Formats of image data files that can be used for routine digital light micrography. Part one

Failing to open computer files that describe image data is not the most frustrating experience that the user of a computer can suffer, but it is high on list of possible aggravations. To ameliorate this, the structure of uncompressed image data files is described here. The various ways in which information that describes a picture can be recorded are related, and a primary distinction between raster or bitmap based and vector or object based image data files is drawn. Bitmap based image data files are the more useful of the two formats for recording complicated images such as digital light micrographs, whereas object based files are better for recording illustrations and cartoons. Computer software for opening a very large variety of different formats of digital image data is recommended, and if these fail, ways are described for opening bitmap based digital image data files whose format is unknown.     

Formats of image data files that can be used in routine digital light micrography. Part two

This is part two of an article that describes the properties of the image data files that are encountered routinely in digital light micrography. In the current part of the article, the differences between saving image data as large intact files and smaller files that have had some information removed, i.e., using lossy compression, are related first. Subsequently, appropriate ways of configuring computers to deal with the large intact image data files are suggested. The structures of the image data files used for recording dynamic sequences and kinematic animations of series of digital light micrographs, i.e., movie formats, are then described. Finally, some information is supplied about choosing file formats for compressing both static and dynamic image data sets.     

Formats of image data files that can be used in routine digital light micrography. Part two

This is part two of an article that describes the properties of the image data files that are encountered routinely in digital light micrography. In the current part of the article, the differences between saving image data as large intact files and smaller files that have had some information removed, i.e., using lossy compression, are related first. Subsequently, appropriate ways of configuring computers to deal with the large intact image data files are suggested. The structures of the image data files used for recording dynamic sequences and kinematic animations of series of digital light micrographs, i.e., movie formats, are then described. Finally, some information is supplied about choosing file formats for compressing both static and dynamic image data sets.     

TLM-Converter: reorganization of long time-lapse microscopy datasets for downstream image analysis

Automated microscopy enables in vivo studies in developmental biology over long periods of time. Time-lapse recordings in three or more dimensions to study the dynamics of developmental processes can produce huge data sets that extend into the terabyte range. However, depending on the available computational resources and software design, downstream processing of very large image data sets can become highly inefficient, if not impossible. To address the lack of available open source and commercial software tools to efficiently reorganize time-lapse data on a desktop computer with limited system resources, we developed TLM-Converter. The software either fragments oversized files or concatenates multiple files representing single time frames and saves the output files in open standard formats. Our application is undemanding on system resources as it does not require the whole data set to be loaded into the system memory. We tested our tool on time-lapse data sets of live Drosophila specimens recorded by laser scanning confocal microscopy. Image data reorganization dramatically enhances the productivity of time-lapse data processing and allows the use of downstream image analysis software that is unable to handle large data sets of ≥2 GB. In addition, saving the outputs in open standard image file formats enables data sharing between independently developed software tools.     

高原鼠兔洞穴区次生斑块面积的测定方法

利用数码相机快速获得高原鼠兔挖掘活动形成的次生斑块图像,运用地理信息系统软件（Arcview） 计算其面积。运用该方法对草地内高原鼠兔洞穴区次生斑块的面积进行了实地测量,结果显示该方法可以快速、准确测量出不同形状次生斑块的面积,具有良好的实用性和可操作性。     

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.     

MuGeN: simultaneous exploration of multiple genomes and computer analysis results

MOTIVATION: The availability of increasing amounts of sequence data about completely sequenced genomes spurs the development of new methods in the fields of automated annotation, and of comparative genomics. Tools allowing the visualization of results produced by analysis methods, superimposed on possibly annotated sequence data, and enabling synchronized navigation in multiple genomes, provide new means for interactive genome exploration. This kind of visual inspection can be used as a basis to assess the quality of new analysis algorithms, or to discover genome portions to be subjected to in-depth studies. RESULTS: We propose a software package, MuGeN, built for navigating through multiple annotated genomes. It is capable of retrieving annotated sequences in several formats, stored in local files, or available in databases over the network. From these, it then generates an interactive display, or an image file, in most common formats suitable for printing, further editing or integrating in Web pages. Genome maps may be mixed with computer analysis results loaded from XML files, whose format is generic enough to be adapted to a majority of sequence oriented analysis methods. AVAILABILITY: MuGeN is available at http://www-mig.jouy.inra.fr/bdsi/MuGeN.     

A suite of Perl modules for handling microarray data

We describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reporters, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well-documented code enables rapid analysis by even inexperienced Perl developers. AVAILABILITY: Software is available at http://sourceforge.net/projects/perlmat     

Image storage for automated crystallization imaging systems

To use crystallography for the determination of the three-dimensional structures of proteins, protein crystals need to be grown. Automated imaging systems are increasingly being used to monitor these crystallization experiments. These present problems of accessibility to the data, repeatability of any image analysis performed and the amount of storage required. Various image formats and techniques can be combined to provide effective solutions to high volume processing problems such as these, however lack of widespread support for the most effective algorithms, such as JPeg2000 which yielded a 64% improvement in file size over the bitmap, currently inhibits the immediate take up of this approach.     

Chimera: construction of chimeric sequences for phylogenetic analysis

SUMMARY: Chimera allows the construction of chimeric protein or nucleic acid sequence files by concatenating sequences from two or more sequence files in PHYLIP formats. It allows the user to interactively select genes and species from the input files. The concatenated result is stored to one single output file in PHYLIP or NEXUS formats. AVAILABILITY: The computer program, including supporting files and example files, is available from http://www.dalicon.com/chimera/.     

Interactive microbial genome visualization with GView

SUMMARY: GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications. AVAILABILITY: GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at http://gview.ca.     

formatomatic: a program for converting diploid allelic data between common formats for population genetic analysis

There has been a great increase in both the number of population genetic analysis programs and the size of data sets being studied with them. Since the file formats required by the most popular and useful programs are variable, automated reformatting or conversion between them is desirable. formatomatic is an easy to use program that can read allelic data files in genepop , raw (csv ) or convert formats and create data files in nine formats: raw (csv ), arlequin , genepop , immanc /bayesass +, migrate , newhybrids , msvar , baps and structure . Use of formatomatic should greatly reduce time spent reformatting data sets and avoid unnecessary errors.     

Web servlet-assisted, dial-in flow cytometry data analysis

BACKGROUND: The obvious benefits of centralized data storage notwithstanding, the size of modern flow cytometry data files discourages their transmission over commonly used telephone modem connections. The proposed solution is to install at the central location a web servlet that can extract compact data arrays, of a form dependent on the requested display type, from the stored files and transmit them to a remote client computer program for display. METHODS: A client program and a web servlet, both written in the Java programming language, were designed to communicate over standard network connections. The client program creates familiar numerical and graphical display types and allows the creation of gates from combinations of user-defined regions. Data compression techniques further reduce transmission times for data arrays that are already much smaller than the data file itself. RESULTS: For typical data files, network transmission times were reduced more than 700-fold for extraction of one-dimensional (1-D) histograms, between 18 and 120-fold for 2-D histograms, and 6-fold for color-coded dot plots. Numerous display formats are possible without further access to the data file. CONCLUSIONS: This scheme enables telephone modem access to centrally stored data without restricting flexibility of display format or preventing comparisons with locally stored files.     

SNPTransformer: a lightweight toolkit for genome-wide association studies

High-throughput genotyping chips have produced huge datasets for genome-wide association studies(GWAS)that have contributed greatly to discovering susceptibility genes for complex diseases.There are two strategies for performing data analysis for GWAS.One strategy is to use open-source or commercial packages that are designed for GWAS.The other is to take advantage of classic genetic programs with specific functions,such as linkage disequilibrium mapping,haplotype inference and transmission disequilibrium tests.However,most classic programs that are available are not suitable for analyzing chip data directly and require custom-made input,which results in the inconvenience of converting raw genotyping files into various data formats.We developed a powerful,user-friendly,lightweight program named SNPTransformer for GWAS that includes five major modules (Transformer,Operator,Previewer,Coder and Simulator).The toolkit not only works for transforming the genotyping files into ten input formats for use with classic genetics packages,but also carries out useful functions such as relational operations on IDs,previewing data files,recoding data formats and simulating marker files,among other functions.It bridges upstream raw genotyping data with downstream genetic programs,and can act as an in-hand toolkit for human geneticists,especially for non-programmers.SNPTransformer is freely available at http://snptransformer.sourceforge.net.     

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de     

A flexible system for microscope fluorometry served by a personal computer

Summary An automated microscope fluorometer based on a modified Leitz MPV I system is described. Automation is mainly attained by the use of a cheap, commercially available personal computer system programmed in extended BASIC supplemented by a few assembly-level subroutines. The automation has resulted in simplified measuring procedures and increased measuring speed. The statistical precision is enhanced because greater cell populations can be analysed within reasonable time. Programs for several biological applications are described. Routines for cell population analysis, including storage of data on disk files, has proved especially useful. Programs for recording of corrected fluorescence emission spectra and of time-dependent fluorescence variables have also been developed. A high flexibility is achieved, as the BASIC programs can readily be modified for specific purposes. Some data on the sensitivity and reproducibility of the instrument alone, and in combination with a staining method, are also presented.Supported by grants from the Swedish Medical Research Council (Project No. 2235) and from the Faculty of Medicine, University of Linköping     

Sharing digital micrographs and other data files between computers

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.     

Sharing digital micrographs and other data files between computers

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.     

Sharing digital micrographs and other data files between computers.

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.     

PEAS V1.0: a package for elementary analysis of SNP data

We have developed a software package named PEAS to facilitate analyses of large data sets of single nucleotide polymorphisms (SNPs) for population genetics and molecular phylogenetics studies. PEAS reads SNP data in various formats as input and is versatile in data formatting; using PEAS, it is easy to create input files for many popular packages, such as STRUCTURE, frappe, Arlequin, Haploview, LDhat, PLINK, EIGENSOFT, PHASE, fastPHASE, MEGA and PHYLIP. In addition, PEAS fills up several analysis gaps in currently available computer programs in population genetics and molecular phylogenetics. Notably, (i) It calculates genetic distance matrices with bootstrapping for both individuals and populations from genome-wide high-density SNP data, and the output can be streamlined to MEGA and PHYLIP programs for further processing; (ii) It calculates genetic distances from STRUCTURE output and generates MEGA file to reconstruct component trees; (iii) It provides tools to conduct haplotype sharing analysis for phylogenetic studies based on high-density SNP data. To our knowledge, these analyses are not available in any other computer program. PEAS for Windows is freely available for academic users from http://www.picb.ac.cn/~xushua/index.files/Download_PEAS.htm.