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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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  3. Content type: Methodology article

    The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accura...

    Authors: Chi Xiao, Weifu Li, Hao Deng, Xi Chen, Yang Yang, Qiwei Xie and Hua Han

    Citation: BMC Bioinformatics 2018 19:263

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  5. Content type: Software

    Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionall...

    Authors: Thomas H. Clarke, Lauren M. Brinkac, Jason M. Inman, Granger Sutton and Derrick E. Fouts

    Citation: BMC Bioinformatics 2018 19:246

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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  19. 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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  20. 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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  21. 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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  22. 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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  24. 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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  27. Content type: Software

    Image segmentation and registration techniques have enabled biologists to place large amounts of volume data from fluorescence microscopy, morphed three-dimensionally, onto a common spatial frame. Existing too...

    Authors: Yong Wan, Hideo Otsuna, Holly A. Holman, Brig Bagley, Masayoshi Ito, A. Kelsey Lewis, Mary Colasanto, Gabrielle Kardon, Kei Ito and Charles Hansen

    Citation: BMC Bioinformatics 2017 18:280

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  28. Content type: Methodology Article

    Histopathology image analysis is a gold standard for cancer recognition and diagnosis. Automatic analysis of histopathology images can help pathologists diagnose tumor and cancer subtypes, alleviating the work...

    Authors: Yan Xu, Zhipeng Jia, Liang-Bo Wang, Yuqing Ai, Fang Zhang, Maode Lai and Eric I-Chao Chang

    Citation: BMC Bioinformatics 2017 18:281

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  29. Content type: Software

    Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually ch...

    Authors: Miles Aron, Richard Browning, Dario Carugo, Erdinc Sezgin, Jorge Bernardino de la Serna, Christian Eggeling and Eleanor Stride

    Citation: BMC Bioinformatics 2017 18:254

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  30. Content type: Research Article

    Image registration is an important research topic in the field of image processing. Applying image registration to vascular image allows multiple images to be strengthened and fused, which has practical value ...

    Authors: Li Chen, Yuxi Lian, Yi Guo, Yuanyuan Wang, Thomas S. Hatsukami, Kristi Pimentel, Niranjan Balu and Chun Yuan

    Citation: BMC Bioinformatics 2017 18:229

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  31. Content type: Methodology article

    Understanding the working mechanism of the brain is one of the grandest challenges for modern science. Toward this end, the BigNeuron project was launched to gather a worldwide community to establish a big dat...

    Authors: Zhijiang Wan, Yishan He, Ming Hao, Jian Yang and Ning Zhong

    Citation: BMC Bioinformatics 2017 18:197

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  32. Content type: Research article

    In recent years, the microscopy technology for imaging cells has developed greatly and rapidly. The accompanying requirements for automatic segmentation and quantification of the imaged cells are becoming more...

    Authors: Zhenzhou Wang and Haixing Li

    Citation: BMC Bioinformatics 2017 18:189

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  33. Content type: Research Article

    Manual assessment and evaluation of fluorescent micrograph cell experiments is time-consuming and tedious. Automated segmentation pipelines can ensure efficient and reproducible evaluation and analysis with co...

    Authors: Veit Wiesmann, Matthias Bergler, Ralf Palmisano, Martin Prinzen, Daniela Franz and Thomas Wittenberg

    Citation: BMC Bioinformatics 2017 18:176

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  34. Content type: Research article

    Cell image segmentation (CIS) is an essential part of quantitative imaging of biological cells. Designing a performance measure and conducting significance testing are critical for evaluating and comparing the...

    Authors: Jin Chu Wu, Michael Halter, Raghu N. Kacker, John T. Elliott and Anne L. Plant

    Citation: BMC Bioinformatics 2017 18:168

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  35. Content type: Software

    In the evaluation of Stereo-Electroencephalography (SEEG) signals, the physicist’s workflow involves several operations, including determining the position of individual electrode contacts in terms of both rel...

    Authors: Massimo Narizzano, Gabriele Arnulfo, Serena Ricci, Benedetta Toselli, Martin Tisdall, Andrea Canessa, Marco Massimo Fato and Francesco Cardinale

    Citation: BMC Bioinformatics 2017 18:124

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  36. Content type: Research Article

    With rapid advances in genome sequencing and editing technologies, systematic and quantitative analysis of animal behavior is expected to be another key to facilitating data-driven behavioral genetics. The nem...

    Authors: Tsukasa Fukunaga and Wataru Iwasaki

    Citation: BMC Bioinformatics 2017 18:46

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  37. Content type: Research Article

    Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately lab...

    Authors: Jiaoyun Yang, Haipeng Wang, Huitong Ding, Ning An and Gil Alterovitz

    Citation: BMC Bioinformatics 2017 18:47

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  40. Content type: Research Article

    Bioimage classification is a fundamental problem for many important biological studies that require accurate cell phenotype recognition, subcellular localization, and histopathological classification. In this ...

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

    Citation: BMC Bioinformatics 2016 17:465

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  41. Content type: Research Article

    New bioimaging techniques capable of visualising the co-location of numerous proteins within individual cells have been proposed to study tumour heterogeneity of neighbouring cells within the same tissue speci...

    Authors: Violeta N. Kovacheva and Nasir M. Rajpoot

    Citation: BMC Bioinformatics 2016 17:430

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  42. Content type: Research article

    Cryo-electron tomography is an important tool to study structures of macromolecular complexes in close to native states. A whole cell cryo electron tomogram contains structural information of all its macromole...

    Authors: Long Pei, Min Xu, Zachary Frazier and Frank Alber

    Citation: BMC Bioinformatics 2016 17:405

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  43. Content type: Software

    Visualization of data generated by high-throughput, high-dimensionality experiments is rapidly becoming a rate-limiting step in computational biology. There is an ongoing need to quickly develop high-quality v...

    Authors: Felix Lam, Christopher M. Lalansingh, Holly E. Babaran, Zhiyuan Wang, Stephenie D. Prokopec, Natalie S. Fox and Paul C. Boutros

    Citation: BMC Bioinformatics 2016 17:401

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  44. Content type: Methodology article

    Soma localization is an important step in computational neuroscience to map neuronal circuits. However, locating somas from large-scale and complicated datasets is challenging. The challenges primarily origina...

    Authors: Shenghua Cheng, Tingwei Quan, Xiaomao Liu and Shaoqun Zeng

    Citation: BMC Bioinformatics 2016 17:375

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  45. Content type: Research article

    Direct volume rendering is one of flexible and effective approaches to inspect large volumetric data such as medical and biological images. In conventional volume rendering, it is often time consuming to set u...

    Authors: Jianlong Zhou, Xiuying Wang, Hui Cui, Peng Gong, Xianglin Miao, Yalin Miao, Chun Xiao, Fang Chen and Dagan Feng

    Citation: BMC Bioinformatics 2016 17:309

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  47. Content type: Methodology article

    Fish tracking is an important step for video based analysis of fish behavior. Due to severe body deformation and mutual occlusion of multiple swimming fish, accurate and robust fish tracking from video image s...

    Authors: Zhi-Ming Qian, Shuo Hong Wang, Xi En Cheng and Yan Qiu Chen

    Citation: BMC Bioinformatics 2016 17:251

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  48. Content type: Research article

    The current practice of histopathology review is limited in speed and accuracy. The current diagnostic paradigm does not fully describe the complex and complicated patterns of cancer. To address these needs, w...

    Authors: Jin Tae Kwak, Stephen M. Hewitt, André Alexander Kajdacsy-Balla, Saurabh Sinha and Rohit Bhargava

    Citation: BMC Bioinformatics 2016 17:227

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  49. Content type: Research Article

    Genomics and proteomics are nowadays the dominant techniques for novel biomarker discovery. However, histopathology images contain a wealth of information related to the tumor histology, morphology and tumor-h...

    Authors: Vlad Popovici, Eva Budinská, Lenka Čápková, Daniel Schwarz, Ladislav Dušek, Josef Feit and Rolf Jaggi

    Citation: BMC Bioinformatics 2016 17:209

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  50. Content type: Research article

    Single particle tracking (SPT) is nowadays one of the most popular technique to probe spatio-temporal dynamics of proteins diffusing within the plasma membrane. Indeed membrane components of eukaryotic cells a...

    Authors: Patrice Dosset, Patrice Rassam, Laurent Fernandez, Cedric Espenel, Eric Rubinstein, Emmanuel Margeat and Pierre-Emmanuel Milhiet

    Citation: BMC Bioinformatics 2016 17:197

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