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A Web2.0 Strategy for the Collaborative Analysis of Complex Bioimages [chapter]

Christian Loyek, Jan Kölling, Daniel Langenkämper, Karsten Niehaus, Tim W. Nattkemper
2011 Lecture Notes in Computer Science  
We present a new, web-based strategy that allows a new way of collaborative bioimage interpretaion through knowledge integration.  ...  Life science research aims at understanding the relationships in genomics, proteomics and metabolomics on all levels of biological self organization, dealing with data of increasing dimension and complexity  ...  Here, several users can communicate about the selected label and the con- Fig. 5 . A clustering based visualization of one three-dimensional HCS bioimage.  ... 
doi:10.1007/978-3-642-24800-9_25 fatcat:a63y2fpghbdjvgtk7xmuzl7fay

Video Bioinformatics Methods for Analyzing Cell Dynamics: A Survey [chapter]

Nirmalya Ghosh
2015 Computational Biology  
segmentation to cellular feature extraction and selection, classification into different phenotypes, and exploration of hidden content-based patterns in bioimaging databases.  ...  Understanding cellular and subcellular interrelations, spatiotemporal dynamic activities, and complex biological processes from quantitative microscopic video is an emerging field of research.  ...  Feature extraction itself is a dimensional reduction to avoid working with every pixels of the high-resolution bioimage.  ... 
doi:10.1007/978-3-319-23724-4_2 fatcat:wjsaagwnpbgmziy662tsmw6hv4

Analyzing multi-tag bioimages with BioIMAX colocation mining tools

Jan Kolling, Magnus Rathke, Dominic Gardner, Tim W. Nattkemper, Sylvie Abouna, Michael Khan
2012 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)  
However, the analysis of such high dimensional bioimages is a difficult task for most of the labs, since software solutions for particular data mining steps are difficult to use or just not available.  ...  Both tools can be used via our recently proposed online bioimage analysis platform BioIMAX, so users can upload their bioimage data, apply the tools and share the results with other invited users based  ...  To visualize MBI, clustering and dimension reduction can be applied to render dynamic pseudo color maps of the images as we have shown in recent works [5, 6] .  ... 
doi:10.1109/isbi.2012.6235802 dblp:conf/isbi/KollingRGNAK12 fatcat:7y5cay4ctzg6zml6snvogqvtzu

Biological imaging software tools

Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurman, Jason R Swedlow (+2 others)
2012 Nature Methods  
Narayanswamy of the Roysam lab for their assistance in preparing figures, and L. Kamentsky and M. Bray of the Carpenter lab for useful input and edits on the manuscript.  ...  A.E.C. and K.W.E. were supported by US National Institutes of  ...  In selective plane illumination microscopy, the dimensionality expansion becomes multiplied as multichannel, multiview data sets are recorded over time for observing dynamics of protein expression and  ... 
doi:10.1038/nmeth.2084 pmid:22743775 pmcid:PMC3659807 fatcat:6wnzuhdrdfd67o72cmcgwwpgka

Mining biomedical images towards valuable information retrieval in biomedical and life sciences

Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
2016 Database: The Journal of Biological Databases and Curation  
Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries.  ...  In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction  ...  We would like to thank all referenced authors and organizations for their valuable efforts and contributions to the field. Funding German Research Foundation (DFG-TR34/Z1). Conflict of interest.  ... 
doi:10.1093/database/baw118 pmid:27538578 pmcid:PMC4990152 fatcat:dlyhrh5nxjhutlvvw2qkgx3wei

Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring

Karsten Wüllems, Annika Zurowietz, Martin Zurowietz, Roland Schneider, Hanna Bednarz, Karsten Niehaus, Tim W. Nattkemper
2021 Scientific Reports  
QUIMBI is an interactive visual exploration tool that provides the user with a convenient and straightforward visual exploration of morphological and spectral features of MSI data.  ...  Here, we present QUIMBI (QUIck exploration tool for Multivariate BioImages) a new tool for the visual analysis of MSI data.  ...  Acknowledgements We acknowledge the financial support of the German Research Foundation (DFG) and the Open Access Publication Fund of Bielefeld University for the article processing charge.  ... 
doi:10.1038/s41598-021-84049-4 pmid:33633175 pmcid:PMC7907387 fatcat:enhen3ulizas3hp5yjsm5o2jvm

Deep learning for bioimage analysis [article]

Adrien Hallou, Hannah Yevick, Bianca Dumitrascu, Virginie Uhlmann
2021 arXiv   pre-print
space and time.  ...  We then review how deep learning has impacted bioimage analysis and explore the open-source resources available to integrate it into a research project.  ...  Acknowledgements AH would like to thank J-B Lugagne for insightful discussions on DL based image analysis and acknowledges the support of Benjamin Simons and his lab.  ... 
arXiv:2107.02584v2 fatcat:45h3x2tw7jhhhdir6lv4wygy2a

Deep learning for bioimage analysis in developmental biology

Adrien Hallou, Hannah G. Yevick, Bianca Dumitrascu, Virginie Uhlmann
2021 Development  
space and time.  ...  We then review how deep learning has impacted bioimage analysis and explore the open-source resources available to integrate it into a research project.  ...  The web-based platform ImJoy hosts a large collection of plug-ins that provide interactive interfaces to generate ground-truth annotations on multi-dimensional images and train various DL algorithms.  ... 
doi:10.1242/dev.199616 pmid:34490888 fatcat:ipqr4yul5reqnlwfumahaub7iy

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution

David W. Knowles, Mark D. Biggin
2013 Wiley Interdisciplinary Reviews: Developmental Biology  
Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis.  ...  We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points.  ...  Pablo Arbelaez, Damir Sudar, Anil Aswani, and Soile V.E. Keränen gave helpful suggestions on the manuscript. It's writting was funded by U.S.  ... 
doi:10.1002/wdev.107 pmid:24123936 pmcid:PMC3819199 fatcat:3uv2t7gvrvduzbamyoje5ypg6m

CMEIAS bioimage informatics that define the landscape ecology of immature microbial biofilms developed on plant rhizoplane surfaces

Frank B Dazzo, Youssef G Yanni, Ashley Jones, Abdelgawad Y Elsadany
2015 AIMS Bioengineering  
spatial scale, indicating that regionalized microbial cell-cell interactions and the local environment can significantly affect their cooperative and competitive colonization behaviors.  ...  Examples of the primary data are obtained by analysis of processed images of rhizoplane biofilm landscapes analyzed at single-cell resolution using the emerging technology of CMEIAS bioimage informatics  ...  This emerging technology of CMEIAS bioimage informatics provides several analytical tools to explore the landscape ecology and bioengineering applications of natural and managed microbial biofilms.  ... 
doi:10.3934/bioeng.2015.4.469 fatcat:ibwnzgpbkbdjpmbi4d53eerqem

Biomedical Visualization [chapter]

Chris R. Johnson, Xavier Tricoche
2009 Advances in Biomedical Engineering  
With the BioImage volume rendering tools we can interactively explore the size and shape of lung tumors without compromising the fidelity of the original high-resolution CT data.  ...  In addition, Bajaj et al. introduced the contour spectrum, which provides a fast isosurface algorithm and a user interface component that improves qualitative user interaction and provides real-time exact  ... 
doi:10.1016/b978-0-444-53075-2.00006-x fatcat:ewd3kgeki5fthj55kfoce6bkcm

Automated Processing of Zebrafish Imaging Data: A Survey

Ralf Mikut, Thomas Dickmeis, Wolfgang Driever, Pierre Geurts, Fred A. Hamprecht, Bernhard X. Kausler, María J. Ledesma-Carbayo, Raphaël Marée, Karol Mikula, Periklis Pantazis, Olaf Ronneberger, Andres Santos (+3 others)
2013 Zebrafish  
larvae, and high-throughput drug screens based on movement patterns.  ...  We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage.  ...  Acknowledgments The authors acknowledge all participants of the Satellite Workshop ''Future image processing platforms'' of the 2nd European Zebrafish Principal Investigator Meeting in Karlsruhe, 108  ... 
doi:10.1089/zeb.2013.0886 pmid:23758125 pmcid:PMC3760023 fatcat:k23sufo6dbdpjj6mqaflrfxbni

Erratum: Visualization of image data from cells to organisms

Thomas Walter, David W Shattuck, Richard Baldock, Mark E Bastin, Anne E Carpenter, Suzanne Duce, Jan Ellenberg, Adam Fraser, Nicholas Hamilton, Steve Pieper, Mark A Ragan, Jurgen E Schneider (+2 others)
2010 Nature Methods  
Advances in imaging techniques and high-throughput technologies are providing scientists with unprecedented possibilities to visualize internal structures of cells, organs and organisms and to collect  ...  visual representation of the data.  ...  One approach to visualizing and interacting with high-dimensional data and microscopy imaging is the iCluster system 62 , developed in association with the Visible Cell 63 .  ... 
doi:10.1038/nmeth0610-479a fatcat:mimxo5gqnrf6zpu2uhfh7iinxm

Bioimage Informatics in the context of Drosophila research

Florian Jug, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak
2014 Methods  
We focus on how state-of-the-art computer vision algorithms are impacting the ability of Drosophila researchers to analyze biological systems in space and time.  ...  Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the Drosophila research community.  ...  Vaa3D excels in 3D image visualization and enables biologist to interact with very large 3D imagery in an interactive manner [140] .  ... 
doi:10.1016/j.ymeth.2014.04.004 pmid:24732429 fatcat:trrhw3bzyjaoljxp7ockcnkdeu

A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

Charles Kervrann, Carlos Oscar Sanchez Sorzano, Scott T. Acton, Jean-Christophe Olivo-Marin, Michael Unser
2016 IEEE Journal on Selected Topics in Signal Processing  
In this area, image processing and analysis methods are now essential to understand the dynamic organization of groups of interacting molecules inside molecular machineries and to address issues in fundamental  ...  A long-term research in bio-imaging at the sub-cellular and cellular scales consists then in inferring the relationships between the dynamics of macromolecules and their functions.  ...  The authors thank the members of the "Space-time imaging of cellular dynamics of organelles and endomembranes" research team (UMR 144 CNRS Institut Curie) and S.  ... 
doi:10.1109/jstsp.2015.2505402 fatcat:fgbrxtuhsfbobluogllqll6q2e
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