Command Menus Research Articles

The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy

Filtration of super-resolved microscopic images brings often troubles with removing undesired image parts like, e.g., noise, inhomogenous background and reconstruction artifacts. Standard filtration techniques, e.g., convolution- or Fourier transform-based methods are not always appropriate, since they may lower image resolution that was acquired by hi-tech and expensive microscopy systems. Thus, in this article it is proposed to filter such images using discrete wavelet transform (DWT). Newly developed Wavelet_Denoise plugin for free available Fiji software package demonstrates important possibilities of applying DWT to images: Decomposition of a filtered picture using various wavelet filters and levels of details with showing decomposed images and visualization of effects of back transformation of the picture with chosen level of suppression or denoising of wavelet coefficients. The Fiji framework allows, for example, using a plethora of various microscopic image formats for data opening, users can easily install the plugin through a menu command and the plugin supports processing 3D images in Z-stacks. The application of the plugin for removal of reconstruction artifacts and undesirable background in images acquired by super-resolved structured illumination microscopy is demonstrated as well.

Natural Language Translation at the Intersection of AI and HCI

The fields of artificial intelligence (AI) and human-computer interaction (HCI) are influencing each other like never before. Widely used systems such as Google Translate, Facebook Graph Search, and RelateIQ hide the complexity of large-scale AI systems behind intuitive interfaces. But relations were not always so auspicious. The two fields emerged at different points in the history of computer science, with different influences, ambitions, and attendant biases. AI aimed to construct a rival, and perhaps a successor, to the human intellect. Early AI researchers such as McCarthy, Minsky, and Shannon were mathematicians by training, so theorem-proving and formal models were attractive research directions. In contrast, HCI focused more on empirical approaches to usability and human factors, both of which generally aim to make machines more useful to humans. Many of the attendees at the first CHI conference in 1983 were psychologists and engineers. Papers were presented with titles such as "Design principles for human-computer interfaces" and "Psychological issues in the use of icons in command menus," hardly appealing fare for most mainstream AI researchers.

Optimal metabolic route search based on atom mappings

A key computational problem in metabolic engineering is finding efficient metabolic routes from a source to a target compound in genome-scale reaction networks, potentially considering the addition of new reactions. Efficiency can be based on many factors, such as route lengths, atoms conserved and the number of new reactions, and the new enzymes to catalyze them, added to the route. Fast algorithms are needed to systematically search these large genome-scale reaction networks. We present the algorithm used in the new RouteSearch tool within the Pathway Tools software. This algorithm is based on a general Branch-and-Bound search and involves constructing a network of atom mappings to facilitate efficient searching. As far as we know, it is the first published algorithm that finds guaranteed optimal routes where atom conservation is part of the optimality criteria. RouteSearch includes a graphical user interface that speeds user understanding of its search results. We evaluated the algorithm on five example metabolic-engineering problems from the literature; for one problem the published solution was equivalent to the optimal route found by RouteSearch; for the remaining four problems, RouteSearch found the published solution as one of its best-scored solutions. These problems were each solved in less than 5 s of computational time. RouteSearch is accessible at BioCyc.org by using the menu command Metabolism --> Metabolic RouteSearch and by downloading Pathway Tools. Pathway Tools software is freely available to academic users, and for a fee to commercial users. Download from: http://biocyc.org/download.shtml.

Which animation effects improve indirect manipulation?

This paper describes an experiment to explore the effectiveness of animation in improving indirect manipulation operations. Indirect manipulation operations are those initiated by command menus and buttons to perform a transformation on a graphical object or set of graphical objects. The particular improvement is an operation's ability to show both what would happen if the operation were committed and what would happen if it were cancelled while an operation is being considered. The experiment required subjects to watch a simple alignment operation for a set of graphical objects. They were then asked to record the original placement of those graphical objects. Each task used one of four visual cues: modified telltale, wiggle, colour, or no visual cue. We found the modified telltale, wiggle, and colour visual effects significantly more effective than no visual feedback for cuing the user as to original position of the graphical objects. The modified telltale and colour effects were significantly more effective than the wiggle effect. The major conclusion drawn from this experiment is the use of visual feedback improves a user's ability to remember the previous position of graphical objects after an alignment operation.

Automatic Page-Layout Scripts for Gatan Digital Micrograph®

The software DigitalMicrograph (DM) by Gatan, Inc., is a popular software platform for digital imaging in microscopy. in a service-oriented microscopy laboratory, a large number of images from many different samples are generated each day. It is critical that each printed image is properly labeled with sample identification and a description before printing. with DM, a script language is provided: from this, various analyses can be designed or customized and repetitive tasks can be automated. This paper presents the procedures and DM scripts needed to perform these tasks. Due to the major software architecture change between version 2.5x and version 3.5x, each will be discussed separately.DM Version 2.5.8 (on Macintosh®)A “Data Bar” mechanism is provided in this version of DM. Using the “Edit→Data Bar→Define and Add Data Bar...“ menu command specifies data bar items (e.g., scale bar, microscope operator) to be included in the image. in addition, other annotations (text, line, rectangle, and oval) can be included as part of “Data Bar.” This is done by first selecting the desired annotation on the image and then using the “Edit→Data Bar→use AS Default Data Bar...” menu command. After defining data bar items, executing the menu command adds these data bar items to the image.

A theory of command language dialogue for a knowledge‐based human‐computer interaction

The flexibility and usability of graphic‐based HCIs can be increased by adding a natural language interface with command menus. Among the several other advantages, such embellishment offers the user an opportunity for direct expression of his or her behaviors, goals, intentions, and objectives along the continuum of the task knowledge. The existing graphic‐based HCIs that operate on active symbologies and icons assume the user's mental models to correlate with perceptual and cognitive levels of the task understanding. This obviously increases mental loads and the frustration of the human adapting to the system. In reality, the system should be designed to adapt to the user's behavior and skill level. In order to improve the current design of graphic‐based HCIs, we have formulated theories of command production language that will enhance the user's ability to interact with the system. The methods developed combine the theory of expert database with formal grammar to develop command‐production rules using a...

A comprehensive current analysis of software look and feel protection — Part III — Recent ‘look’ cases plus commencement of analysis of the ‘feel’ cases

The ‘look’ cases focused on copyright infringement claims based primarily on the appearance of various screen display elements of the computer program user interfaces at issue. By contrast, the ‘feel’ cases discussed later in this Part III focus on infringement claims based on non-visible or less visible ‘nonliteral’ aspects of computer programs — such as the structure of the code itself, the structure of the menu command system or ‘menu tree’ of the program, and the overall dynamic behaviour or flow of the program and the underlying methodologies and program features.

Trade Dress Protection for Computer User Interface "Look and Feel"

An employee on way back to his office glances at illuminated screen of a nearby computer. He sees small trash can in lower right corner; graphics of labeled folders, documents, and applications in center; and a strip of words across top of screen. He immediately assumes that computer is an Apple Macintosh. A spreadsheet programmer determines that an application program requires her to use a backslash to access multi-layered command menus and to strike first letter of layered menu items in sequence in order to execute any series of commands. She knows software must be Lotus 1-2-3. Apple and Lotus realize that computer users rely on these elements to identify computer programs.' Accordingly, both companies have invested time and money to build consumer recognition of their programs and have sought legal protection for their user interfaces.2 A personal computer's user interface is the means by which software and user interact.' Audio-visual displays are most obvious means of communicating with user, but user interface also includes other elements of computer system such as keyboard and printer.4 The look and feel of

Transfer of knowledge across computer command menus

Two experiments are reported that examine the effects of menu organization and command naming on performance within and across computer command menus. The work on performance within menus extends prior work on information retrieval (IR) menus to computer command menus. We found that selection of computer commands conforms to the same laws that govern selection of IR categories and object names, with alphabetic organization leading to shorter search times in early trials when users knew the names of the commands. When users did not know the exact names of the commands, the functional organization led to shorter search times. More importantly, we found that the knowledge of the functional organization transferred from one application menu to another, thereby reducing search time in the menu of the second application.

The user interface to CD-ROM databases

The article discusses CD-ROM user interfaces under the following headings: 'Dialogue transaction' (command languages, full-screen menus, pull-down/pop-up menus, command menus, direct manipula tion and natural language); 'Input devices' (keyboard, mouse, touch- screen and voice); 'Display features' (layout, colour, sound and response time); 'User assistance' (error mes sages, on-screen help, on-screen tutorials and manuals/quick refer ence cards) and 'Reliability and robustness'.

Transfer across Computer Command Menus

Two experiments are reported which examine the effects of menu organization and command naming on performance across computer command menus. Results indicate that different menu organizations are best for different selection tasks when switching between applications. Surprisingly, different sources for command names have no effect on selection times. When users know the exact names of the commands that they are searching for, an alphabetic organization produces faster search times in early trials. However, when users know only the definitions of the commands that they are searching for, a conceptual organization leads to faster search times in early trials. Knowledge of this conceptual organization transfers to a new application and speeds selection time in the second application. Also, similar names for identical commands transfers to the second application and improves performance there. However, keeping identical commands in the same position across applications has no effect on performance.

An access interface for the MS-DOS diskette format of GenBank(R), a gene sequence database

An interface program has been developed for users of MS-DOS computers and the GenBank(R) gene sequence files in their diskette format. With the program a user is able to produce keyword, author and entry name listings of GenBank items or to select GenBank sequences for viewing, printing or decoding. The decode option uncompresses sequence data and yields a character file which has the format used on GenBank magnetic tapes. Program options are chosen by selecting items from command menus. While the program is designed primarily for hard disk operation, it also allows users of diskette-based computers to work with GenBank files.

Progress on the Flexible Data Acquisition System at Two Plasma Physics Laboratories

RSX-DAS is a flexible CAMAC-based data acquisition software system that runs on a variety of PDP-11 architectures and under RSX-11 operating systems. Since 1983, five versions of RSX-DAS have been developed at the Plasma Physics Laboratory, University of California, Los Angeles, U.S.A. and the Institute of Plasma Physics, Academia Sinica, China. The system has modular, multi-tasking and concurrent processing features. The communication among seventeen tasks is accomplished through parent/offspring tasking, event flags and shared regions. The user interface to RSX-DAS consists of a set of user friendly commands, indirect command files and menus. The database consists of four static shared regions for the control of data acquisition and display, one dynamic shared region for the data of current shot, and data files for previous shots. The modularity of the CAMAC interface software allows operation on several CAMAC organizations, for example a parallel branch or some dedicated crates, and allows easy addition and subtraction of CAMAC hardware.