Bio-imaging Toolkit for Indexing, Searching, Navigation, Discovery and Annotation

Bio-imaging toolkit is an application for biological imaging community that will bring in the latest efforts in indexing, searching, navigation, discovery, analysis and annotation for both biological image and video collections. This paper discusses both metadata-based and content-based representation, indexing, querying, navigation, discovery, and retrieval, as well as video segmentation and image/video annotations. It also discusses image retrieval by texture similarity, shape similarity, color similarity, and spatio-temporal relationships for the bio-imaging database. A highly interactive multimedia information retrieval system has been developed which is based on Service Oriented Architecture (SOA) that relies on the REST based web-service model to create efficient web components. Application designed is a light weight container application that can be deployed easily without any expertise and easy to understand for novice users.

[1]  Afzal A. Godil VISA: Video Segmentation and Annotation , 2004 .

[2]  Stuart Macdonald,et al.  User Engagement in Research Data Curation , 2009, ECDL.

[3]  Simone Santini,et al.  The cell-centered database , 2007, Neuroinformatics.

[4]  David Bargeron,et al.  Annotations for streaming video on the web , 1999, CHI Extended Abstracts.

[5]  Erik Brauner,et al.  Informatics and Quantitative Analysis in Biological Imaging , 2003, Science.

[6]  A. Prata,et al.  Algorithm for computation of Zernike polynomials expansion coefficients. , 1989, Applied optics.

[7]  Ilya G. Goldberg,et al.  Open microscopy environment , 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

[8]  Bertram Ludäscher,et al.  A cell-centered database for electron tomographic data. , 2002, Journal of structural biology.

[9]  Andreas Girgensohn,et al.  A genetic algorithm for video segmentation and summarization , 2000, 2000 IEEE International Conference on Multimedia and Expo. ICME2000. Proceedings. Latest Advances in the Fast Changing World of Multimedia (Cat. No.00TH8532).

[10]  Maryann E Martone,et al.  Database resources for cellular electron microscopy. , 2007, Methods in cell biology.

[11]  P. Beek,et al.  Text of 15938-5 FCD Information Technology-Multimedia Content Description Interface-Pard 5 Multimedia Description Schemes , 2001 .

[12]  Jitendra Malik,et al.  Scale-Space and Edge Detection Using Anisotropic Diffusion , 1990, IEEE Trans. Pattern Anal. Mach. Intell..

[13]  Jane Hunter,et al.  An Indexing, Browsing, Search and Retrieval System for Audiovisual Libraries , 1999, ECDL.

[14]  Maryann E Martone,et al.  The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. , 2008, Journal of structural biology.

[15]  B. S. Manjunath,et al.  Texture Features for Browsing and Retrieval of Image Data , 1996, IEEE Trans. Pattern Anal. Mach. Intell..

[16]  Shih-Fu Chang,et al.  Overview of the MPEG-7 standard , 2001, IEEE Trans. Circuits Syst. Video Technol..

[17]  Jane Hunter,et al.  Adding Multimedia to the Semantic Web: Building an MPEG-7 ontology , 2001, SWWS.

[18]  David Bargeron,et al.  Annotations for Streaming Video on the Web: System Design and Usage Studies , 1999, Comput. Networks.

[19]  Robert M. Haralick,et al.  Textural Features for Image Classification , 1973, IEEE Trans. Syst. Man Cybern..

[20]  N. Otsu A threshold selection method from gray level histograms , 1979 .