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Imaging, image analysis and data visualization

Section edited by Hanchuan Peng

This section incorporates all aspects of imaging and bioimage informatics, including but not limited to: microscopic and biomedical image acquisition methods and applications, methods and applications of image analysis and related machine learning, pattern recognition and data mining techniques, image oriented multidimensional data and metadata visualization techniques, methods and applications of bioimage annotation and ontology generation.

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  1. Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data repres...

    Authors: Jean-Baptiste Pettit and John C Marioni

    Citation: BMC Bioinformatics 2013 14:185

    Content type: Software

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  2. Segmenting cell nuclei in microscopic images has become one of the most important routines in modern biological applications. With the vast amount of data, automatic localization, i.e. detection and segmentati...

    Authors: Yang Song, Weidong Cai, Heng Huang, Yue Wang, David Dagan Feng and Mei Chen

    Citation: BMC Bioinformatics 2013 14:173

    Content type: Research article

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  3. Calcium (Ca2+) propagates within tissues serving as an important information carrier. In particular, cilia beat frequency in oviduct cells is partially regulated by Ca2+ changes. Thus, measuring the calcium de...

    Authors: Carlos Milovic, Carolina Oses, Manuel Villalón, Sergio Uribe, Carlos Lizama, Claudia Prieto, Marcelo E Andia, Pablo Irarrazaval and Cristian Tejos

    Citation: BMC Bioinformatics 2013 14:162

    Content type: Methodology article

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  4. Vibrational spectroscopic imaging is now used in several fields to acquire molecular information from microscopically heterogeneous systems. Recent advances have led to promising applications in tissue analysi...

    Authors: David Mayerich, Michael Walsh, Matthew Schulmerich and Rohit Bhargava

    Citation: BMC Bioinformatics 2013 14:156

    Content type: Research article

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  5. Microscopy image segmentation lays the foundation for shape analysis, motion tracking, and classification of biological objects. Despite its importance, automated segmentation remains challenging for several w...

    Authors: Boguslaw Obara, Mark AJ Roberts, Judith P Armitage and Vicente Grau

    Citation: BMC Bioinformatics 2013 14:134

    Content type: Methodology article

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  6. Phytoplankton communities are often used as a marker for the determination of fresh water quality. The routine analysis, however, is very time consuming and expensive as it is carried out manually by trained p...

    Authors: Katja Schulze, Ulrich M Tillich, Thomas Dandekar and Marcus Frohme

    Citation: BMC Bioinformatics 2013 14:115

    Content type: Methodology article

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  7. Automatic 3D digital reconstruction (tracing) of neurons embedded in noisy microscopic images is challenging, especially when the cell morphology is complex.

    Authors: Jinzhu Yang, Paloma T Gonzalez-Bellido and Hanchuan Peng

    Citation: BMC Bioinformatics 2013 14:93

    Content type: Research article

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  8. Motion analysis is one of the tools available to biologists to extract biologically relevant information from image datasets and has been applied to a diverse range of organisms. The application of motion anal...

    Authors: Oliver Tills, Tabitha Bitterli, Phil Culverhouse, John I Spicer and Simon Rundle

    Citation: BMC Bioinformatics 2013 14:37

    Content type: Research article

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  9. Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illu...

    Authors: Daniel Wüstner, Lukasz M Solanko, Frederik W Lund, Daniel Sage, Hans J Schroll and Michael A Lomholt

    Citation: BMC Bioinformatics 2012 13:296

    Content type: Methodology article

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  10. Automated classification of histopathology involves identification of multiple classes, including benign, cancerous, and confounder categories. The confounder tissue classes can often mimic and share attribute...

    Authors: Scott Doyle, Michael D Feldman, Natalie Shih, John Tomaszewski and Anant Madabhushi

    Citation: BMC Bioinformatics 2012 13:282

    Content type: Research article

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  11. Correct segmentation is critical to many applications within automated microscopy image analysis. Despite the availability of advanced segmentation algorithms, variations in cell morphology, sample preparation...

    Authors: William J Cukierski, Kaustav Nandy, Prabhakar Gudla, Karen J Meaburn, Tom Misteli, David J Foran and Stephen J Lockett

    Citation: BMC Bioinformatics 2012 13:232

    Content type: Research article

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  12. Quantitative analysis of changes in dendritic spine morphology has become an interesting issue in contemporary neuroscience. However, the diversity in dendritic spine population might seriously influence the r...

    Authors: Błażej Ruszczycki, Zsuzsanna Szepesi, Grzegorz M Wilczynski, Monika Bijata, Katarzyna Kalita, Leszek Kaczmarek and Jakub Wlodarczyk

    Citation: BMC Bioinformatics 2012 13:213

    Content type: Methodology article

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  13. The enteric pathogen Salmonella is the causative agent of the majority of food-borne bacterial poisonings. Resent research revealed that colonization of plants by Salmonella is an active infection process. Salmon...

    Authors: Marek Schikora, Balram Neupane, Satish Madhogaria, Wolfgang Koch, Daniel Cremers, Heribert Hirt, Karl-Heinz Kogel and Adam Schikora

    Citation: BMC Bioinformatics 2012 13:171

    Content type: Research article

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