A computer system automatic analysis of vectorcardiograms.

This computer system performs the analysis of orthogonal electrocardiograms for vectorcardiographic (VCG) display and classification. The data acquisition can be performed 'on-line' with the complete analysis in 'real-time', or off-line by processing a magnetic tape. The original computational methods for beat averaging and wave recognition are described. Some features, such as the quality of the visual display of the VCG traces, the availability of a measurement matrix allowing the quantitative analysis of the VCG and the use of a data bank for storage, retrieval and statistical studies make this system very efficient for clinical purposes, introducing the concept of 'Computer Assisted Vectorcardiography'.     

Two-parameter data acquisition system for rapid slit-scan analysis of mammalian chromosomes

A data acquisition system is described for recording two independent signals simultaneously from a laser-based flow cytometer for rapid slit-scan chromosome analysis. High-aperture microscope optics allow recording of fluorescence distributions along the longest axis of metaphase chromosomes with a spatial resolution better than 1 micron. Fluorescence and small angle forward light scatter as well as dual-wavelength fluorescence signals from Indian muntjac chromosomes stained with propidium iodide (PI) or acridine orange (AO) have been recorded simultaneously. While maintaining the multi-user operation of the computer, photomultiplier signals are digitized at a rate of 400 signals per second, stored temporarily in high-speed cache memories, and transferred subsequently to a minicomputer for further storage. Extensive software packages for data acquisition, analysis, and display of the results are described. Data acquisition is generally done in list mode, allowing complete reconstruction of individual signals (profiles) at any time. The distribution of stained constituents along the chromosomes can be displayed. Furthermore, histograms of various parameters of the input signals may be generated.     

MUST, a computer package of Management Utilities for Sequences and Trees.

The MUST package is a phylogenetically oriented set of programs for data management and display, allowing one to handle both raw data (sequences) and results (trees, number of steps, bootstrap proportions). It is complementary to the main available software for phylogenetic analysis (PHYLIP, PAUP, HENNING86, CLUSTAL) with which it is fully compatible. The first part of MUST consists of the acquisition of new sequences, their storage, modification, and checking of sequence integrity in files of aligned sequences. In order to improve alignment, an editor function for aligned sequences offers numerous options, such as selection of subsets of sequences, display of consensus sequences, and search for similarities over small sequence fragments. For phylogenetic reconstruction, the choice of species and portions of sequences to be analyzed is easy and very rapid, permitting fast testing of numerous combinations of sequences and taxa. The resulting files can be formatted for most programs of tree construction. An interactive tree-display program recovers the output of all these programs. Finally, various modules allow an in-depth analysis of results, such as comparison of distance matrices, variation of bootstrap proportions with respect to various parameters or comparison of the number of steps per position. All presently available complete sequences of 28S rRNA are furnished aligned in the package. MUST therefore allows the management of all the operations required for phylogenetic reconstructions.     

Open, reconfigurable cytometric acquisition system: ORCAS.

A digital signal processing (DSP)-based digital data acquisition system has been developed to support novel flow cytometry efforts. The system flexibility includes how it detects, captures, and processes event data. Custom data capture boards utilizing analog to digital converters (ADCs) and field programmable gate arrays (FPGA) detect events and capture correlated event data. A commercial DSP board processes the captured data and sends the results over the IEEE 1394 bus to the host computer that provides a user interface for acquisition, display, analysis, and storage. The system collects list mode data, correlated pulse shapes, or streaming data from a variety of detector types using Linux, Mac OS X, and Windows host computers. It extracts pulse features not found on commercial systems with excellent sensitivity and linearity over a wide dynamic range. List mode data are saved in FCS 3.0 formatted files while streaming or correlated waveform data are saved in custom format files for postprocessing. Open, reconfigurable cytometric acquisition system is compact, scaleable, flexible, and modular. Programmable feature extraction algorithms have exciting possibilities for both new and existing applications. The recent availability of a commercial data capture board will enable general availability of similar systems.     

A low-cost microcomputer-based data acquisition and analysis system for an electron spin resonance spectrometer: data handling of dilute spin labeled nucleic acids

This article describes the construction of an inexpensive and reliable data acquisition system for a Varian E-line Century Series ESR spectrometer utilizing an Apple II Plus microcomputer. All necessary hardware is readily available and used without modification. A BASIC program for routine collection, display, plotting and disk storage of experimental data has been written and subsequently compiled into machine code for high speed operation. The interface offers distinct advantages in spectral resolution as well as instrument control. An example of signal enhancement via computer controlled time averaging is presented for a spin labeled DNA experiment. The technique has recently been applied to studies of relative binding affinities of gene-32 protein for various spin-labeled polynucleotides.     

Computer graphics presentation modes for biologic data. Types and examples

New advances in automated cytology, computer microscopy, densitometry and other instrumentation for feature/scene acquisition or analysis have resulted in higher information densities than heretofore encountered. Two-, three- and four-space computer graphics provide favorable bandwidth conditions for transforming complex, large-scale data sets into visual displays that allow a human observer, utilizing the brain's efficient processing of visual information, to rapidly grasp relationships and synthesize concepts. Examples of multidimensional displays are presented, all developed by neuroscientists who are not computer specialists. Because modern graphics and image-synthesis techniques can now be implemented on any one of several commercially available very-high-speed integrated-circuit-based display systems, at moderate cost, exploitation of specifically visual presentation should be carefully considered in any system generating information in high density.     

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a ‘digital twin’ software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.     

Time-Gated Optical Projection Tomography Allows Visualization of Adult Zebrafish Internal Structures

Optical imaging through biological samples is compromised by tissue scattering and currently various approaches aim to overcome this limitation. In this paper we demonstrate that an all optical technique, based on non-linear upconversion of infrared ultrashort laser pulses and on multiple view acquisition, allows the reduction of scattering effects in tomographic imaging. This technique, namely Time-Gated Optical Projection Tomography (TGOPT), is used to reconstruct three dimensionally the internal structure of adult zebrafish without staining or clearing agents. This method extends the use of Optical Projection Tomography to optically diffusive samples yielding reconstructions with reduced artifacts, increased contrast and improved resolution with respect to those obtained with non-gated techniques. The paper shows that TGOPT is particularly suited for imaging the skeletal system and nervous structures of adult zebrafish.     

Developmental maps of acetylcholinesterase and G4-antigen of the early chicken brain: long-distance tracts originate from AChE-producing cell bodies

After approaching the outer surface of the neuroepithelium, postmitotic cell bodies abruptly start to synthesize acetylcholinesterase (AChE). Their easy histochemical detection allows us to trace sensitively spatiotemporal patterns of differentiation processes of the chicken nervous system. To investigate the relationship between postmitotic AChE production and the first formation of neurites, AChE histochemistry is combined here with immunohistochemistry using the neurite-specific G4-antibody. Spatial computer reconstructions from double-stained serial sections of whole brains of H.H. stages 10-20 demonstrate that G4-neurite expression spatio-temporally follows the expression of AChE in its complex polycentric pattern closely, the details of which have been described earlier. By comparing both differentiative steps at the single cell level reveals that a great majority (if not all) of the G4-positive neurites originate from AChE-positive cell bodies. Based on both the computer reconstructions as well as single cell analysis, including [3H]-thymidine pulse-experiments followed by autoradiography, we conclude, that AChE expression precedes formation of G4-neurites by about 15 h. In addition, the reconstructions provide the first detailed maps of G4-fiber tract formation and shows that G4-neurites form fascicles, most of which travel over long distances to targets within or without the central nervous system (CNS). This is the first demonstration for the entire young chicken brain which verifies that AChE-expressing cells, generally, are those that will establish efferents to distant targets.     

Three-dimensional video analysis of facial movements: a new method to assess the quantity and quality of the smile

The results of neuromuscular reconstructions of the paralyzed face are difficult to assess. Very sophisticated methods are necessary to measure the motor deficits of facial paralysis or the functional recovery in the face. The aim of this development was a relatively simple system for data acquisition, which is easy to handle and which makes it relatively cheap to delegate data acquisition to centers all over the world, which will not be able to derive a data analysis on their own, but will send their data to a center with specialized equipment. A complex mirror system was developed to get three different views of the face at the same time on the video screen. At each investigation, a digital video is taken from a calibration grid and from standardized facial movements of the patient. Secondary analysis of the digital videofilm is made possible at any time later on by the support of a computer program, which calculates distances and movements three-dimensionally from the frontal image and the right and left mirror images. Pathologies of the mimic movements can be identified as well as improvements after surgical procedures by this system. The significant advantage is the possibility to watch the same movement on the video which is under study and to apply any kind of study later on. Taking the video needs only a few minutes, and fatigue of the patient's mimic system is prevented. Measurements usually at the endpoints of the movements give excellent information on the quantity of the movement or the degree of the facial palsy, whereas the video itself is very informative regarding the quality of the smile. Specific computer software was developed for standardized three-dimensional analysis of the video-documented facial movements and for data presentation. There are options like two-dimensional graphs of single moving points in the face or three-dimensional graphs of the movements of all measured points at the same time during a standardized facial movement. By a comparison of the right- and left-sided alterations of specific distances between two points during the facial movements, the degree of normal symmetry or pathologic asymmetry is quantified. This system is more suitable for detailed scientific multicenter studies than any other system previously established. A very sensitive instrument for exact evaluation of mimic function is now available.     

A computer-assisted cell identification system

A computer and optical microscope image processing system for the acquisition, editing and analysis of quantitative, multivariate, cell nuclear data is described. The experimental equipment and methods are discussed, the mathematics used are presented, and the additions, modifications and deletions to the TICAS 11/45 set of computer programs for the analysis of the data are outlined.     

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.     

General purpose, field-portable cell-based biosensor platform.

There are several groups of researchers developing cell-based biosensors for chemical and biological warfare agents based on electrophysiologic monitoring of cells. In order to transition such sensors from the laboratory to the field, a general-purpose hardware and software platform is required. This paper describes the design, implementation, and field-testing of such a system, consisting of cell-transport and data acquisition instruments. The cell-transport module is a self-contained, battery-powered instrument that allows various types of cell-based modules to be maintained at a preset temperature and ambient CO(2) level while in transit or in the field. The data acquisition module provides 32 channels of action potential amplification, filtering, and real-time data streaming to a laptop computer. At present, detailed analysis of the data acquired is carried out off-line, but sufficient computing power is available in the data acquisition module to enable the most useful algorithms to eventually be run real-time in the field. Both modules have sufficient internal power to permit realistic field-testing, such as the example presented in this paper.     

Towards neural circuit reconstruction with volume electron microscopy techniques

Electron microscopy is the only currently available technique with a resolution adequate to identify and follow every axon and dendrite in dense neuropil. Reconstructions of large volumes of neural tissue, necessary to reconstruct even local neural circuits, have, however, been inhibited by the daunting task of serially sectioning and reconstructing thousands of sections. Recent technological developments have improved the quality of volume electron microscopy data and automated its acquisition. This opens up the prospect of reconstructing almost complete invertebrate and sizable fractions of vertebrate nervous systems. Such reconstructions of complete neural wiring diagrams could rekindle the tradition of relating neural function to the underlying neuroanatomical circuitry.     

Development of a fully integrated microdistillation flow injection system for the determination of trace level ammonia

An in-housed designed computerised flow injection system comprised a fully integrated microdistillation flow injection (MDFI) system for low level ammonia analysis was reported. In this system, the microdistillation separation step was incorporated into the flow injection manifold and the ammonia gas sensing probe sensing element was replaced by a flow-through micro-pH electrode which sensed the change in pH of a flowing collector solution caused by the dissolution of distilled ammonia gas, in a process analogous to that occurring in the internal solution of the gas sensing probe. A computerised control and data acquisition system was constructed for this system using a commercially available data acquisition card which offered many advantages such as improved data acquisition rates and control over the system components, as well as good graphics display and data processing options. The system was optimised using a multi-variable simplex optimisation technique.     

Low cost multi user multi platform accessible HPLC data acquisition system

Summary A low cost multi user multi platform accessible HPLC data acquisition system has been designed for use in a laboratory environment. This system uses available HPLC measurement systems that lack modern network communication tools and a low cost computer with reliable software. HPLC data are portable to any other computer by means of File Transport Protocol (FTP) communication and can then be used for data analysis. Off line analysis of ethanol data showed a substantial improvement over the old system in terms of data accuracy and skewness. Furthermore, off line data analysis could resolve hidden acetaldehyde peaks which revealed to be oscillatory.     

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.     

On-line data acquisition and evaluation of long-term measurements of circadian rhythms in individual cells of Acetabularia

A multitasking time-sharing computer system was implemented for studies of different circadian rhythms in individual cells of the unicellular green alga, Acetabularia. This fully automatized system allows simultaneous data acquisition and analysis. Graphical presentation of untreated and mathematically treated data is permanently available on three graphic displays and on a digital plotter. The sampling rate for the data acquisition in each of the 60 channels connected to the system is 720/24 h. Provisions have been made to guarantee uninterrupted data uptake for these long-term measurements by including an auto-restart module and by providing extremely reliable software for the experimenter using menu techniques.     

A computerized system for scoring primate behavior using standard keyboards

A scoring system has been developed for primate behavior which uses standard keyboards and minicomputers or microcomputers. The mnemonic, alphanumeric code used is easily learned, highly flexible, and can be recorded in longhand for later entry into a computer if a keyboard is not immediately available. The software consists of two programs, both of which can be written in BASIC. SCORE is used for data acquisition and appends the test time to each behavioral sequence. DATSUM decodes and summarizes the test data using table-driven logic. The minimum hardware required is a 16K microcomputer, an alphanumeric keyboard, a display, and cassette storage.     

On-line data acquisition and evaluation of long-term measurements of circadian rhythms in individual cells ofAcetabularia

A multitasking time-sharing computer system was implemented for studies of different circadian rhythms in individual cells of the unicellular green alga,Acetabularia. This fully automatized system allows simultaneous data acquisition and analysis. Graphical presentation of untreated and mathematically treated data is permanently available on three graphic displays and on a digital plotter. The sampling rate for the data acquisition in each of the 60 channels connected to the system is 720/24 h. Provisions have been made to guarantee uninterrupted data uptake for these long-term measurements by including an auto-restart module and by providing extremely reliable software for the experimenter using menu techniques.