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TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays (vol 46, pg 265, 2009)

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BIOTECHNIQUES 2009年第6期46卷 383-383页

作者： Gebaeck Swiss Federal Institute of Technology ETH Zurich Zurich Switzerland.

Cell migration plays a major role in development, physiology, and disease, and is frequently evaluated in vitro by the monolayer wound healing assay. The assay analysis, however, is a time-consuming task that is often performed manually. In order to accelerate this analysis, we have developed TScratch, a new, freely available image analysis technique and associated software tool that uses the fast discrete curvelet transform to automate the measurement of the area occupied by cells in the images. This tool helps to significantly reduce the time needed for analysis and enables objective and reproducible quantification of assays. The software also offers a graphical user interface which allows easy inspection of analysis results and, if desired, manual modification of analysis parameters. The automated analysis was validated by comparing its results with manual-analysis results for a range of different cell lines. The comparisons demonstrate a close agreement for the vast majority of images that were examined and indicate that the present computational tool can reproduce statistically significant results in experiments with well-known cell migration inhibitors and enhancers.

关键词： Algorithms Animals Cell Line, Tumor Cell Migration Assays Cell Migration Assays Cell Movement/physiology Cells/classification Cells, Cultured computer Graphics Data Interpretation, Statistical Humans image processing, computer-assisted/methods Mice Software User-computer Interface Wound Healing/physiology

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Shortened Dental Arch and Cerebral Regional Blood Volume: An Experimental Pilot Study with Optical Topography

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CRANIO-THE JOURNAL OF CRANIOMANDIBULAR & SLEEP PRACTICE 2009年第2期27卷 94-100页

作者： Miyamoto, Ikuya Yoshida, Kazuya Bessho, Kazuhisa Kyushu Dent Coll Dept Oral & Maxillofacial Surg Div Oral & Maxillofacial Reconstruct Surg Kokura Kita Ku Kitakyushu Fukuoka 8038580 Japan Natl Hosp Org Kyoto Med Ctr Dept Oral & Maxillofacial Surg Kyoto Japan Kyoto Univ Hosp Dept Oral & Maxillofacial Surg Kyoto Japan

A shortened dental arch without posterior occlusal support has been thought to maintain sufficient oral function. The mechanism of occlusal adaptation with a shortened dental arch is unclear. For a better understanding of the effects of molar teeth on brain function, the authors combined experimentally-shortened dental arches and a neuro-imaging technique. Regional cerebral blood volume was measured using near-infrared optical topography during maximum voluntary clenching tasks from 10 subjects on individually fabricated oral appliances, which can create experimentally complete and shortened dental arches. Results suggested that clenching on the complete dental arch showed a significantly higher brain blood volume than that on the shortened dental arch. Moreover, there were no differences between the two splints in the latency to the maximum oxyhemoglobin concentration. These findings suggest that occlusal status is closely related to brain blood flow and lack of occlusal molar support rapidly reduces cerebral blood volume in the maximum voluntary clenching condition.

关键词： Adult Blood Volume/physiology Cerebrovascular Circulation/physiology Dental Arch/pathology Female Hemoglobins/analysis Humans image processing, computer-assisted/methods Jaw, Edentulous, Partially/pathology Male Molar Muscle Contraction/physiology Occlusal Splints Oxyhemoglobins/analysis Pilot Projects Reaction Time/physiology Temporal Lobe/blood supply Tomography, Optical/methods Tomography, Optical/methods

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Digitalization of post-mortem coronary angiography

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HISTOPATHOLOGY 2009年第6期55卷 760-761页

作者： Kornegoor, Robert Brosens, Lodewijk A. A. Roothaan, Suzan M. Smits, Alexander J. J. Vink, Aryan Univ Med Ctr Utrecht Dept Pathol Utrecht Netherlands

The article discusses the efficiency of post-mortem coronary angiography technique in evaluating coronary artery disease in sudden heart death. It states that the method can provide a permanent overview of coronary distribution, patency and the formation of collateral blood vessels. It adds that the use of barium sulphate/gelatin suspension in angiography can prevent settlement of the suspension in the vessel lumen.

关键词： Autopsy Autopsy Coronary Angiography/methods Coronary Angiography/methods Humans image processing, computer-assisted/methods

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A neurite quality index and machine vision software for improved quantification of neurodegeneration

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BIOTECHNIQUES 2009年第4期47卷 III-VIII页

作者： Romero, Peggy L. Miller, Ted Garakani, Arman M. Reify Corp Saratoga CA USA Sirtris Cambridge MA USA

Current methods to assess neurodegradation in dorsal root ganglion cultures as a model for neurodegenerative diseases are imprecise and time-consuming. Here we describe two new methods to quantify neuroprotection in these cultures. The neurite quality index (NQI) builds upon earlier manual methods, incorporating additional morphological events to increase detection sensitivity for the detection of early degeneration events. Neurosight is a machine vision-based method that recapitulates many of the strengths of NQI while enabling high-throughput screening applications with decreased costs.

关键词： Cells, Cultured Ganglia, Spinal/cytology Humans image processing, computer-assisted/methods NAD/metabolism Nerve Degeneration/pathology Neurites/pathology Neurites/ultrastructure Software

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Five-dimensional neuroimaging: Localization of the time-frequency dynamics of cortical activity

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NEUROimage 2008年第4期40卷 1686-1700页

作者： Dalal, Sarang S. Guggisberg, Adrian G. Edwards, Erik Sekihara, Kensuke Findlay, Anne M. Canolty, Ryan T. Berger, Mitchel S. Knight, Robert T. Barbaro, Nicholas M. Kirsch, Heidi E. Nagarajana, Srikantan S. Univ Calif San Francisco Dept Radiol Biomagnet Imaging Lab San Francisco CA 94143 USA Univ Calif Berkeley Helen Wills Neurosci Inst Berkeley CA 94720 USA Univ Calif San Francisco Joint Grad Grp Bioengn San Francisco CA 94143 USA Univ Calif San Francisco Dept Neurol Surg San Francisco CA 94143 USA Univ Calif San Francisco Dept Neurol San Francisco CA 94143 USA Univ Calif Berkeley Dept Psychol Berkeley CA 94720 USA Tokyo Metropolitan Univ Dept Syst Design & Engn Tokyo 1910065 Japan Univ Bern Inselspital Dept Neurol CH-3010 Bern Switzerland

The spatiotemporal dynamics of cortical oscillations across human brain regions remain poorly understood because of a lack of adequately validated methods for reconstructing such activity from noninvasive electrophysiological data. In this paper, we present a novel adaptive spatial filtering algorithm optimized for robust source time frequency reconstruction from magnetoencephalography (MEG) and electroencephalography ( EEG) data. The efficacy of the method is demonstrated with simulated sources and is also applied to real MEG data from a self-paced finger movement task. The algorithm reliably reveals modulations both in the beta band (12-30 Hz) and high gamma band (65-90 Hz) in sensorimotor cortex. The performance is validated by both across-subjects statistical comparisons and by intracranial electrocorticography (ECoG) data from two epilepsy patients. Interestingly, we also reliably observed high frequency activity (30-300 Hz) in the cerebellum, although with variable locations and frequencies across subjects. The proposed algorithm is highly parallelizable and runs efficiently on modern high-performance computing clusters. This method enables the ultimate promise of MEG and EEG for five-dimensional imaging of space, time, and frequency activity in the brain and renders it applicable for widespread studies of human cortical dynamics during cognition. (c) 2008 Elsevier Inc. All rights reserved.

关键词： Adult Algorithms Beta Rhythm Beta Rhythm Cerebellum/anatomy & histology Cerebellum/physiology Cerebral Cortex/anatomy & histology Cerebral Cortex/physiology Data Interpretation, Statistical Electroencephalography Electrophysiology Female Fingers/innervation Fingers/physiology Humans image processing, computer-assisted/methods Magnetoencephalography Magnetoencephalography Male Motor Cortex/anatomy & histology Motor Cortex/physiology Psychomotor Performance/physiology Somatosensory Cortex/anatomy & histology Somatosensory Cortex/physiology

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Differential neural activation for updating rule versus stimulus information in working memory

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NEURON 2008年第1期59卷 173-182页

作者： Montojo, Caroline A. Courtney, Susan M. Johns Hopkins Univ Dept Psychol & Brain Sci Baltimore MD 21218 USA Johns Hopkins Univ Dept Neurosci Baltimore MD 21218 USA Kennedy Krieger Inst FM Kirby Res Ctr Funct Brain Imaging Baltimore MD 21218 USA

Establishing what information is actively maintained in working memory (WM) and how it is represented and controlled is essential to understanding how such information guides future behavior. WM has traditionally been investigated in terms of the maintenance of stimulus-specific information, such as locations or words. More recently, investigators have emphasized the importance of rules that establish relationships between those stimuli and the pending response. The current study used a mental arithmetic task with fMRI to test whether updating of numbers (i.e., stimuli) and updating of mathematical operations (i.e., rules) in WM relies on the same neural system. Results indicate that, while a common network is activated by both types of updating, rule updating preferentially activates prefrontal cortex while number updating preferentially activates parietal cortex. The results suggest that both numbers and rules are maintained in WM but that they are different types of information that are controlled independently.

关键词： Adult Analysis of Variance Brain/blood supply Brain/physiology Brain Mapping Brain Mapping Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Male Mathematics Memory, Short-Term/physiology Mental Processes/physiology Oxygen/blood Photic Stimulation/methods Reaction Time/physiology

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Optical analysis of computed tomography images of the liver predicts fibrosis stage and distribution in chronic hepatitis C

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HEPATOLOGY 2008年第3期47卷 810-816页

作者： Romero-Gomez, Manuel Gomez-Gonzalez, Emilio Madrazo, Ana Vera-Valencia, Marina Rodrigo, Luis Perez-Alvarez, Ramon Perez-Lopez, Rosa Castellano-Megias, Victor M. Nevado-Santos, Manuel Alcon, Juan C. Sola, Ricard Perez-Moreno, Jose M. Navarro, Jose M. Andrade, Raul J. Salmeron, Javier Fernandez-Lopez, Manuel Aznar, Rafael Diago, Moises Hosp Univ Valme Unit Clin Management Digest Dis Seville 41014 Spain Hosp Univ Valme CIBEREHD Seville 41014 Spain Univ Seville Dept Appl Phys 3 ESI Interdisciplinary Phys Grp Seville Spain Univ Oviedo Hosp Cent Asturias Digest Serv E-33080 Oviedo Spain Hosp Fuenlabrada Pathol Unit Madrid Spain Fdn Hosp Alcorcon Pathol Unit Madrid Spain Hosp Univ Valme Radiol Unit Seville 41014 Spain Hosp del Mar Hepatol Sect Barcelona Spain Hosp Univ Puerto Real Digest Unit Cadiz Spain Hosp Costa Sol Digest Unit Malaga Spain Hosp Virgen Victoria Hepatol Unit Malaga Spain Hosp Univ San Cecilio Digest Unit Granada Spain Univ Valencia Gen Hosp Hepatol Sect Valencia Spain

This study was undertaken to evaluate an image processing method for assessing liver fibrosis in conventional computed tomography (CT) scans in patients with chronic hepatitis C. Two cohorts (designated "estimation," n = 34;and "validation," n = 107) of chronic hepatitis C patients were assessed using digitized conventional helical CT. Weighted CT mean fibrosis (Fibro-CT) was calculated as a nonlinear weighted mean F-score for each sample. Fibrosis was defined according to Scheuer on the F0 to F4 scale by 2 pathologists blinded regarding the Fibro-CT data. Fibrosis according to Fibro-CT correlated with histology-determined fibrosis (r = 0.69;P < 0.001) and with increasing F-stage: FO = 0.23 +/- 0.39;F1 = 0.90 +/- 0.99;F2 = 1.41 +/- 0.94;F3 = 2.79 +/- 0.55;F4 = 3.15 +/- 0.35 [analysis of variance: P < 0.0001). The receiver operating characteristics curve to diagnose significant fibrosis (>= F2) was 0.83;95% confidence interval (95%CI), 0.75 to 0.91;and, to diagnose advanced fibrosis (>= F3), was 0.86, 95%CI: 0.80 to 0.93. The correlation between Fibro-CT and fibrosis was higher in patients with homogeneous distribution of fibrosis than in patients with heterogeneous distribution (r = 0.77 versus r = 0.43;P < 0.05). Conclusion: Optical digital analysis of CT images of the liver is effective in determining the stage and distribution of liver fibrosis in chronic hepatitis C. In patients with homogeneous fibrosis distribution, the correlation between Fibro-CT and histology was better than in patients with heterogeneous distribution. Fibro-CT is a simple to use, readily available, and useful method for the diagnosis of fibrosis in patients with chronic hepatitis C.

关键词： Adult Aged Cohort Studies Female Hepatitis C, Chronic/complications Hepatitis C, Chronic/pathology Humans image processing, computer-assisted/methods Liver Cirrhosis/pathology Liver Cirrhosis/radiography Liver Cirrhosis/virology Male Middle Aged Prognosis Tomography, X-Ray Computed/methods

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Detecting change in BOLD signal between sessions for atlas-based anatomical ROIs

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NEUROimage 2008年第3期40卷 1157-1165页

作者： Buck, Robert Singhal, Harsh Arora, Jagriti Schlitt, Heidi Constable, R. Todd Pfizer Inc Ann Arbor MI USA Yale Univ MRCC New Haven CT USA Amgen Inc Thousand Oaks CA 91320 USA

An algorithm using pre-defined regions of interest (ROIs) to detect differences between sessions in Blood Oxygen-Level Dependent (BOLD) signal is proposed and results from a reproducibility study are reported here. It is important to know whether tests for change have the desired statistical properties, e. g., low variability between sessions and unbiased false-positive rates, under null conditions so one is confident in any conclusions based on the metric and test used. This study examined three cognitive tasks: Stroop, response inhibition, Sternberg digits, and a visually-cued finger tapping task, in 20 healthy subjects. Each subject had two fMRI sessions, one week apart. A series of ROI summaries was constructed by choosing different proportions of voxels from the ROI and calculating the mean of t values for the selected voxels. The choice of voxels was based on the magnitude of the t values, selecting the maximum value, then the top 1%, and so on until all voxels in the ROI were included. No ROIs were found to have significant differences between sessions based on paired comparison t tests. Generally, the observed false-positive rates were near the expected rates for all summaries and tasks, although the Sternberg and Response Inhibition tasks did have higher false-positive rates when alpha >= 0.1 for some ROI summaries. This study indicates results are reproducible and also have the desired statistical properties under null conditions. (C) 2008 Elsevier Inc. All rights reserved.

关键词： Adolescent Adult Aged Algorithms Artifacts Brain/anatomy & histology False Positive Reactions Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Magnetic Resonance Imaging/statistics & numerical data Male Middle Aged Neuropsychological Tests Oxygen/blood Psychomotor Performance/physiology Reproducibility of Results

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Partial volume corrected image derived input functions for dynamic PET brain studies:: Methodology and validation for [¹¹C] flumazenil

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NEUROimage 2008年第3期39卷 1041-1050页

作者： Mourik, Jurgen E. M. Lubberink, Mark Klumpers, Ursula M. H. Comans, Emile F. Lammertsma, Adriaan A. Boellaard, Ronald Vrije Univ Amsterdam Med Ctr Dept Nucl Med & PET Res NL-1007 MB Amsterdam Netherlands Vrije Univ Amsterdam Med Ctr Dept Psychiat Amsterdam Netherlands

Extraction of arterial input functions from dynamic brain scans may obviate the need for arterial sampling and would increase the clinical applicability of quantitative PET studies. The aim of the present study was to evaluate applicability and accuracy of image derived input functions (IDIFs) following reconstruction based partial volume correction (PVC). Settings for the PVC ordered subset expectation maximization (PVC-OSEM) reconstruction algorithm were varied. In addition, different methods for defining arterial regions of interest (1101) in order to extract IDIFs were evaluated. [C-11]flumazenil data of 10 subjects were used in the present study. Results obtained with IDIFs were compared with those using standard on-line measured arterial input functions. These included areas under the curve (AUC) for peak (1-2 min) and tail (2-60 min), volume of distribution (V-T) obtained using Logan analysis, and VT and K, obtained with a basis function implementation of a single tissue compartment model. Best results were obtained with PVC-OSEM using 4 iterations and 16 subsets. Based on 11 C point source measurements, a 4.5 non FWHM (full width at half maximum) resolution kernel was used to correct for partial volume effects. A ROI consisting of the four hottest pixels per plane (over the carotid arteries) was the best method to extract IDIFs. Excellent peak AUC ratios (0.99 +/- 0.09) between IDIF and blood sampler input function (BSIF) were found. Furthermore, extracted IDIFs provided V-T, and K-1 values that were very similar to those obtained using BSIFs. The proposed method appears to be suitable for analysing [C-11] flumazenil data without the need for online arterial sampling. (c) 2007 Elsevier Inc. All rights reserved.

关键词： Area Under Curve Brain/radionuclide imaging Calibration Carotid Arteries/radionuclide imaging Flumazenil/diagnostic use Flumazenil/pharmacokinetics Fourier Analysis Fourier Analysis GABA Modulators/diagnostic use GABA Modulators/pharmacokinetics Humans image processing, computer-assisted/methods Radiopharmaceuticals/diagnostic use Radiopharmaceuticals/diagnostic use Radiopharmaceuticals/pharmacokinetics Radiopharmaceuticals/pharmacokinetics

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A comparison of methods for the automated calculation of volumes and atrophy rates in the hippocampus

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NEUROimage 2008年第4期40卷 1655-1671页

作者： Barnes, J. Foster, J. Boyes, R. G. Pepple, T. Moore, E. K. Schott, J. M. Frost, C. Scahill, R. I. Fox, N. C. UCL Dementia Res Ctr Natl Hosp Neurol & Neurosurg London WC1N 3BG England London Sch Hyg & Trop Med Med Stat Unit London WC1 England

Hippocampal atrophy rates have been used in a number of studies in Alzheimer's disease ( AD) to assess disease progression and are being increasingly utilized as an outcome measure in clinical trials of new pharmaceutical agents. Owing to the labor-intensive nature of hippocampal segmentation, more automated approaches are required for such analysis. In this study we compared methods of automatically segmenting the hippocampus (single-person template and template library) on the baseline image in a group of probable AD (n = 36) and control (n = 19) subjects with serial images. Using the method that gave most similar results to manual, three automated methods of calculating change within the hippocampal region were compared: fluid change calculated using ( 1) Jacobian change or ( 2) region propagation and ( 3) boundary shift. Rates were compared with manual measures. We found that segmentation of baseline hippocampus was most accurate using a template library combined with morphological operations ( intensity thresholding plus one conditional dilation). This gave a voxel similarity of 0.69 (0.05) and 0.72 (0.06) in controls and probable AD subjects respectively compared with manual measures. Atrophy rates within these regions were most similar to the manual rates using the boundary shift integral ( mean difference from manual rate 0.03% (1.29) in controls and 0.48% (2.44) in AD). A template library segmentation approach, together with morphological operations, provides a segmentation accurate enough to quantify relative change over time. The change over time can then be calculated automatically using boundary shift or fluid measures, with boundary shift giving most similar results to manual. (c) 2008 Elsevier Inc. All rights reserved.

关键词： Aged Algorithms Alzheimer Disease/pathology Atrophy/pathology Biological Markers Cross-Sectional Studies Disease Progression Female Hippocampus/pathology Humans image processing, computer-assisted/methods Linear Models Logistic Models Longitudinal Studies Magnetic Resonance Imaging Male Neuropsychological Tests Nonlinear Dynamics

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