MicroMeasure: a new computer program for the collection and analysis of cytogenetic data.

The ability to identify individual chromosomes in cytological preparations is an essential component of many investigations. While several computer software applications have been used to facilitate such quantitative karyotype analysis, most of these programs are limited by design for specific types of analyses, or can be used only with specific hardware configurations. MicroMeasure is a new image analysis application that may be used to collect data for a wide variety of chromosomal parameters from electronically captured or scanned images. Unlike similar applications, MicroMeasure may be individually configured by the end user to suit a wide variety of research needs. This program can be used with most common personal computers, and requires no unusual or specific hardware. MicroMeasure is made available to the research community without cost by the Department of Biology at Colorado State University via the World Wide Web at http://www.biology.colostate.edu/MicroMeasure.     

Portable telepathology: methods and tools

Telepathology is becoming easier to implement in most pathology departments. In fact e-mail image transmit can be done from almost any pathologist as a simplistic telepathology system. We tried to develop a way to improve capabilities of communication among pathologists with the idea that the system should be affordable for everybody. We took the premise that any pathology department would have microscopes and computers with Internet connection, and selected a few elements to convert them into a telepathology station. Needs were reduced to a camera to collect images, a universal microscope adapter for the camera, a device to connect the camera to the computer, and a software for the remote image transmit. We found out a microscope adapter (MaxView Plus) that allowed us connect almost any domestic digital camera to any microscope. The video out signal from the camera was sent to the computer through an Aver Media USB connector. At last, we selected a group of portable applications that were assembled into a USB memory device. Portable applications are computer programs that can be carried generally on USB flash drives, but also in any other portable device, and used on any (Windows) computer without installation. Besides, when unplugging the device, none of personal data is left behind. We selected open-source applications, and based the pathology image transmission to VLC Media Player due to its functionality as streaming server, portability and ease of use and configuration. Audio transmission was usually done through normal phone lines. We also employed alternative videoconferencing software, SightSpeed for bi-directional image transmission from microscopes, and conventional cameras allowing visual communication and also image transmit from gross pathology specimens. All these elements allowed us to install and use a telepathology system in a few minutes, fully prepared for real time image broadcast.     

Applications of a signal averager for neurophysiological investigations in clinical function laboratories using a general signal-processing unit

A general 'coherent signal averager' software package which can be run on a small laboratory computer is presented as an application of a new approach to medical instrumentation. The combination of the minicomputer, preprocessing hardware and the above-mentioned software yields a flexible multipurpose averaging system for electrophysiological signals. The possibilities of the system are discussed with reference to visual evoked potential measurements in a clinical function laboratory.     

DScan - a high-performance digital scanning system for entomological collections

Here we describe a high-performance imaging system for creating high-resolution images of whole insect drawers. All components of the system are industrial standard and can be adapted to meet the specific needs of entomological collections. A controlling unit allows the setting of imaging area (drawer size), step distance between individual images, number of images, image resolution, and shooting sequence order through a set of parameters. The system is highly configurable and can be used with a wide range of different optical hardware and image processing software.     

Computer-assisted sperm analysis (CASA): Capabilities and potential developments

Computer-assisted sperm analysis (CASA) systems have evolved over approximately 40 years, through advances in devices to capture the image from a microscope, huge increases in computational power concurrent with amazing reduction in size of computers, new computer languages, and updated/expanded software algorithms. Remarkably, basic concepts for identifying sperm and their motion patterns are little changed. Older and slower systems remain in use. Most major spermatology laboratories and semen processing facilities have a CASA system, but the extent of reliance thereon ranges widely. This review describes capabilities and limitations of present CASA technology used with boar, bull, and stallion sperm, followed by possible future developments. Each marketed system is different. Modern CASA systems can automatically view multiple fields in a shallow specimen chamber to capture strobe-like images of 500 to >2000 sperm, at 50 or 60 frames per second, in clear or complex extenders, and in <2 minutes, store information for ≥30 frames and provide summary data for each spermatozoon and the population. A few systems evaluate sperm morphology concurrent with motion. CASA cannot accurately predict ‘fertility’ that will be obtained with a semen sample or subject. However, when carefully validated, current CASA systems provide information important for quality assurance of semen planned for marketing, and for the understanding of the diversity of sperm responses to changes in the microenvironment in research. The four take-home messages from this review are: (1) animal species, extender or medium, specimen chamber, intensity of illumination, imaging hardware and software, instrument settings, technician, etc., all affect accuracy and precision of output values; (2) semen production facilities probably do not need a substantially different CASA system whereas biology laboratories would benefit from systems capable of imaging and tracking sperm in deep chambers for a flexible period of time; (3) software should enable grouping of individual sperm based on one or more attributes so outputs reflect subpopulations or clusters of similar sperm with unique properties; means or medians for the total population are insufficient; and (4) a field-use, portable CASA system for measuring one motion and two or three morphology attributes of individual sperm is needed for field theriogenologists or andrologists working with human sperm outside urban centers; appropriate hardware to capture images and process data apparently are available.     

Future directions in computer simulation

Developments in computer hardware and software are making significant improvements in the availability of simulation for biomedical researchers. This paper reviews past and present techniques for digital computer simulation and looks at improvements likely in the near future. In the area of hardware, personal computers are making computing and simulation more widely available and at the same time, supercomputers and special-purpose numerical processors are making it possible to solve larger problems. Software developments for simulation are reducing the time, effort and special skills required to produce a simulation program. A new hierarchical linker is proposed to make it easy to synthesize a global model by combining existing submodels. In the more distant future, computer models may be constructed graphically and with the assistance of intelligent programs capable of analysis and information retrieval.     

An Innovative Method for Obtaining Consistent Images and Quantification of Histochemically Stained Specimens

Obtaining digital images of color brightfield microscopy is an important aspect of biomedical research and the clinical practice of diagnostic pathology. Although the field of digital pathology has had tremendous advances in whole-slide imaging systems, little effort has been directed toward standardizing color brightfield digital imaging to maintain image-to-image consistency and tonal linearity. Using a single camera and microscope to obtain digital images of three stains, we show that microscope and camera systems inherently produce image-to-image variation. Moreover, we demonstrate that post-processing with a widely used raster graphics editor software program does not completely correct for session-to-session inconsistency. We introduce a reliable method for creating consistent images with a hardware/software solution (ChromaCal™; Datacolor Inc., NJ) along with its features for creating color standardization, preserving linear tonal levels, providing automated white balancing and setting automated brightness to consistent levels. The resulting image consistency using this method will also streamline mean density and morphometry measurements, as images are easily segmented and single thresholds can be used. We suggest that this is a superior method for color brightfield imaging, which can be used for quantification and can be readily incorporated into workflows.     

Rationale and methodology for testing auditory cognition in songbirds

Songbirds, and in particular zebra finches, present a wonderful opportunity to study cognition in species that have evolved specialized abilities and brain structures for auditory cognition. The authors describe the rationale, methods, and apparatus used to test the auditory perceptual and cognitive abilities of songbirds. They have developed an operant conditioning system for conducting discrimination experiments simultaneously with several songbirds. The system uses specialized single-board computers, standard personal computers, CD-ROMs, and custom-written software to present stimuli, control training, and record responses. Also, the authors describe software to produce high-quality synthesized and naturally occurring acoustic stimuli for use in studies of auditory cognition. Typical results from a challenging frequency-range discrimination are included.     

Reference master: A microcomputer-based storage and retrieval system for bibliographic references

A complete system for housekeeping and retrieval of bibliographic references managing individual reprint collections is described. By the use of special hardware and individual data base software even large reprint collections in the range up to 65 000 papers are handled economically. A fast 8-bit microprocessor (HD 64180) in combination with a Winchester hard disk drive serves as the basis for rapid access to the desired information. An efficient string search algorithm written in assembly language guarantees a fast operation with a search speed of more than 6,000 entries/ minute. The system cannot only prepare reference lists and reference files, but also incorporates an editor and maintains the control whether reprints are already on file or requested. The implementation of back-up schemes assure against data losses. Using a state of the art design single board computer and the most recent mass storage device technology, the system is as well small and cost effective, and thus suitable for personal use. In addition, some general questions and pitfalls concerning the management of scientific literature collections are touched upon.     

Quantitation of phospholipids on thin layer chromatographic plates using a desk-top scanner

Amethod for quantitating phospholipids separated on thin layer chromatographic plates by computer-assisted photodensitometry is described. After development, the plates are stained with molibdic reagent and the image obtained is acquired as TIFF file in the memory of a personal computer. The color intensity of the single spots of the digitalized image is analyzed using a dedicated software.Sensitivity and reproducibility are adequate for most of the needs of lipid chemist. When compared to conventional photodensitometric procedures, the present method offers the advantage of requiring a much cheaper hardware.     

Personal computer-based visualization of molecular models by available ray-tracing software

Developed primarily for the graphic arts, ray-tracing algorithms offer a high level of flexibility with reference to photorealistic and surrealistic image rendering. The utility of these programs is further enhanced by portability (i.e., compatibility with a number of operating systems), accessibility through various sources, and low cost. This report documents, through the use of existing software, the application of these ray-tracing attributes to molecular graphics on a desktop computer. This application is especially pertinent in view of rapid speed enhancements in personal computers (PCs), which have enabled molecular modeling and dynamics on these systems. In this regard, ray tracing on a PC provides enhanced capabilities for molecular graphics rendering that are potentially equivalent to those achieved by workstations.     

Personal access to sequence databases on personal computers.

A comprehensive package of software has been developed to access nucleic acid and protein sequence databases on stand-alone IBM personal computers. The software combines keyword search on the annotation fields of the data with pattern matching algorithms on the biological sequences. Sequences containing complex sites like promoters or kink sites can be identified as well as sequences that are similar to a query sequence. Protein sequences with particular patterns of amino acids such as hydrophobic regions can be identified as well. Considering the relatively inexpensive hard disks now available, personal computers have become a cost-effective alternative to mainframe processing for sequence databases.     

Using medical genetics applications to educate for computer competence.

This article proposes specific areas of computing competence and illustrates how these skills can be acquired as an integral part of the curriculum of medical genetics. Geneticists are at the forefront in the use of computers for medical care, because of the driving force of the Human Genome Project. Computer searching of international data bases is the most efficient method to keep current with the explosion in molecular genetics data and with its immediate relevance to clinical care. The use of computers in genetics education could go far beyond the use of computer-assisted instruction (CAI) to show how to use computer systems to assist with clinical decisions. The proposed basic computer skills can be obtained using genetics software. The six proposed skills include the use of (1) microcomputers, (2) productivity software, (3) CAI, patient simulations and specific application programs, (4) remote computers, (5) data bases and knowledge bases, and (6) computers to improve the clinical care of patients.     

A new ImageJ plug-in "ActogramJ" for chronobiological analyses

While the rapid development of personal computers and high-throughput recording systems for circadian rhythms allow chronobiologists to produce huge amounts of data, the software to analyze them often lags behind. Here, we announce newly developed chronobiology software that is easy to use, compatible with many different systems, and freely available. Our system can perform the most frequently used analyses: actogram drawing, periodogram analysis, and waveform analysis. The software is distributed as a pure Java plug-in for ImageJ and so works on the 3 main operating systems: Linux, Macintosh, and Windows. We believe that this free software raises the speed of data analyses and makes studying chronobiology accessible to newcomers.     

Voxx: a PC-based, near real-time volume rendering system for biological microscopy

Confocal and two-photon fluorescence microscopyhave advanced the exploration of complex, three-dimensional biologicalstructures at submicron resolution. We have developed a voxel-basedthree-dimensional (3-D) imaging program (Voxx) capable of nearreal-time rendering that runs on inexpensive personal computers. Thislow-cost interactive 3-D imaging system provides a powerful tool foranalyzing complex structures in cells and tissues and encourages a morethorough exploration of complex biological image data.

     

Automated comet assay analysis.

BACKGROUND: Recently the "comet assay" or "single-cell gel electrophoresis assay" has been established as a sensitive method for the detection of DNA damage and repair. Most of the software now available to quantify various parameters for DNA damage requires the interaction of a human observer. In this report, we describe an automated analysis system that is based on self-developed software and hardware and needs minimal human interaction. METHODS: The image analysis is divided into two parts: 1) automatic cell recognition and comet classification and 2) quantification of desired comet parameters. Image preprocessing, segmentation, and feature classification were developed with algorithms based on mathematical morphology. To enhance evaluation speed, we have introduced parallel processing of data under the Windows NT operating system (Microsoft Corporation, Redmond, WA). Use of an analogue real-time autofocus unit (B?cker et al.: Phys Med Biol 1997;42:1981-1992) allows for faster analysis. RESULTS: Our recognition software shows a sensitivity of 95.2% and a specificity of 92.7% when tested on test samples from routine work with DNA damage by low-dose radiation (0-2 Gy). The parallel hardware and software concept enables us to analyze 100 comets on one slide in less than 15 min. CONCLUSIONS: A comparison of measurements made on the same samples by manual and automated analysis systems revealed that there are no significant differences. The slope of the dose-response curves and the repair kinetics are very similar and demonstrate that automatic comet assay analysis is possible.     

An optical recording system based on a fast CCD sensor for biological imaging.

This paper presents technical details, hardware and software of a complete imaging system which uses a fast CCD sensor and a 41 Msample/s A/D converter to acquire full-frame 12 bit/pixel digitized images with a time resolution of 1.25 ms/image. This apparatus permits to resolve intracellular Ca2+ gradients in individual cells as well as the spatio-temporal pattern of neural activity of cell assemblies in neural tissue.