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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. 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

    Content type: Research article

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  2. 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

    Content type: Research article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Software

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  5. 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

    Content type: Research article

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  6. 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

    Content type: Research article

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  7. 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

    Content type: Research article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Methodology article

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  11. 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

    Content type: Research article

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  12. 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

    Content type: Methodology article

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  13. 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

    Content type: Research article

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  14. 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

    Content type: Software

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  15. Artificial neural networks (ANNs) have been used to classify eye diseases, such as diabetic retinopathy (DR) and glaucoma. DR is the leading cause of blindness in working-age adults in the developed world. The...

    Authors: Gábor Márk Somfai, Erika Tátrai, Lenke Laurik, Boglárka Varga, Veronika Ölvedy, Hong Jiang, Jianhua Wang, William E Smiddy, Anikó Somogyi and Delia Cabrera DeBuc

    Citation: BMC Bioinformatics 2014 15:106

    Content type: Research article

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  16. Visualization of protein-ligand complex plays an important role in elaborating protein-ligand interactions and aiding novel drug design. Most existing web visualizers either rely on slow software rendering, or...

    Authors: Hongjian Li, Kwong-Sak Leung, Takanori Nakane and Man-Hon Wong

    Citation: BMC Bioinformatics 2014 15:56

    Content type: Software

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  17. True date palms (Phoenix dactylifera L.) are impressive trees and have served as an indispensable source of food for mankind in tropical and subtropical countries for centuries. The aim of this study is to differ...

    Authors: Vladimir Arinkin, Ilya Digel, Dariusz Porst, Aysegül Temiz Artmann and Gerhard M Artmann

    Citation: BMC Bioinformatics 2014 15:55

    Content type: Research article

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  18. Structural study of retinal blood vessels provides an early indication of diseases such as diabetic retinopathy, glaucoma, and hypertensive retinopathy. These studies require accurate tracing of retinal vessel...

    Authors: Jaydeep De, Huiqi Li and Li Cheng

    Citation: BMC Bioinformatics 2014 15:20

    Content type: Research article

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  19. Studying how individual cells spatially and temporally organize within the embryo is a fundamental issue in modern developmental biology to better understand the first stages of embryogenesis. In order to perf...

    Authors: Jaza Gul-Mohammed, Ignacio Arganda-Carreras, Philippe Andrey, Vincent Galy and Thomas Boudier

    Citation: BMC Bioinformatics 2014 15:9

    Content type: Research article

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  20. Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of ...

    Authors: Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar and Shuiwang Ji

    Citation: BMC Bioinformatics 2013 14:372

    Content type: Methodology article

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  21. Absorption and refraction induced signal attenuation can seriously hinder the extraction of quantitative information from confocal microscopic data. This signal attenuation can be estimated and corrected by al...

    Authors: Thorsten Schmidt, Jasmin Dürr, Margret Keuper, Thomas Blein, Klaus Palme and Olaf Ronneberger

    Citation: BMC Bioinformatics 2013 14:366

    Content type: Research article

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  22. Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by...

    Authors: Qian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar and Jieping Ye

    Citation: BMC Bioinformatics 2013 14:350

    Content type: Research article

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  23. Unsupervised segmentation of multi-spectral images plays an important role in annotating infrared microscopic images and is an essential step in label-free spectral histopathology. In this context, diverse clu...

    Authors: Qiaoyong Zhong, Chen Yang, Frederik Großerüschkamp, Angela Kallenbach-Thieltges, Peter Serocka, Klaus Gerwert and Axel Mosig

    Citation: BMC Bioinformatics 2013 14:333

    Content type: Research article

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  24. Recently a series of algorithms have been developed, providing automatic tools for tracing C. elegans embryonic cell lineage. In these algorithms, 3D images collected from a confocal laser scanning microscope wer...

    Authors: Long Chen, Leanne Lai Hang Chan, Zhongying Zhao and Hong Yan

    Citation: BMC Bioinformatics 2013 14:328

    Content type: Methodology article

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  25. The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux,...

    Authors: Qi Wang, Biao Tang, Lifu Song, Biao Ren, Qun Liang, Feng Xie, Ying Zhuo, Xueting Liu and Lixin Zhang

    Citation: BMC Bioinformatics 2013 14:322

    Content type: Software

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  26. DCE@urLAB is a software application for analysis of dynamic contrast-enhanced magnetic resonance imaging data (DCE-MRI). The tool incorporates a friendly graphical user interface (GUI) to interactively select ...

    Authors: Juan E Ortuño, María J Ledesma-Carbayo, Rui V Simões, Ana P Candiota, Carles Arús and Andrés Santos

    Citation: BMC Bioinformatics 2013 14:316

    Content type: Software

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  27. The combination of time-lapse imaging of live cells with high-throughput perturbation assays is a powerful tool for genetics and cell biology. The Mitocheck project employed this technique to associate thousan...

    Authors: Gregoire Pau, Thomas Walter, Beate Neumann, Jean-Karim Hériché, Jan Ellenberg and Wolfgang Huber

    Citation: BMC Bioinformatics 2013 14:308

    Content type: Research article

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  28. In recent years, high-throughput microscopy has emerged as a powerful tool to analyze cellular dynamics in an unprecedentedly high resolved manner. The amount of data that is generated, for example in long-ter...

    Authors: Felix Buggenthin, Carsten Marr, Michael Schwarzfischer, Philipp S Hoppe, Oliver Hilsenbeck, Timm Schroeder and Fabian J Theis

    Citation: BMC Bioinformatics 2013 14:297

    Content type: Research article

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  29. Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possi...

    Authors: Cheng-Jin Du, Phillip T Hawkins, Len R Stephens and Till Bretschneider

    Citation: BMC Bioinformatics 2013 14:296

    Content type: Research article

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  30. Segmenting electron microscopy (EM) images of cellular and subcellular processes in the nervous system is a key step in many bioimaging pipelines involving classification and labeling of ultrastructures. Howev...

    Authors: Saket Navlakha, Parvez Ahammad and Eugene W Myers

    Citation: BMC Bioinformatics 2013 14:294

    Content type: Methodology article

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  31. We briefly identify several critical issues in current computational neuroscience, and present our opinions on potential solutions based on bioimage informatics, especially automated image computing.

    Authors: Hanchuan Peng, Badrinath Roysam and Giorgio A Ascoli

    Citation: BMC Bioinformatics 2013 14:293

    Content type: Commentary

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  32. Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes. To provide effectiv...

    Authors: Jie Zhou, Santosh Lamichhane, Gabriella Sterne, Bing Ye and Hanchuan Peng

    Citation: BMC Bioinformatics 2013 14:291

    Content type: Software

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  33. Whole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and...

    Authors: Ruby Lee, Jonathan R Karr and Markus W Covert

    Citation: BMC Bioinformatics 2013 14:253

    Content type: Software

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  34. Laserscanning recently has become a powerful and common method for plant parameterization and plant growth observation on nearly every scale range. However, 3D measurements with high accuracy, spatial resoluti...

    Authors: Stefan Paulus, Jan Dupuis, Anne-Katrin Mahlein and Heiner Kuhlmann

    Citation: BMC Bioinformatics 2013 14:238

    Content type: Research article

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  35. Two-dimensional gel electrophoresis (2DE) is a powerful technique for studying protein isoforms and their modifications. Existing commercial 2D image analysis tools rely on spot detection that limits analysis ...

    Authors: Ola Kristoffer Øye, Katarina M Jørgensen, Sigrun M Hjelle, André Sulen, Dag Magne Ulvang and Bjørn Tore Gjertsen

    Citation: BMC Bioinformatics 2013 14:215

    Content type: Software

    Published on:

2018 Journal Metrics

  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
    1.374 - SCImago Journal Rank (SJR)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

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