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LEIBNIZ INSTITUTE PLANT GENETICS KULTURPFLANZENFORCHUNG, Germany
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6 Papers

VISUAL ANALYTICS OF MULTIMODAL BIOLOGICAL DATA

Topics: Visual Data Analysis and Knowledge Discovery; Biomedical Visualization and Applications; Information and Scientific Visualization; Visualization Applications

Authors: Hendrik Rohn 1 , Christian Klukas 1 and Falk Schreiber 2

Affiliations: 1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany , 2 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and Martin Luther University, Germany

Digital Object Identifier: 10.5220/0003354202560261

Proceedings of IVAPP 2011/VISIGRAPP, ISBN: 978-989-8425-46-1

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Biological data is measured in increasing quantity and quality, resulting in data describing biological systems from different perspectives. Based on data integration methods, visual data mining and visual analytics can be used to promote the understanding of combined biological data and facilitate the exploration process. In this paper a number of view types are presented and integrated into a comprehensive software tool, in order to support researchers in visualizing flexible combinations of multimodal biological data and to create integrated views on comprehensive datasets spanning multiple “omics” areas. A number of interaction techniques accompany these views, enabling the efficient exploration of the data.
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Abstract Data Visualization

General Data Visualization

Visual Data Analysis and Knowledge Discovery

Biomedical Visualization and Applications

Information and Scientific Visualization

Visualization Applications
Computer Vision, Visualization and Computer Graphics

Spatial Data Visualization

ARRAY-BASED GENOME COMPARISON OF ARABIDOPSIS ECOTYPES USING HIDDEN MARKOV MODELS

Topics: Pattern Recognition; Bioinformatics

Authors: Michael Seifert 1 , Ali Banaei 1 , Jens Keilwagen 1 , Michael Florian Mette 1 , Andreas Houben 1 , François Roudier 2 , Vincent Colot 2 , Ivo Grosse 3 and Marc Strickert 4

Affiliations: 1 Leibniz Institute of Plant Genetics and Crop Plant Research, Germany , 2 Ecole Normale Superieure, France , 3 Martin Luther University, Germany , 4 Institute of Plant Genetics and Crop Plant Research, Germany

Digital Object Identifier: 10.5220/0001123700030011

Proceedings of BIOSIGNALS 2009/BIOSTEC, ISBN: 978-989-8111-65-4

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Arabidopsis thaliana is an important model organism in plant biology with a broad geographic distribution including ecotypes from Africa, America, Asia, and Europe. The natural variation of different ecotypes is expected to be reflected to a substantial degree in their genome sequences. Array comparative genomic hybridization ( ACGH ) can be used to quantify the natural variation of different ecotypes at the DNA level. Besides, such ACGH data provides the basics to establish a genome-wide map of DNA copy number variation for different ecotypes. Here, we present a new approach based on Hidden Markov Models (HMMs) to predict copy number variations in ACGH experiments. Using this approach, an improved genome-wide characterization of DNA segments with decreased or increased copy numbers is obtained in comparison to the routinely used segMNT algorithm. The software and the data set used in this case study can be downloaded from http://dig.ipk-gatersleben.de/HMMs/ACGH/ACGH.html.
Collapse Button Related Ontology Subjects/Areas/Topics (14)
Artificial Intelligence

Health Engineering and Technology Applications

Pattern Recognition

Bioinformatics

Human-Computer Interaction

Physiological Computing Systems

Biomedical Engineering

Methodologies and Methods

Sensor Networks

Biomedical Signal Processing

Neurocomputing

Soft Computing
Data Manipulation

Neurotechnology, Electronics and Informatics

FROM INDIVIDUAL INTENSITY VOXEL DATA TO INTER-INDIVIDUAL PROBABILISTIC ATLASES OF BIOLOGICAL OBJECTS BY AN INTERLEAVED REGISTRATION-SEGMENTATION APPROACH

Topics: Image-Based Modeling and 3D Reconstruction; Image Registration; Enhancement and Restoration; Segmentation and Grouping; Image Formation, Acquisition Devices and Sensors

Authors: Felix Bollenbeck 1 , Diana Weier 2 , Wolfram Schoor 1 and Udo Seiffert 1

Affiliations: 1 Fraunhofer Institute for Factory Operation and Automation (IFF), Germany , 2 Leibniz Institute of Plant Genetics and Crop Plant Research, Germany

Digital Object Identifier: 10.5220/0001767001250128

Proceedings of VISAPP 2009/VISIGRAPP, ISBN: 978-989-8111-69-2

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In this paper we describe an automated processing of plant serial section data for high-resolution 3-D models of internal structures. The processing pipeline includes standardization and registration of large image stacks as well as multiple tissue recognition by a joint registration-segmentation approach. By integrating segmented data from multiple individuals in a common reference, a statistical three-dimensional description is used to represent the inherent biodiversity amongst specimen. Inter-individual 3-D models are a novelty in the context of plant microscopy, and along with meaningful visualisation they deliver new insights into growth and development as well as provide a framework for the integration of functional data.
Collapse Button Related Ontology Subjects/Areas/Topics (12)
Applications

Image and Video Analysis

Image-Based Modeling

Computer Vision, Visualization and Computer Graphics

Image Formation and Preprocessing

Pattern Recognition

Enhancement and Restoration

Image Formation, Acquisition Devices and Sensors

Segmentation and Grouping

Geometry and Modeling

Image Registration

Software Engineering

MULTIMODAL REGISTRATION OF NMR-VOLUMES AND HISTOLOGICAL CROSS-SECTIONS OF BARLEY GRAINS ON THE CELL BROADBAND ENGINE PROCESSOR

Topics: Feature Extraction; Image Registration; Structural and Syntactic Approach

Authors: Rainer Pielot 1 , Udo Seiffert 2 , Bertram Manz 3 , Diana Weier 1 , Frank Volke 3 , Falk Schreiber 1 and Winfriede Weschke 1

Affiliations: 1 Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Germany , 2 Fraunhofer Institut für Fabrikbetrieb und -automatisierung (IFF), Germany , 3 Fraunhofer Institut für Biomedizinische Technik (IBMT), Germany

Digital Object Identifier: 10.5220/0001767102410244

Proceedings of VISAPP 2009/VISIGRAPP, ISBN: 978-989-8111-69-2

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Representation of developmental gradients in biological structures requires visualization of storage compounds, metabolites or mRNA hybridization patterns in a 3D morphological framework. NMR imaging can generate such a 3D framework by non-invasive scanning of living structures. Histology provides the distribution of developmental markers as 2D cross-sections. Multimodal alignment tries to put such different image modalities into correspondence. Here we compare different methods for rigid registration of 3D NMR datasets and 2D cross-sections of developing barley grains. As metrics for similarity measurements mutual information, cross correlation and overlap index are used. In addition, different filters are applied to the images before the alignment. The algorithms are parallelized, partially vectorized and implemented on the Cell Broadband Engine processor in a Playstation® 3. Evaluation is done by a comparison of the results to a manually defined gold standard of a NMR dataset and a corresponding 2D cross-section of the same grain. The results show, that best alignment is achieved by application of mutual information on sobel-filtered images and, compared to the implementation on a standard single-core CPU, the computation is accelerated by a factor up to 1.95.
Collapse Button Related Ontology Subjects/Areas/Topics (8)
Computer Vision, Visualization and Computer Graphics

Image and Video Analysis

Signal Processing, Sensors, Systems Modeling and Control

Feature Extraction

Image Registration

Structural and Syntactic Approach
Features Extraction

Informatics in Control, Automation and Robotics

REMOTE RENDERING OF LARGE BIOLOGICAL DATASETS

Topics: Real-Time Rendering; Systems and Software Architectures for Rendering

Authors: Wolfram Schoor 1 , Rüdiger Mecke 1 , Udo Seiffert 1 , Felix Bollenbeck 2 and Uwe Scholz 2

Affiliations: 1 Fraunhofer Institute for Factory Operation and Automation (IFF), Germany , 2 Leibniz Institute of Plant Genetics and Crop Plant Research, Germany

Digital Object Identifier: 10.5220/0001802102230227

Proceedings of GRAPP 2009/VISIGRAPP, ISBN: 978-989-8111-67-8

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This paper presents remote rendering technologies to support the analysis and information exploration of large biological datasets. Reconstructed three-dimensional models and other data domains stored in a database are the foundation for the visualization. Remote Rendering via a clients web interface enables a widespread access to the data with interactive frame rates and high-quality rendering results without the demand of new client hardware. Moreover, the rendering server has the capability to manage multiple independent or collaborative sessions and has a very small bandwidth consumption over time.
Collapse Button Related Ontology Subjects/Areas/Topics (4)
Computer Vision, Visualization and Computer Graphics

Rendering

Systems and Software Architectures for Rendering
Real-Time Rendering

4D WARPING FOR ANALYSING MORPHOLOGICAL CHANGES IN SEED DEVELOPMENT OF BARLEY GRAINS

Topic: Image Registration

Authors: Rainer Pielot 1 , Udo Seiffert 1 , Bertram Manz 2 , Diana Weier 1 , Frank Volke 2 and Winfriede Weschke 1

Affiliations: 1 Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Germany , 2 Fraunhofer Institut für Biomedizinische Technik (IBMT), Germany

Digital Object Identifier: 10.5220/0001073803350340

Proceedings of VISAPP 2008/VISIGRAPP, ISBN: 978-989-8111-21-0

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NMR imaging allows to obtain 3D-images by non-invasive treatment of biological structures. In this study intensity-based warping is evaluated by comparing it to landmark-based warping for a four-dimensional analysis of morphological changes in seed development of barley. The datasets of barley grains are obtained at certain development stages by NMR. Warping algorithms reconstruct intermediate physically nonmeasured stages. The landmark-based procedure consists of automatic definition of landmarks and subsequent distance-weighted warping. The intensity-based approach uses iterative intensity-based warping for definition of the displacement vector field and distance-weighted volume warping for generation of the virtual intermediate dataset. The approaches were tested with four datasets of barley at different development stages. As a result, the intensity-based approach is highly applicable for analysis of morphological changes in NMR datasets and serves as a tool for an extensive 4D analysis of seed development in barley grains.
Collapse Button Related Ontology Subjects/Areas/Topics (3)
Computer Vision, Visualization and Computer Graphics

Image and Video Analysis

Image Registration

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