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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. Content type: Methodology article

    There is growing interest in utilizing artificial intelligence, and particularly deep learning, for computer vision in histopathology. While accumulating studies highlight expert-level performance of convoluti...

    Authors: Kevin Faust, Quin Xie, Dominick Han, Kartikay Goyle, Zoya Volynskaya, Ugljesa Djuric and Phedias Diamandis

    Citation: BMC Bioinformatics 2018 19:173

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  2. Content type: Software

    Standard cone-beam computed tomography (CBCT) involves the acquisition of at least 360 projections rotating through 360 degrees. Nevertheless, there are cases in which only a few projections can be taken in a ...

    Authors: Claudia de Molina, Estefania Serrano, Javier Garcia-Blas, Jesus Carretero, Manuel Desco and Monica Abella

    Citation: BMC Bioinformatics 2018 19:171

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  3. Content type: Methodology article

    Zebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic simila...

    Authors: Chia-Pin Kang, Hung-Chi Tu, Tzu-Fun Fu, Jhe-Ming Wu, Po-Hsun Chu and Darby Tien-Hao Chang

    Citation: BMC Bioinformatics 2018 19:169

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  4. Content type: Methodology article

    Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a col...

    Authors: Hoai Nam Nguyen, Vincent Paveau, Cyril Cauchois and Charles Kervrann

    Citation: BMC Bioinformatics 2018 19:148

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  5. Content type: Methodology article

    Morphological features are widely used in the study of neuronal function and pathology. Invertebrate neurons are often structurally stereotypical, showing little variance in gross spatial features but larger v...

    Authors: Ajayrama Kumaraswamy, Kazuki Kai, Hiroyuki Ai, Hidetoshi Ikeno and Thomas Wachtler

    Citation: BMC Bioinformatics 2018 19:143

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  6. Content type: Research article

    Studying the patterns of protein-protein interactions (PPIs) is fundamental for understanding the structure and function of protein complexes. The exploration of the vast space of possible mutual configuration...

    Authors: Katarína Furmanová, Jan Byška, Eduard M. Gröller, Ivan Viola, Jan J. Paleček and Barbora Kozlíková

    Citation: BMC Bioinformatics 2018 19:125

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  7. Content type: Software

    AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release...

    Authors: Braden Katzman, Doris Tang, Anthony Santella and Zhirong Bao

    Citation: BMC Bioinformatics 2018 19:121

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  8. Content type: Research Article

    Pathological angiogenesis has been identified in many malignancies as a potential prognostic factor and target for therapy. In most cases, angiogenic analysis is based on the measurement of microvessel density...

    Authors: Faliu Yi, Lin Yang, Shidan Wang, Lei Guo, Chenglong Huang, Yang Xie and Guanghua Xiao

    Citation: BMC Bioinformatics 2018 19:64

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  9. Content type: Software

    ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions f...

    Authors: Curtis T. Rueden, Johannes Schindelin, Mark C. Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena and Kevin W. Eliceiri

    Citation: BMC Bioinformatics 2017 18:529

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  10. Content type: Research Article

    Cell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e....

    Authors: Peter Bajcsy, Soweon Yoon, Stephen J. Florczyk, Nathan A. Hotaling, Mylene Simon, Piotr M. Szczypinski, Nicholas J. Schaub, Carl G. Simon Jr, Mary Brady and Ram D. Sriram

    Citation: BMC Bioinformatics 2017 18:526

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  11. Content type: Research Article

    Brain disorders are one of the top causes of human death. Generally, neurologists analyze brain medical images for diagnosis. In the image analysis field, corners are one of the most important features, which ...

    Authors: Linlin Gao, Haiwei Pan, Qing Li, Xiaoqin Xie, Zhiqiang Zhang, Jinming Han and Xiao Zhai

    Citation: BMC Bioinformatics 2017 18:505

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  12. Content type: Research Article

    Aging is characterized by a gradual breakdown of cellular structures. Nuclear abnormality is a hallmark of progeria in human. Analysis of age-dependent nuclear morphological changes in Caenorhabditis elegans is o...

    Authors: Mengdi Zhao, Jie An, Haiwen Li, Jiazhi Zhang, Shang-Tong Li, Xue-Mei Li, Meng-Qiu Dong, Heng Mao and Louis Tao

    Citation: BMC Bioinformatics 2017 18:412

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  13. Content type: Software

    With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method th...

    Authors: Michael Kern, Alexander Lex, Nils Gehlenborg and Chris R. Johnson

    Citation: BMC Bioinformatics 2017 18:406

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  14. Content type: Research Article

    Traction Force Microscopy (TFM) is a widespread technique to estimate the tractions that cells exert on the surrounding substrate. To recover the tractions, it is necessary to solve an inverse problem, which i...

    Authors: Alejandro Suñé-Auñón, Alvaro Jorge-Peñas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares, Hans Van Oosterwyck and Arrate Muñoz-Barrutia

    Citation: BMC Bioinformatics 2017 18:365

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  15. Content type: Research Article

    Histopathology images are critical for medical diagnosis, e.g., cancer and its treatment. A standard histopathology slice can be easily scanned at a high resolution of, say, 200,000×200,000 pixels. These high ...

    Authors: Yan Xu, Yeshu Li, Zhengyang Shen, Ziwei Wu, Teng Gao, Yubo Fan, Maode Lai and Eric I-Chao Chang

    Citation: BMC Bioinformatics 2017 18:360

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  16. Content type: Software

    Drosophila melanogaster is an important organism used in many fields of biological research such as genetics and developmental biology. Drosophila wings have been widely used to study ...

    Authors: Sheng Yang Michael Loh, Yoshitaka Ogawa, Sara Kawana, Koichiro Tamura and Hwee Kuan Lee

    Citation: BMC Bioinformatics 2017 18:319

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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    Usage 
    3784657 downloads
    1405 Usage Factor


    Social Media Impact
    816 mentions

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