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A Web2.0 Strategy for the Collaborative Analysis of Complex Bioimages
[chapter]
2011
Lecture Notes in Computer Science
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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]
2015
Computational Biology
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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
2012
2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)
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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
2012
Nature Methods
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2021
Scientific Reports
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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]
2021
arXiv
pre-print
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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
2021
Development
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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
2013
Wiley Interdisciplinary Reviews: Developmental Biology
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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
2015
AIMS Bioengineering
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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]
2009
Advances in Biomedical Engineering
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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
2013
Zebrafish
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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
2010
Nature Methods
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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
2014
Methods
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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
2016
IEEE Journal on Selected Topics in Signal Processing
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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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