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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. 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

    Content type: Software

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  2. 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

    Content type: Research Article

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  3. 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

    Content type: Methodology article

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  4. 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

    Content type: Research article

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  5. 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

    Content type: Research Article

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  6. 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

    Content type: Research article

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  7. 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

    Content type: Software

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  8. 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

    Content type: Research Article

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  9. 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

    Content type: Research Article

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  10. 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

    Content type: Research Article

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  11. 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

    Content type: Research Article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Software

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  14. 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

    Content type: Methodology article

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Methodology article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Research Article

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Methodology Article

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  21. 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

    Content type: Software

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  22. 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

    Content type: Methodology Article

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  23. 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

    Content type: Software

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  24. 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

    Content type: Research Article

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  25. 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

    Content type: Research article

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  26. 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

    Content type: Methodology article

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  27. 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

    Content type: Methodology Article

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  28. 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

    Content type: Software

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  29. 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

    Content type: Software

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  30. 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

    Content type: Software

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research Article

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  34. 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

    Content type: Software

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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2019 Journal Metrics

  • Citation Impact
    3.242 - 2-year Impact Factor
    3.213 - 5-year Impact Factor
    1.156 - Source Normalized Impact per Paper (SNIP)
    1.626 - SCImago Journal Rank (SJR)

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