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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: 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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  2. 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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  3. Content type: Methodology Article

    Endocytosis is regarded as a mechanism of attenuating the epidermal growth factor receptor (EGFR) signaling and of receptor degradation. There is increasing evidence becoming available showing that breast canc...

    Authors: Lu Cao, Marjo de Graauw, Kuan Yan, Leah Winkel and Fons J. Verbeek

    Citation: BMC Bioinformatics 2016 17:196

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  4. Content type: Software

    DNA methylation at a gene promoter region has the potential to regulate gene transcription. Patterns of methylation over multiple CpG sites in a region are often complex and cell type specific, with the region...

    Authors: Nicholas C. Wong, Bernard J. Pope, Ida L. Candiloro, Darren Korbie, Matt Trau, Stephen Q. Wong, Thomas Mikeska, Xinmin Zhang, Mark Pitman, Stefanie Eggers, Stephen R. Doyle and Alexander Dobrovic

    Citation: BMC Bioinformatics 2016 17:98

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  5. Content type: Methodology Article

    Robust methods for the segmentation and analysis of cells in 3D time sequences (3D+t) are critical for quantitative cell biology. While many automated methods for segmentation perform very well, few generalize...

    Authors: Diana L. Delibaltov, Utkarsh Gaur, Jennifer Kim, Matthew Kourakis, Erin Newman-Smith, William Smith, Samuel A. Belteton, Daniel B. Szymanski and B. S. Manjunath

    Citation: BMC Bioinformatics 2016 17:88

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  6. Content type: Software

    Automated classification using machine learning often relies on features derived from segmenting individual objects, which can be difficult to automate. WND-CHARM is a previously developed classification algor...

    Authors: Virginie Uhlmann, Shantanu Singh and Anne E. Carpenter

    Citation: BMC Bioinformatics 2016 17:51

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  7. Content type: Research Article

    Microarray analysis represents a powerful way to test scientific hypotheses on the functionality of cells. The measurements consider the whole genome, and the large number of generated data requires sophistica...

    Authors: Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch and Ovidiu Balacescu

    Citation: BMC Bioinformatics 2015 16:412

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  8. Content type: Research article

    We describe a suite of tools and methods that form a core set of capabilities for researchers and clinical investigators to evaluate multiple analytical pipelines and quantify sensitivity and variability of th...

    Authors: Tahsin Kurc, Xin Qi, Daihou Wang, Fusheng Wang, George Teodoro, Lee Cooper, Michael Nalisnik, Lin Yang, Joel Saltz and David J. Foran

    Citation: BMC Bioinformatics 2015 16:399

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  9. Content type: Methodology Article

    In recent years, hyperspectral microscopy techniques such as infrared or Raman microscopy have been applied successfully for diagnostic purposes. In many of the corresponding studies, it is common practice to ...

    Authors: Chen Yang, Daniel Niedieker, Frederik Großerüschkamp, Melanie Horn, Andrea Tannapfel, Angela Kallenbach-Thieltges, Klaus Gerwert and Axel Mosig

    Citation: BMC Bioinformatics 2015 16:396

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  10. Content type: Methodology article

    Analysis of single cells in their native environment is a powerful method to address key questions in developmental systems biology. Confocal microscopy imaging of intact tissues, followed by automatic image s...

    Authors: Michael Chiang, Sam Hallman, Amanda Cinquin, Nabora Reyes de Mochel, Adrian Paz, Shimako Kawauchi, Anne L. Calof, Ken W. Cho, Charless C. Fowlkes and Olivier Cinquin

    Citation: BMC Bioinformatics 2015 16:397

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  11. Content type: Software

    The number of γH2AX foci per nucleus is an accepted measure of the number of DNA double-strand breaks in single cells. One of the experimental techniques for γH2AX detection in cultured cells is immunofluoresc...

    Authors: Anastasiya Lapytsko, Gabriel Kollarovic, Lyubomira Ivanova, Maja Studencka and Jörg Schaber

    Citation: BMC Bioinformatics 2015 16:392

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  12. Content type: Software

    For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of i...

    Authors: Martin Nettling, Hendrik Treutler, Jan Grau, Jens Keilwagen, Stefan Posch and Ivo Grosse

    Citation: BMC Bioinformatics 2015 16:387

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  13. Content type: Software

    Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structu...

    Authors: Kimmo Kartasalo, Risto-Pekka Pölönen, Marisa Ojala, Jyrki Rasku, Jukka Lekkala, Katriina Aalto-Setälä and Pasi Kallio

    Citation: BMC Bioinformatics 2015 16:344

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  14. Content type: Research article

    Reconstruction of neuron anatomy structure is a challenging and important task in neuroscience. However, few algorithms can automatically reconstruct the full structure well without manual assistance, making i...

    Authors: Gongning Luo, Dong Sui, Kuanquan Wang and Jinseok Chae

    Citation: BMC Bioinformatics 2015 16:342

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  15. Content type: Research article

    The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammal...

    Authors: Peter Bajcsy, Antonio Cardone, Joe Chalfoun, Michael Halter, Derek Juba, Marcin Kociolek, Michael Majurski, Adele Peskin, Carl Simon, Mylene Simon, Antoine Vandecreme and Mary Brady

    Citation: BMC Bioinformatics 2015 16:330

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  16. Content type: Research Article

    The detection of the glomeruli is a key step in the histopathological evaluation of microscopic images of the kidneys. However, the task of automatic detection of the glomeruli poses challenges owing to the di...

    Authors: Tsuyoshi Kato, Raissa Relator, Hayliang Ngouv, Yoshihiro Hirohashi, Osamu Takaki, Tetsuhiro Kakimoto and Kinya Okada

    Citation: BMC Bioinformatics 2015 16:316

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  17. Content type: Software

    DNA fingerprinting is a technique for comparing DNA patterns that has applications in a wide variety of contexts. Several commercial and freely-available tools can be used to analyze DNA fingerprint gel images...

    Authors: Jónathan Heras, César Domínguez, Eloy Mata, Vico Pascual, Carmen Lozano, Carmen Torres and Myriam Zarazaga

    Citation: BMC Bioinformatics 2015 16:270

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  18. Content type: Research article

    Rapid improvements in light and electron microscopy imaging techniques and the development of 3D anatomical atlases necessitate new approaches for the visualization and analysis of image data. Pixel-based repr...

    Authors: Albina Asadulina, Markus Conzelmann, Elizabeth A. Williams, Aurora Panzera and Gáspár Jékely

    Citation: BMC Bioinformatics 2015 16:229

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  19. Content type: Research article

    Many cell lines currently used in medical research, such as cancer cells or stem cells, grow in confluent sheets or colonies. The biology of individual cells provide valuable information, thus the separation o...

    Authors: Joe Chalfoun, Michael Majurski, Alden Dima, Christina Stuelten, Adele Peskin and Mary Brady

    Citation: BMC Bioinformatics 2014 15:431

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  20. Content type: Research article

    Recent advances in microscopy enable the acquisition of large numbers of tomographic images from living tissues. Three-dimensional microscope images are often displayed with volume rendering by adjusting the t...

    Authors: Megumi Nakao, Shintaro Takemoto, Tadao Sugiura, Kazuaki Sawada, Ryosuke Kawakami, Tomomi Nemoto and Tetsuya Matsuda

    Citation: BMC Bioinformatics 2014 15:415

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  21. Content type: Research article

    Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. Illustra...

    Authors: Ivan Kolesar, Julius Parulek, Ivan Viola, Stefan Bruckner, Anne-Kristin Stavrum and Helwig Hauser

    Citation: BMC Bioinformatics 2014 15:345

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  22. Content type: Research article

    Neural stem cells are motile and proliferative cells that undergo mitosis, dividing to produce daughter cells and ultimately generating differentiated neurons and glia. Understanding the mechanisms controlling...

    Authors: Eric Wait, Mark Winter, Chris Bjornsson, Erzsebet Kokovay, Yue Wang, Susan Goderie, Sally Temple and Andrew R Cohen

    Citation: BMC Bioinformatics 2014 15:328

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  23. Content type: Research article

    Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such m...

    Authors: John E Wenskovitch Jr., Leonard A Harris, Jose-Juan Tapia, James R Faeder and G Elisabeta Marai

    Citation: BMC Bioinformatics 2014 15:316

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  24. Content type: Research article

    Flow cytometry (FC)-based computer-aided diagnostics is an emerging technique utilizing modern multiparametric cytometry systems.The major difficulty in using machine-learning approaches for classification of ...

    Authors: Murat Dundar, Ferit Akova, Halid Z Yerebakan and Bartek Rajwa

    Citation: BMC Bioinformatics 2014 15:314

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  25. Content type: Research article

    Non-small cell lung cancer (NSCLC), the most common type of lung cancer, is one of serious diseases causing death for both men and women. Computer-aided diagnosis and survival prediction of NSCLC, is of great ...

    Authors: Hongyuan Wang, Fuyong Xing, Hai Su, Arnold Stromberg and Lin Yang

    Citation: BMC Bioinformatics 2014 15:310

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  26. Content type: Research article

    Vision-based surveillance and monitoring is a potential alternative for early detection of respiratory disease outbreaks in urban areas complementing molecular diagnostics and hospital and doctor visit-based a...

    Authors: Tuan Hue Thi, Li Wang, Ning Ye, Jian Zhang, Sebastian Maurer-Stroh and Li Cheng

    Citation: BMC Bioinformatics 2014 15:300

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  27. Content type: Research article

    The sensitivity of Optical Coherence Tomography (OCT) images to identify retinal tissue morphology characterized by early neural loss from normal healthy eyes is tested by calculating structural information an...

    Authors: Gábor Márk Somfai, Erika Tátrai, Lenke Laurik, Boglárka E Varga, Vera Ölvedy, William E Smiddy, Robert Tchitnga, Anikó Somogyi and Delia Cabrera DeBuc

    Citation: BMC Bioinformatics 2014 15:295

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  28. Content type: Software

    Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus...

    Authors: Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp

    Citation: BMC Bioinformatics 2014 15:293

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  29. Content type: Research article

    The development of digital imaging technology is creating extraordinary levels of accuracy that provide support for improved reliability in different aspects of the image analysis, such as content-based image ...

    Authors: Xin Qi, Daihou Wang, Ivan Rodero, Javier Diaz-Montes, Rebekah H Gensure, Fuyong Xing, Hua Zhong, Lauri Goodell, Manish Parashar, David J Foran and Lin Yang

    Citation: BMC Bioinformatics 2014 15:287

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  30. Content type: Research article

    Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphologica...

    Authors: Paul D Shaw, Martin Graham, Jessie Kennedy, Iain Milne and David F Marshall

    Citation: BMC Bioinformatics 2014 15:259

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  31. Content type: Research article

    Biological data often originate from samples containing mixtures of subpopulations, corresponding e.g. to distinct cellular phenotypes. However, identification of distinct subpopulations may be difficult if bi...

    Authors: Justin Feigelman, Fabian J Theis and Carsten Marr

    Citation: BMC Bioinformatics 2014 15:240

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  32. Content type: Research article

    The biological world is replete with phenomena that appear to be ideally modeled and analyzed by one archetypal statistical framework - the Graphical Probabilistic Model (GPM). The structure of GPMs is a uniqu...

    Authors: William C Ray, Samuel L Wolock, Nicholas W Callahan, Min Dong, Q Quinn Li, Chun Liang, Thomas J Magliery and Christopher W Bartlett

    Citation: BMC Bioinformatics 2014 15:202

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  33. Content type: Research article

    Biological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwo...

    Authors: Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J Smit, Michel A Westenberg and Gunnar W Klau

    Citation: BMC Bioinformatics 2014 15:201

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  34. Content type: Methodology article

    Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are e...

    Authors: Rongjian Li, Wenlu Zhang and Shuiwang Ji

    Citation: BMC Bioinformatics 2014 15:209

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  35. Content type: Research article

    Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area i...

    Authors: Jan M Brauner, Teja W Groemer, Armin Stroebel, Simon Grosse-Holz, Timo Oberstein, Jens Wiltfang, Johannes Kornhuber and Juan Manuel Maler

    Citation: BMC Bioinformatics 2014 15:181

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  36. Content type: Methodology article

    The ability of science to produce experimental data has outpaced the ability to effectively visualize and integrate the data into a conceptual framework that can further higher order understanding. Multidimens...

    Authors: Marianna Budnikova, Jeffrey W Habig, Daniel Lobo, Nicolas Cornia, Michael Levin and Tim Andersen

    Citation: BMC Bioinformatics 2014 15:178

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  37. Content type: Research article

    Retinal ganglion cell (RGC) loss is one of the earliest and most important cellular changes in glaucoma. The DARC (Detection of Apoptosing Retinal Cells) technology enables in vivo real-time non-invasive imaging ...

    Authors: Mukhtar Bizrah, Steve C Dakin, Li Guo, Farzana Rahman, Miles Parnell, Eduardo Normando, Shereen Nizari, Benjamin Davis, Ahmed Younis and M Francesca Cordeiro

    Citation: BMC Bioinformatics 2014 15:169

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  38. Content type: Software

    Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes...

    Authors: Gustavo A Salazar, Ayton Meintjes, Gaston K Mazandu, Holifidy A Rapanoël, Richard O Akinola and Nicola J Mulder

    Citation: BMC Bioinformatics 2014 15:129

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

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