Finally, we conduct a leave-one-out cross-validation of hippocampal subfield segmentation in standard 3T T1-weighted images, using five high-resolution manually

关键词： Adolescent Adult Aged Aged, 80 and over Aging/pathology Alzheimer Disease/pathology Atlases as Topic Female Hippocampus/anatomy & histology Hippocampus/pathology Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Magnetic Resonance Imaging/methods Magnetic Resonance Imaging/standards Male Middle Aged Monte Carlo Method Psychotic Disorders/pathology Young Adult

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Accurate cell segmentation in microscopy images using membrane patterns

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BIOINFORMATICS 2014年第18期30卷 2644-2651页

作者： Dimopoulos, Sotiris Mayer, Christian E. Rudolf, Fabian Stelling, Joerg ETH Dept Biosyst Sci & Engn CH-4058 Basel Switzerland ETH Swiss Inst Bioinformat CH-4058 Basel Switzerland

Motivation: Identifying cells in an image (cell segmentation) is essential for quantitative single-cell biology via optical microscopy. Although a plethora of segmentation methods exists, accurate segmentation is challenging and usually requires problem-specific tailoring of algorithms. In addition, most current segmentation algorithms rely on a few basic approaches that use the gradient field of the image to detect cell boundaries. However, many microscopy protocols can generate images with characteristic intensity profiles at the cell membrane. This has not yet been algorithmically exploited to establish more general segmentation methods. Results: We present an automatic cell segmentation method that decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques. In quantitative benchmarks and comparisons with established methods on synthetic and real images, we demonstrate significantly improved segmentation performance despite cell-shape irregularity, cell-to-cell variability and image noise. As a proof of concept, we monitor the internalization of green fluorescent protein-tagged plasma membrane transporters in single yeast cells.

关键词： Algorithms Cell Membrane/metabolism Computational Biology/methods image processing, computer-assisted/methods Microscopy/methods

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Comparison of human septal nuclei MRI measurements using automated segmentation and a new manual protocol based on histology

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NEUROimage 2014年 97卷 245-251页

作者： Butler, Tracy Zaborszky, Laszlo Pirraglia, Elizabeth Li, Jinyu Wang, Xiuyuan Hugh Li, Yi Tsui, Wai Talos, Delia Devinsky, Orrin Kuchna, Izabela Nowicki, Krzysztof French, Jacqueline Kuzniecky, Rubin Wegiel, Jerzy Glodzik, Lidia Rusinek, Henry deLeon, Mony J. Thesen, Thomas NYU Sch Med Ctr Brain Hlth Dept Psychiat New York NY 10016 USA NYU Sch Med Comprehens Epilepsy Ctr Dept Neurol New York NY 10016 USA Rutgers State Univ Ctr Mol & Behav Neurosci Newark NJ 07102 USA New York State Inst Basic Res Dev Disabil Staten Isl NY 10314 USA

Septal nuclei, located in basal forebrain, are strongly connected with hippocampi and important in learning and memory, but have received limited research attention in human MRI studies. While probabilistic maps for estimating septal volume on MRI are now available, they have not been independently validated against manual tracing of MRI typically considered the gold standard for delineating brain structures. We developed a protocol for manual tracing of the human septal region on MRI based on examination of neuroanatomical specimens. We applied this tracing protocol to T1 MRI scans (n = 86) from subjects with temporal epilepsy and healthy controls to measure septal volume. To assess the inter-rater reliability of the protocol, a second tracer used the same protocol on 20 scans that were randomly selected from the 72 healthy controls. In addition to measuring septal volume, maximum septal thickness between the ventricles was measured and recorded. The same scans (n = 86) were also analyzed using septal probabilistic maps and DARTEL toolbox in SPM. Results show that our manual tracing algorithm is reliable, and that septal volume measurements obtained via manual and automated methods correlate significantly with each other (p<.001). Both manual and automated methods detected significantly enlarged septal nuclei in patients with temporal lobe epilepsy in accord with a proposed compensatory neuroplastic process related to the strong connections between septal nuclei and hippocampi. Septal thickness, which was simple to measure with excellent inter-rater reliability, correlated well with both manual and automated septal volume, suggesting it could serve as an easy-to-measure surrogate for septal volume in future studies. Our results call attention to the important though understudied human septal region, confirm its enlargement in temporal lobe epilepsy, and provide a reliable new manual delineation protocol that will facilitate continued study of this critical region.

关键词： Adolescent Adult Automation Brain Mapping Brain Mapping Epilepsy, Temporal Lobe/pathology Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Male Middle Aged Observer Variation Septal Nuclei/anatomy & histology Septal Nuclei/pathology Young Adult

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