STESYS2: extended STESYS software for MS Windows

The STESYS2 software is a new version of the IBM PC software supporting interactive stereological measurements. In comparison with the previous STESYS, it is enhanced by a number of useful options, e.g. on-line image input via a TV camera coupled with a microscope operating under MS Windows OS. The main advantage, when compared with other such software packages, is the design of the STESYS2 as a module of the freeware image processing system Image Tool which provides a user-friendly environment including a number of image processing and preprocessing routines. Capabilities of the STESYS2 are illustrated by a practical example: estimation of the surface area of capillaries in the terminal villi of human placenta by the Sandau spatial grid method.     

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.     

MITICS (MALDI Imaging Team Imaging Computing System): a new open source mass spectrometry imaging software

MITICS is a new software developed for MALDI imaging. We tried to render this software compatible with all types of instruments. MITICS is divided in two parts: MITICS control for data acquisition and MITICS Image for data processing and images reconstruction. MITICS control is available for Applied BioSystems MALDI-TOF instruments and MITICS Image for both Applied BioSystems and Bruker Daltonics ones. MITICS Control provides an interface to the user for setting the acquisition parameters for the imaging sequence, namely set instruments acquisition parameters, create the raster of acquisition and control post-acquisition data processing, and provide this settings to the automatic acquisition software of the MALDI instrument. MITICS Image ensures image reconstruction, files are first converted to XML files before being loaded in a database. In MITICS image we have chosen to implement different data representations and calculations for image reconstruction. MITICS Image uses three different representations that have shown to ease extraction of information from the whole data set. It also offers image reconstruction base either on the maximum peak intensity or the peak area. Image reconstruction is possible for single ions but also by summing signals of different ions. MITICS was validated on biological cases.     

Automated Turbidimetric Bioassay Readout Instrument Using a Multiple Flow-Cell System

An instrument has been developed which permits the automatic quantitation of the turbidities of microbiological assay samples. Assay tubes were fed to the instrument at the end of the incubation period. The turbidity readings were automatically converted to digital data which were printed on International Business Machines (IBM) cards and from which potencies were calculated by an IBM computer. The instrument operated at a speed of over 240 tube readings per hour and was totally automatic in sample-mixing, readout, and data recording. The instrument is being used routinely at The Upjohn Co. for the turbidimetric bioassay of vitamins, with a coefficient of variation among repeated turbidity readings of 0.12 to 0.23%.     

Software development of the EMI head scanner.

A method has been developed to run the general purpose operating system RDOS on the same disc of the head scanner computer as is used for scanner software and data. This made it possible to develop additional software in high level programming language for image processing, based on original image data on the disc. All new images produced by the program are stored on the disc in the same format as the original images. This makes it possible to handle processed images exactly as the original ones and to do multiple operations. The following processing has been included in the program so far: subtraction, smoothing, density profiles, vertical reconstructions, magnification and labelling. A set of operator commands has been developed which are very similar to the ordinary commands for the scanner, which makes the program to appear being a direct extension of the standard scanner software.     

Efficient clustering of large EST data sets on parallel computers

Clustering expressed sequence tags (ESTs) is a powerful strategy for gene identification, gene expression studies and identifying important genetic variations such as single nucleotide polymorphisms. To enable fast clustering of large-scale EST data, we developed PaCE (for Parallel Clustering of ESTs), a software program for EST clustering on parallel computers. In this paper, we report on the design and development of PaCE and its evaluation using Arabidopsis ESTs. The novel features of our approach include: (i) design of memory efficient algorithms to reduce the memory required to linear in the size of the input, (ii) a combination of algorithmic techniques to reduce the computational work without sacrificing the quality of clustering, and (iii) use of parallel processing to reduce run-time and facilitate clustering of larger data sets. Using a combination of these techniques, we report the clustering of 168 200 Arabidopsis ESTs in 15 min on an IBM xSeries cluster with 30 dual-processor nodes. We also clustered 327 632 rat ESTs in 47 min and 420 694 Triticum aestivum ESTs in 3 h and 15 min. We demonstrate the quality of our software using benchmark Arabidopsis EST data, and by comparing it with CAP3, a software widely used for EST assembly. Our software allows clustering of much larger EST data sets than is possible with current software. Because of its speed, it also facilitates multiple runs with different parameters, providing biologists a tool to better analyze EST sequence data. Using PaCE, we clustered EST data from 23 plant species and the results are available at the PlantGDB website.     

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.     

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.     

MUCIDS: an operative C environment for acquisition and processing of polarized-light scattered from biological specimens

In this work, we describe a software package, MUCIDS, completelydeveloped in our laboratory, for acquisition and processingof differential polarizxition light-scattering data from specimensof biophysical interest. MUCIDS is a C environment that managesthe whole activity of an instrument used for measurements ofMueller matrix scattering elements. It allows one to capture,analyse, process and display data from this or from other similarlight-scattering experiments. The entire system is suitablefor routine measurements in a general biophysical (or microbiological)laboratory because of its easy handling and maintenance. Thesoftware was written in C lattice and will run on IBM personalcomputers and similar. It uses IBM/DAC and GPIB/IBM interfacecards. Received on October 3, 1989; accepted on March 26, 1990     

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.     

An off-line system for in-time analysis of cardiac catheterization data and for establishment of a cardiological database for retrospective studies.

The system described may be divided in two major parts: (i) automatic analysis of cardiac catheterization data running off-line on a Siemens 305 computer; (ii) storage and retrieval of the results from these analyses and additional data from related departments (thoracic surgery, internal medicine and clinical physiology) in a cardiological database on an IBM 370/155 computer. The first part is described with special regard to (i) operation and control during the phases of data collection, pre-processing, processing and storage of results; (ii) the presentation of the results in a complete and readable form and (iii) the modular design of the software. The results of an evaluation of the computer methods versus manual methods are also presented. The second part has been described with regard to the type of data entered in the cardiological database. The structure of the database and the programs used for storage and retrieval have not been described in detail in the present publication.     

“Omnidia”: software for taxonomy,calculation of diatom indices and inventories management

Software for calculation of 6 diatom indices and diversity indices has been created for both Macintosh and IBM compatible computers. This software runs with the data base Omnis 5 under Windows 3.0. It includes three taxonomic files: families, genera and species, and an inventories file. Four types of data inputs are possible. It is always possible to operate simulations and to carry out investigations with simple or combined characters. All files and results of investigations can be listed in different ways. This data base is compatible with both word processing and spreadsheet systems.     

beadarray: R classes and methods for Illumina bead-based data

The R/Bioconductor package beadarray allows raw data from Illumina experiments to be read and stored in convenient R classes. Users are free to choose between various methods of image processing, background correction and normalization in their analysis rather than using the defaults in Illumina's; proprietary software. The package also allows quality assessment to be carried out on the raw data. The data can then be summarized and stored in a format which can be used by other R/Bioconductor packages to perform downstream analyses. Summarized data processed by Illumina's; BeadStudio software can also be read and analysed in the same manner. Availability: The beadarray package is available from the Bioconductor web page at www.bioconductor.org. A user's guide and example data sets are provided with the package.     

2dx_merge: data management and merging for 2D crystal images

Electron crystallography of membrane proteins determines the structure of membrane-reconstituted and two-dimensionally (2D) crystallized membrane proteins by low-dose imaging with the transmission electron microscope, and computer image processing. We have previously presented the software system 2dx, for user-friendly image processing of 2D crystal images. Its central component 2dx_image is based on the MRC program suite, and allows the optionally fully automatic processing of one 2D crystal image. We present here the program 2dx_merge, which assists the user in the management of a 2D crystal image processing project, and facilitates the merging of the data from multiple images. The merged dataset can be used as a reference to re-process all images, which usually improves the resolution of the final reconstruction. Image processing and merging can be applied iteratively, until convergence is reached. 2dx is available under the GNU General Public License at http://2dx.org.     

Distributed computing in image analysis using open source frameworks and application to image sharpness assessment of histological whole slide images

Background

Automated image analysis on virtual slides is evolving rapidly and will play an important role in the future of digital pathology. Due to the image size, the computational cost of processing whole slide images (WSIs) in full resolution is immense. Moreover, image analysis requires well focused images in high magnification.

Methods

We present a system that merges virtual microscopy techniques, open source image analysis software, and distributed parallel processing. We have integrated the parallel processing framework JPPF, so batch processing can be performed distributed and in parallel. All resulting meta data and image data are collected and merged. As an example the system is applied to the specific task of image sharpness assessment. ImageJ is an open source image editing and processing framework developed at the NIH having a large user community that contributes image processing algorithms wrapped as plug-ins in a wide field of life science applications. We developed an ImageJ plug-in that supports both basic interactive virtual microscope and batch processing functionality. For the application of sharpness inspection we employ an approach with non-overlapping tiles. Compute nodes retrieve image tiles of moderate size from the streaming server and compute the focus measure. Each tile is divided into small sub images to calculate an edge based sharpness criterion which is used for classification. The results are aggregated in a sharpness map.

Results

Based on the system we calculate a sharpness measure and classify virtual slides into one of the following categories - excellent, okay, review and defective. Generating a scaled sharpness map enables the user to evaluate sharpness of WSIs and shows overall quality at a glance thus reducing tedious assessment work.

Conclusions

Using sharpness assessment as an example, the introduced system can be used to process, analyze and parallelize analysis of whole slide images based on open source software.

     

CellAnimation: an open source MATLAB framework for microscopy assays

MOTIVATION: Advances in microscopy technology have led to the creation of high-throughput microscopes that are capable of generating several hundred gigabytes of images in a few days. Analyzing such wealth of data manually is nearly impossible and requires an automated approach. There are at present a number of open-source and commercial software packages that allow the user to apply algorithms of different degrees of sophistication to the images and extract desired metrics. However, the types of metrics that can be extracted are severely limited by the specific image processing algorithms that the application implements, and by the expertise of the user. In most commercial software, code unavailability prevents implementation by the end user of newly developed algorithms better suited for a particular type of imaging assay. While it is possible to implement new algorithms in open-source software, rewiring an image processing application requires a high degree of expertise. To obviate these limitations, we have developed an open-source high-throughput application that allows implementation of different biological assays such as cell tracking or ancestry recording, through the use of small, relatively simple image processing modules connected into sophisticated imaging pipelines. By connecting modules, non-expert users can apply the particular combination of well-established and novel algorithms developed by us and others that are best suited for each individual assay type. In addition, our data exploration and visualization modules make it easy to discover or select specific cell phenotypes from a heterogeneous population. AVAILABILITY: CellAnimation is distributed under the Creative Commons Attribution-NonCommercial 3.0 Unported license (http://creativecommons.org/licenses/by-nc/3.0/). CellAnimationsource code and documentation may be downloaded from www.vanderbilt.edu/viibre/software/documents/CellAnimation.zip. Sample data are available at www.vanderbilt.edu/viibre/software/documents/movies.zip. CONTACT: walter.georgescu@vanderbilt.edu SUPPLEMENTARY INFORMATION: Supplementary data available at Bioinformatics online.     

Two-dimensional electrophoresis computerized processing

This paper describes various methods suitable for implementation of two-dimensional processing software. The different steps leading to a complete processing are described, from the digitalization of the image to the processing of the resulting data. The characteristics of a convenient digitalization system are discussed. The different software devoted to spot detection is reviewed with respect to the presence or otherwise of a spot model and its characteristics. The major techniques for gel matching are compared as are designs for database structures suitable for tabulation of measurements. Finally, the need for a sophisticated system of data processing is stressed and its main requirements are described.     

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology

Background

The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container.

Methods

In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server.

Results

The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8GHz 4GB RAM server with 768x576 pixel size, 1.28Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server – 3.5 seconds, at remote analysis – 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds.

Conclusions

The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system.