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INFOBIOMED

INFOBIOMED. NoE. Activity 5.2 Image visualization and analysis Univ. Aveiro /IEETA. INFOBIOMED. NoE. Activity work plan - first 12 months. Activity code and title: A5.2 Image visualization and analysis Responsible partner: UAVR – Univ. Aveiro / IEETA Activity objectives:

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INFOBIOMED

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  1. INFOBIOMED NoE Activity 5.2 Image visualization and analysis Univ. Aveiro /IEETA

  2. INFOBIOMED NoE Activity work plan - first 12 months • Activity code and title: A5.2 Image visualization and analysis • Responsible partner: UAVR – Univ. Aveiro / IEETA • Activity objectives: • Identification of state of the art tools on Image visualization and analysis, and existing expertise and needs within the consortium. • Identification of new tools to be developed taking into account outputs of WP 4 and WP 6. • INFOBIOMED repository of Image visualization and analysis tools • Expected results: • Month 6: Report on Image visualization and analysis tools • Month 12:INFOBIOMED repository with existing Image visualization and analysis tools • Relationships with other activities (input/output): WP 4, WP 6

  3. INFOBIOMED NoE A5.2 – Image visualization and analysis • Microarray image analysis and compression • Survey on existing techniques; compression of microarray images has got relatively little attention • Number of microarray experiments is increasing rapidly, putting high pressure no storages devices and communication networks • Existing analytic methods are still evolving, being imprudent to discard the raw data, keeping only parameters obtained through analysis • Lack of representative set of microarray images for methods testing and comparison

  4. INFOBIOMED NoE A5.2 – Image visualization and analysis • Microarray image compression • Jörnsten et al. (2002, 2003). • Compression of cDNA and inkjet microarray images. • Microarray image compression: SLOCO and the effect of information loss. • Hua et al. (2002, 2003). • Fast segmentation and lossy-to-lossless compression of DNA microarray images. • Microarray BASICA: background adjustment, segmentation, image compression and analysis of microarray images. • N. Faramarzpour et al. (2003, 2004). • Lossless DNA microarray image compression. • Lossless and lossy compression of DNA microarray images. • Lonardi et al. (2004). • Gridding and compression of microarray images.

  5. INFOBIOMED NoE A5.2 – Image visualization and analysis • Microarray image compression • Segmentation of spot area from background area for separate coding. • Both predictive and transform-based approaches have been tried for encoding. • The possible correlation existing between the "red" and "green" images is not exploited. • Lack of representative, public, set of microarray images for fair comparison of the methods. • Difficulties in obtaining software from the authors for testing.

  6. INFOBIOMED NoE A5.2 – Image visualization and analysis Red image Green image

  7. INFOBIOMED NoE A5.2 – Image visualization and analysis • Microarray image compression • Assembling a set of public microarray images with the aim of being used as a reference for comparing microarray image processing, analysis and compression methods (already existing or future ones). • Implementing and/or making available tools for microarray image compression based on patent-free methods. This might also be extended to some analysis methods if found appropriate. • Developing new methods for microarray image compression, exploiting aspects neglected by existing techniques, such as the correlation between the "red" and "green" images.

  8. INFOBIOMED NoE A5.2 – Image visualization and analysis • Future activities • Contribution to SOA in WP5 • BMI supported by GRID • …… • Identification of needed tools resulting from pilot requirements • Development of repository for images and tools • Collaboration with pilots

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