High Throughput Screening of Gene Expression Signatures

This paper focuses on microarray image analysis and discusses a completely automated approach to image processing, which eliminates human intervention. A system for automated image processing is described, which is capable of processing image files in a batch-mode thus allowing high-throughput of microarray image analysis. Grid-placement and spot finding are achieved without operator's help. The software eliminates noise signals from the data analysis process and minimizes operator's involvement in the procedure.     

A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection

Separation of complex mixtures of proteins by two-dimensional gel electrophoresis (2-DE) is a fundamental component of current proteomic technology. Quantitative analysis of the images generated by digitization of such gels is critical for the identification of alterations in protein expression within a given biological system. Despite the availability of several commercially available software packages designed for this purpose, image analysis is extremely resource intensive, subjective and remains a major bottleneck. In addition to reducing throughput, the requirement for manual intervention results in the introduction of operator subjectivity, which can limit the statistical significance of the numerical data generated. A key requirement of image analysis is the accurate definition of protein spot boundaries using a suitable method of image segmentation. We describe a method of spot detection applicable to 2-DE image files using a segmentation method involving pixel value collection via serial analysis of the image through its range of density levels. This algorithm is reproducible, sensitive, accurate and primarily designed to be automatic, removing operator subjectivity. Furthermore, it is believed that this method may offer the potential for improved spot detection over currently available software.     

A software system to record and analyze digitized cell images

This paper describes basic software for digitization and processing of microscopic cell images used at the Department of Clinical Cytology at Uppsala University Hospital. A family of programs running on a PDP-8 minicomputer which is connected to a Leitz Orthoplan microscope with two image scanners, one diode-array scanner and a moving-stage photometer, is used for data collection. The digitized image data is converted by converted by conversion program to IBM compatible format. The data structures for image processing and statistical evaluation on the IBM system are also described. Finally, some experiences from the use of the software in cytology automation are discussed.     

Using statistical image models for objective evaluation of spot detection in two-dimensional gels

Protein spot detection is central to the analysis of two-dimensional electrophoresis gel images. There are many commercially available packages, each implementing a protein spot detection algorithm. Despite this, there have been relatively few studies comparing the performance characteristics of the different packages. This is in part due to the fact that different packages employ different sets of user-adjustable parameters. It is also partly due to the fact that the images are complex. To carry out an evaluation, "ground truth" data specifying spot position, shape and intensities needs to be defined subjectively on selected test images. We address this problem by proposing a method of evaluation using synthetic images with unambiguous interpretation. The characteristics of the spots in the synthetic images are determined from statistical models of the shape, intensity, size, spread and location of real spot data. The distribution of parameters is described using a Gaussian mixture model obtained from training images. The synthetic images allow us to investigate the effects of individual image properties, such as signal-to-noise ratios and degree of spot overlap, by measuring quantifiable outcomes, e.g. accuracy of spot position, false positive and false negative detection. We illustrate the approach by carrying out quantitative evaluations of spot detection on a number of widely used analysis packages.     

Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels

Efficient analysis of protein expression by using two-dimensional electrophoresis (2-DE) data relies on the use of automated image processing techniques. The overall success of this research depends critically on the accuracy and the reliability of the analysis software. In addition, the software has a profound effect on the interpretation of the results obtained, and the amount of user intervention demanded during the analysis. The choice of analysis software that best meets specific needs is therefore of interest to the research laboratory. In this paper we compare two advanced analysis software packages, PDQuest and Progenesis. Their evaluation is based on quantitative tests at three different levels of standard 2-DE analysis: spot detection, gel matching and spot quantitation. As test materials we use three gel sets previously used in a similar comparison of Z3 and Melanie, and three sets of gels from our own research. It was observed that the quality of the test gels critically influences the spot detection and gel matching results. Both packages were sensitive to the parameter or filter settings with respect to the tendency of finding true positive and false positive spots. Quantitation results were very accurate for both analysis software packages.     

智能化鼠多功能行为训练系统的研究

目的：研制一种微机控制的大鼠多功能行为训练检测系统－梯度电压自动驱动大鼠及微机适时显示,记录和分析实验结果。方法：采用仿windows界面,以TurboC2．0编制,利用TC直接对硬件端口操作,完成信号的采集,处理和对实验仪器的控制。结果：本系统实现了：①梯度电压自动驱动;②声,光,电不同条件刺激;③多路径自动设置;④所没数据建立数据库以SAS软件处理其结果。结论：本系统自动化程度高,操作简便,数据处理科学、准确,尤其是还可用于听觉、视觉等特殊鼠记忆模型的建立。     

Easily assembled digital data acquisition system for the analytical ultracentrifuge

A system for the acquisition of digital data from the analytical ultracentrifuge which uses a commercially available data acquisition board, a standard IBM compatible personal computer (PC), and an interface circuit has been developed. The system uses the signal from the standard Beckman scanner. Preliminary analysis and data reduction are performed at the PC within minutes of data acquisition using simple commercially available software, and final data fitting is performed with a mainframe computer. Procedures are described which allow approach to equilibrium to be followed and attainment of equilibrium to be demonstrated. Data density of 200 points per millimeter column height (500 points per 100 μ1 of sample) allows the use of short columns and hence short run times. Only 2 min are required to collect a complete scan, which is recorded in a format suitable for direct analysis by standard spreadsheet software. This allows multiple sequential scans to be quickly recorded at equilibrium and averaged to reduce noise prior to analysis. The combination of characteristics allows molecular weight determinations to be performed relatively quickly with only a few micrograms of protein. The system is inexpensive and easy to assemble given the centrifuge and a PC.     

Software for quantitation and visualization of expression array data

Software is described that facilitates the analysis of phosphoimages from large array hybridizations. The Macintosh PowerPC-compatible application and its manual are available at no charge from http:?people.bu.edu/strehlow. The software is compatible with both custom formats and array filters from three commercial manufacturers. It allows the rapid quantitation of every spot on images of hybridizations to large arrays. The user drags grids of squares over the spots on the image to define the coordinates of each spot, then aligns and edits the position of the grid. The software then corrects the positions as necessary and quantitates up to 27,000 spots per image. It stores the numerical values for each signal in a format called the fingerprint file. Fingerprint files can be directly averaged or compared, allowing the user to find mean values or differences in data from independent hybridization experiments. Data can be recalled from the fingerprint file and can be output in a variety of spreadsheet formats with several options for background correction. Finally, the software offers an output format that allows the convenient visualization of data points using animated, three-dimensional graphs.     

Modular PC-based data acquisition and processing system for biological signals]

The data acquisition system described here is designed for biomedical research and permits the recording of up to eight biological signals simultaneously. A personal computer using the Windows 95 operating system is employed for data monitoring, data processing and analysis during experiments. The system has been designed for reliability, economy, flexibility and ease of handling, with the aim of achieving universal application. To avoid interface incompatibility, problems with transfer protocols and the data formats of commercially available products, analog signals are used for further processing. The individual input channels are electrically isolated from one another and the PC to avoid ground loops, and for reasons of safety. An isolated voltage supply is available for pre-amplifiers and bridges. A bandwidth of 0-5 kHz and the maximum sampling rate of 12.5 kHz suffice to pick up higher frequency signals such as EMG and ENG. The modular software and hardware concepts permit the use of almost any desktop or laptop PC as a central processing unit. The PC handless documentation, data acquisition, data analysis and the preparation of publications. If needed, further analytical functions can be added in modular form. Finally, the option of saving data in the ASCII format permits processing of results with such standard software packages as Excel, Access, Matlab and Origin.     

Improving gene quantification by adjustable spot-image restoration

MOTIVATION: One of the major factors that complicate the task of microarray image analysis is that microarray images are distorted by various types of noise. In this study a robust framework is proposed, designed to take into account the effect of noise in microarray images in order to assist the demanding task of microarray image analysis. The proposed framework, incorporates in the microarray image processing pipeline a novel combination of spot adjustable image analysis and processing techniques and consists of the following stages: (1) gridding for facilitating spot identification, (2) clustering (unsupervised discrimination between spot and background pixels) applied to spot image for automatic local noise assessment, (3) modeling of local image restoration process for spot image conditioning (adjustable wiener restoration using an empirically determined degradation function), (4) automatic spot segmentation employing seeded-region-growing, (5) intensity extraction and (6) assessment of the reproducibility (real data) and the validity (simulated data) of the extracted gene expression levels. RESULTS: Both simulated and real microarray images were employed in order to assess the performance of the proposed framework against well-established methods implemented in publicly available software packages (Scanalyze and SPOT). Regarding simulated images, the novel combination of techniques, introduced in the proposed framework, rendered the detection of spot areas and the extraction of spot intensities more accurate. Furthermore, on real images the proposed framework proved of better stability across replicates. Results indicate that the proposed framework improves spots' segmentation and, consequently, quantification of gene expression levels. AVAILABILITY: All algorithms were implemented in Matlab (The Mathworks, Inc., Natick, MA, USA) environment. The codes that implement microarray gridding, adaptive spot restoration and segmentation/intensity extraction are available upon request. Supplementary results and the simulated microarray images used in this study are available for download from: ftp://users:bioinformatics@mipa.med.upatras.gr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Data acquisition in thermal physiology: Measurements of shivering

1. 1.|Simple electronics for measurement of shivering, which include direct and mean rectified EMG (U_mrv), are suggested.

2. 2.|A software system (LabGraph) for measurement and analysis is described.

3. 3.|Three different electrode designs were tested with the system by recording electromyography (EMG) from m. iliotibialis with subdermal, intramuscular and safety pin electrodes in bantam hens exposed to cold eggs. The signal characteristics of EMG are discussed in relation to electrode design and signal processing.

4. 4.|A method for normalizing EMG activity within an experiment to units of heat production is presented and was tested successfully in bantam hens.

Software package for automatic microarray image analysis (MAIA)

Although various software solutions are currently available for microarray image analysis, one would still expect to develop algorithms ensuring higher level of intelligence and robustness. We present a fully functional software package for automatic processing of the two-color microarray images including spot localization, quantification and quality control. The developed algorithms aim at making ratio estimates more resistant to array contamination and offer automatic tools to evaluate spot quality. Availability: A demo version of the software can be downloaded from http://bioinfo.curie.fr/projects/maia. A full version is freely available to non-commercial users upon request from the authors.     

A microprocessor-based underwater data acquisition system

Summary A microprocessor-based data-acquisition system has been developed to meet the requirements of a range of oceanic sensor inputs. The system described is specially suitable for low-power, long-period underwater applications. Details are given of the hardware and software design, and examples of interface to propeller current sensor and pressure transducer. Preliminary field results in the Northern Great Barrier Reef are described.     

High resolution nanomechanical characterization of multi‐domain model membranes by fast Force Volume

Plasma membrane is a complex structure, mainly composed by lipids and proteins, which plays a pivotal role in cell metabolism by regulating its selective permeability to ions and molecules. According to the “raft hypothesis”, lipids in the bilayer are not forming a structurally passive solvent, but are rather organized in specific domains, which present different structural and functional characteristics. The mechanical properties of the lipid part of plasma membrane have been recently characterized through Atomic Force Microscopy, by analyzing the features of force vs distance curves collected on supported lipid bilayers (SLBs). In case of lipid domains sizing from tens to hundreds of nanometers, which mimic in a good way the lateral organization of real membranes, a high lateral resolution and a large number of curves are often required for properly expressing the complexity of the system, with a consequent exponential growth of acquisition and processing time. In this paper we propose a method, based on a recently developed high speed Force Volume technique and on home‐built data processing software, for the mechanical characterization of nanostructured SLBs. With our software we have been able to process data set composed by tens of thousands of curves, collected with a spatial resolution ranging from 8 to 40 nm/pixel. Multiparametric maps and distribution histograms produced by our analysis allowed identifying a specific behavior for each lipid phase in the investigated model membranes, even in presence of nanosized features. Copyright © 2015 John Wiley & Sons, Ltd.     

Image analysis for monitoring the barley tempeh fermentation process

AIMS: To develop a fast, accurate, objective and nondestructive method for monitoring barley tempeh fermentation. METHODS AND RESULTS: Barley tempeh is a food made from pearled barley grains fermented with Rhizopus oligosporus. Rhizopus oligosporus growth is important for tempeh quality, but quantifying its growth is difficult and laborious. A system was developed for analysing digital images of fermentation stages using two image processing methods. The first employed statistical measures sensitive to image colour and surface structure, and these statistical measures were highly correlated (r=0.92, n=75, P<0.001) with ergosterol content of tempeh fermented with R. oligosporus and lactic acid bacteria (LAB). In the second method, an image-processing algorithm optimized to changes in images of final tempeh products was developed to measure number of visible barley grains. A threshold of 5 visible grains per Petri dish indicated complete tempeh fermentation. When images of tempeh cakes fermented with different inoculation levels of R. oligosporus were analysed the results from the two image processing methods were in good agreement. CONCLUSION: Image processing proved suitable for monitoring barley tempeh fermentation. The method avoids sampling, is nonintrusive, and only requires a digital camera with good resolution and image analysis software. SIGNIFICANCE AND IMPACT OF THE STUDY: The system provides a rapid visualization of tempeh product maturation and qualities during fermentation. Automated online monitoring of tempeh fermentation by coupling automated image acquisition with image processing software could be further developed for process control.     

A double scanning microphotometer for image analysis: hardware, software and biomedical applications.

A new image processing system designed for densitometry and pattern analysis of microscopic specimens is described with special regard to the hardware, the software and the biologic applications. The data acquisition procedure involves the combination between the scanning of the preparation by means of a motorized stage and the scanning of successive fields by a mechanical device. The signal provided by the photomultiplier is converted into digital values which are directed to an on-line computer. The data processing is based on a one-pass computation involving automata theory and therefore it avoids the storage of the image in the computer memory. In so doing, an entire and continuous image of the whole preparation can be processed at the highest magnification of the microscope whatever the size of the analyzed specimen may be. A biologic application of the system is reported and concerns the automatic identification and counting of cells in the various phases of the mitotic cycle.     

A general-purpose system for the rapid acquisition and computer processing of optical and scanning electron microscope images—II. Software

The design and implementation of software for the operation of a general-purpose optical and electron microscope image processing system is described. The software is a group of programs, controlled by a command-line interpreter called IPR (Image PRocessing). The interpreter may be used interactively, or groups of commands may be issued indirectly after placing them in files. Programs for specialized image processing applications may obtain the services of the system's memory-resident programs, through the same interprogram communication methods that are used by the command-line interpreter.     

A computerized respiratory system including test functions of lung and circulation

The design of a microcomputer-controlled ventilator for automatic performance of lung function and circulatory tests has been described. It incorporates the characteristics of normal mechanical ventilation and also allows one to perform a multitude of test procedures for lung function and circulatory studies in paralyzed animals. The major components of the setup are a pump assembly with solenoid valves to direct gas flow, an electromechanical servo system, and a MS-DOS microcomputer system. The pump assembly has been constructed as a relatively simple device. Great versatility is created by the use of a microcomputer for the control of the ventilator. The software can be easily adapted to several other types of experimental studies. Besides the keyboard input the ventilator can be controlled by a remote computer system. This allows one to run an experimental protocol automatically and to use it in closed-loop servo ventilation. The flexibility in the choice of the respiratory parameters makes the ventilator suitable for lung function and circulatory studies during artificial ventilation. The ventilator has been successfully used in different animal studies during the last 6 yr.