EBImage—an R package for image processing with applications to cellular phenotypes
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TLDR
EBImage provides general purpose functionality for reading, writing, processing and analysis of images and in the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors.Abstract:
Summary: EBImage provides general purpose functionality for reading, writing, processing and analysis of images. Furthermore, in the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization.
Availability: EBImage is free and open source, released under the LGPL license and available from the Bioconductor project (http://www.bioconductor.org/packages/release/bioc/html/EBImage.html).
Contact: gregoire.pau/at/ebi.ac.ukread more
Citations
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Journal ArticleDOI
Biological imaging software tools
Kevin W. Eliceiri,Michael R. Berthold,Ilya G. Goldberg,Luis Ibanez,B.S. Manjunath,Maryann E. Martone,Robert F. Murphy,Hanchuan Peng,Anne L. Plant,Badrinath Roysam,Nico Stuurman,Jason R. Swedlow,Pavel Tomancak,Anne E. Carpenter +13 more
TL;DR: Each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics are reviewed, focusing on open-source options.
Journal ArticleDOI
Data-analysis strategies for image-based cell profiling
Juan C. Caicedo,Sam Cooper,Florian Heigwer,Scott Warchal,Peng Qiu,Csaba Molnar,Aliaksei Vasilevich,Joseph Barry,Harmanjit Singh Bansal,Oren Kraus,Mathias Wawer,Lassi Paavolainen,Markus D. Herrmann,Mohammad Hossein Rohban,Jane Hung,Jane Hung,Holger Hennig,John Concannon,Ian Smith,Paul A. Clemons,Shantanu Singh,Paul Rees,Paul Rees,Peter Horvath,Peter Horvath,Roger G. Linington,Anne E. Carpenter +26 more
TL;DR: The steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images are introduced and techniques that have proven useful in each stage of the data analysis process are recommended on the basis of the experience of 20 laboratories worldwide that are refining their image- based cell-profiling methodologies.
Journal ArticleDOI
Finding the sources of missing heritability in a yeast cross
Joshua S. Bloom,Ian M. Ehrenreich,Ian M. Ehrenreich,Wesley T. Loo,Thúy-Lan Võ Lite,Leonid Kruglyak,Leonid Kruglyak +6 more
TL;DR: A large cross between two yeast strains is used to accurately estimate different sources of heritable variation for 46 quantitative traits, and to detect underlying loci with high statistical power, and it is found that the detected loci explain nearly the entire additive contribution to heritability for the traits studied.
Journal ArticleDOI
Directional tissue migration through a self-generated chemokine gradient
Erika Donà,Joseph Barry,Guillaume Valentin,Guillaume Valentin,Charlotte Quirin,Anton Khmelinskii,Andreas Kunze,Sevi Durdu,Lionel R. Newton,Ana Fernandez-Minan,Ana Fernandez-Minan,Wolfgang Huber,Michael Knop,Darren Gilmour +13 more
TL;DR: The in vivo dynamics of one key guidance molecule, the chemokine Cxcl12a, are defined by applying a fluorescent timer approach to measure ligand-triggered receptor turnover in living animals and this study provides the first in vivo proof for self-directed tissue migration through local shaping of an extracellular cue.
Journal ArticleDOI
Software tools for automated transmission electron microscopy
Martin Schorb,Isabella Haberbosch,Isabella Haberbosch,Wim J. H. Hagen,Yannick Schwab,David N. Mastronarde +5 more
TL;DR: A combination of software tools that enable automated acquisition guided by image analysis for a variety of transmission electron microscopy acquisition schemes, Py-EM and SerialEM, which enable automated microscope control for high-throughput data acquisition in diverse transmission electron microscopeopy imaging experiments.
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