A Content Based Pattern Analysis System for a Biological Specimen Collection

Over the years many research collections of biological specimen have been developed for research in biological sciences. Number of specimens in some of these collections can be as high as several millions. There is a move to convert these physical specimens into digital images. This research is motivated by the need to develop techniques to mine useful information from these large collections of specimen images. Specific focus of this research is on the collection of parasites in the Harold W. Manter Laboratory (HWML) Parasite Collection, one of the top four parasite collections in the world. These parasites closely resemble in shape and have flexible bodies with rigid extremities. They have only a few specific structural differences. In this paper we present a technique to retrieve specimens based on shape of a given sample. This form of mining based on the shape of the specimen has the potential to discover linkages between specimens not otherwise known

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Extending the 5S Framework of Digital Libraries to support Complex Objects, Superimposed Information, and Content-Based Image Retrieval Services

Advanced services in digital libraries (DLs) have been developed and widely used to address the required capabilities of an assortment of systems as DLs expand into diverse application domains. These systems may require support for images (e.g., Content-Based Image Retrieval), Complex (information) Objects, and use of content at fine grain (e.g., Superimposed Information). Due to the lack of consensus on precise theoretical definitions for those services, implementation efforts often involve ad hoc development, leading to duplication and interoperability problems. This article presents a methodology to address those problems by extending a precisely specified minimal digital library (in the 5S framework) with formal definitions of aforementioned services. The theoretical extensions of digital library functionality presented here are reinforced with practical case studies as well as scenarios for the individual and integrative use of services to balance theory and practice. This methodology has implications that other advanced services can be continuously integrated into our current extended framework whenever they are identified. The theoretical definitions and case study we present may impact future development efforts and a wide range of digital library researchers, designers, and developers

Encoding of arbitrary micrometric complex illumination patterns with reduced speckle

In nonlinear microscopy, phase-only spatial light modulators (SLMs) allow achieving simultaneous two-photon excitation and fluorescence emission from specific regionof-interests (ROIs). However, as iterative Fourier transform algorithms (IFTAs) can only approximate the illumination of selected ROIs, both image formation and/or signal acquisition can be largely affected by the spatial irregularities of the illumination patterns and the speckle noise. To overcome these limitations, we propose an alternative complex illumination method (CIM) able to generate simultaneous excitation of large-area ROIs with full control over the amplitude and phase of light and reduced speckle. As a proof-of-concept we experimentally demonstrate single-photon and second harmonic generation (SHG) with structured illumination over large-area ROIs

Analysis and Synthesis of Metadata Goals for Scientific Data

The proliferation of discipline-specific metadata schemes contributes to artificial barriers that can impede interdisciplinary and transdisciplinary research. The authors considered this problem by examining the domains, objectives, and architectures of nine metadata schemes used to document scientific data in the physical, life, and social sciences. They used a mixed-methods content analysis and Greenberg’s (2005) metadata objectives, principles, domains, and architectural layout (MODAL) framework, and derived 22 metadata-related goals from textual content describing each metadata scheme. Relationships are identified between the domains (e.g., scientific discipline and type of data) and the categories of scheme objectives. For each strong correlation (\u3e0.6), a Fisher’s exact test for nonparametric data was used to determine significance (p \u3c .05). Significant relationships were found between the domains and objectives of the schemes. Schemes describing observational data are more likely to have “scheme harmonization” (compatibility and interoperability with related schemes) as an objective; schemes with the objective “abstraction” (a conceptual model exists separate from the technical implementation) also have the objective “sufficiency” (the scheme defines a minimal amount of information to meet the needs of the community); and schemes with the objective “data publication” do not have the objective “element refinement.” The analysis indicates that many metadata-driven goals expressed by communities are independent of scientific discipline or the type of data, although they are constrained by historical community practices and workflows as well as the technological environment at the time of scheme creation. The analysis reveals 11 fundamental metadata goals for metadata documenting scientific data in support of sharing research data across disciplines and domains. The authors report these results and highlight the need for more metadata-related research, particularly in the context of recent funding agency policy changes

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals