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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. Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta...

    Authors: Wei Wang, Xi Yang, Chengkun Wu and Canqun Yang

    Citation: BMC Bioinformatics 2020 21:544

    Content type: Methodology article

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  2. Calling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling sing...

    Authors: Lei Cai, Yufeng Wu and Jingyang Gao

    Citation: BMC Bioinformatics 2019 20:665

    Content type: Research article

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  3. Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in ...

    Authors: Olalekan Agbolade, Azree Nazri, Razali Yaakob, Abdul Azim Ghani and Yoke Kqueen Cheah

    Citation: BMC Bioinformatics 2019 20:619

    Content type: Research article

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  4. Nucleus or cell detection is a fundamental task in microscopy image analysis and supports many other quantitative studies such as object counting, segmentation, tracking, etc. Deep neural networks are emerging...

    Authors: Fuyong Xing, Yuanpu Xie, Xiaoshuang Shi, Pingjun Chen, Zizhao Zhang and Lin Yang

    Citation: BMC Bioinformatics 2019 20:472

    Content type: Research Article

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    The Correction to this article has been published in BMC Bioinformatics 2019 20:509

  5. An important task of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is the identification of single particles in micrographs (particle picking). Due to the necessity of human invo...

    Authors: Adil Al-Azzawi, Anes Ouadou, John J. Tanner and Jianlin Cheng

    Citation: BMC Bioinformatics 2019 20:326

    Content type: Methodology article

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  7. Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments an...

    Authors: Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa and Ivan Viola

    Citation: BMC Bioinformatics 2019 20:187

    Content type: Research article

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  9. The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cr...

    Authors: Wei Li Wang, Zhou Yu, Luis R. Castillo-Menendez, Joseph Sodroski and Youdong Mao

    Citation: BMC Bioinformatics 2019 20:169

    Content type: Research article

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  11. The segmentation of a 3D image is a task that can hardly be automatized in certain situations, notably when the contrast is low and/or the distance between elements is small. The existing supervised methods re...

    Authors: Bastien Kovac, Jérôme Fehrenbach, Ludivine Guillaume and Pierre Weiss

    Citation: BMC Bioinformatics 2019 20:142

    Content type: Software

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  12. High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track c...

    Authors: Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev and Ivan V. Kulakovskiy

    Citation: BMC Bioinformatics 2019 20:113

    Content type: Software

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  13. Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With ...

    Authors: Kaisa Liimatainen, Lauri Kananen, Leena Latonen and Pekka Ruusuvuori

    Citation: BMC Bioinformatics 2019 20:80

    Content type: Methodology article

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  16. The biomedical literature is expanding at ever-increasing rates, and it has become extremely challenging for researchers to keep abreast of new data and discoveries even in their own domains of expertise. We i...

    Authors: Patricia Maraver, Rubén Armañanzas, Todd A. Gillette and Giorgio A. Ascoli

    Citation: BMC Bioinformatics 2019 20:50

    Content type: Software

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  17. We introduce BPG, a framework for generating publication-quality, highly-customizable plots in the R statistical environment.

    Authors: Christine P’ng, Jeffrey Green, Lauren C. Chong, Daryl Waggott, Stephenie D. Prokopec, Mehrdad Shamsi, Francis Nguyen, Denise Y. F. Mak, Felix Lam, Marco A. Albuquerque, Ying Wu, Esther H. Jung, Maud H. W. Starmans, Michelle A. Chan-Seng-Yue, Cindy Q. Yao, Bianca Liang…

    Citation: BMC Bioinformatics 2019 20:42

    Content type: Software

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  18. Cryo-electron microscopy (cryo-EM) has become a widely used tool for determining the structures of proteins and macromolecular complexes. To acquire the input for single-particle cryo-EM reconstruction, resear...

    Authors: Jingrong Zhang, Zihao Wang, Yu Chen, Renmin Han, Zhiyong Liu, Fei Sun and Fa Zhang

    Citation: BMC Bioinformatics 2019 20:41

    Content type: Methodology article

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  19. Image segmentation and quantification are essential steps in quantitative cellular analysis. In this work, we present a fast, customizable, and unsupervised cell segmentation method that is based solely on Fij...

    Authors: Mischa Schwendy, Ronald E. Unger, Mischa Bonn and Sapun H. Parekh

    Citation: BMC Bioinformatics 2019 20:39

    Content type: Methodology article

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  20. Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance...

    Authors: Charlotte Debus, Ralf Floca, Michael Ingrisch, Ina Kompan, Klaus Maier-Hein, Amir Abdollahi and Marco Nolden

    Citation: BMC Bioinformatics 2019 20:31

    Content type: Software

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  21. Single-molecule localization microscopy is a super-resolution microscopy technique that allows for nanoscale determination of the localization and organization of proteins in biological samples. For biological...

    Authors: Maarten W. Paul, H. Martijn de Gruiter, Zhanmin Lin, Willy M. Baarends, Wiggert A. van Cappellen, Adriaan B. Houtsmuller and Johan A. Slotman

    Citation: BMC Bioinformatics 2019 20:30

    Content type: Software

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  23. Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the dat...

    Authors: Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Kam, German E. Novakovsky, Jasper Wong, Dylan Aïssi and Li Yao

    Citation: BMC Bioinformatics 2018 19:303

    Content type: Software

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  26. 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

    Content type: Methodology article

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  28. 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

    Content type: Software

    Published on:

  29. 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

    Content type: Methodology article

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  30. 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

    Content type: Software

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  31. 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

    Content type: Methodology article

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  32. 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

    Content type: Methodology article

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  33. 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

    Content type: Methodology article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Software

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  36. 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

    Content type: Research Article

    Published on:

  37. 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

    Content type: Software

    Published on:

  38. 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

    Content type: Research Article

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  39. 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

    Content type: Research Article

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  42. 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

    Content type: Research Article

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  43. 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

    Content type: Software

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  44. 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

    Content type: Research Article

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  45. 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

    Content type: Research Article

    Published on:

  47. 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

    Content type: Software

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  50. 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

    Content type: Methodology Article

    Published on:

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BMC Bioinformatics

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