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
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TLDR
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.Abstract:
Representative members of the bioimage informatics community review the computational steps and some of the primary software tools available to biologists who are acquiring and analyzing microscopy-based digital image data, with a focus on open-source options. Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.read more
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ImageJ2: ImageJ for the next generation of scientific image data
Curtis Rueden,Johannes Schindelin,Johannes Schindelin,Mark Hiner,Barry E. DeZonia,Alison E. Walter,Alison E. Walter,Ellen T. Arena,Ellen T. Arena,Kevin W. Eliceiri,Kevin W. Eliceiri +10 more
TL;DR: ImageJ2 as mentioned in this paper is the next generation of ImageJ, which provides a host of new functionality and separates concerns, fully decoupling the data model from the user interface.
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ImageJ2: ImageJ for the next generation of scientific image data
Curtis Rueden,Johannes Schindelin,Johannes Schindelin,Mark Hiner,Barry E. DeZonia,Alison E. Walter,Alison E. Walter,Ellen T. Arena,Ellen T. Arena,Kevin W. Eliceiri,Kevin W. Eliceiri +10 more
TL;DR: The entire ImageJ codebase was rewrote, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements.
Journal ArticleDOI
The ImageJ ecosystem: An open platform for biomedical image analysis
TL;DR: The ImageJ project is used as a case study of how open‐source software fosters its suites of software tools, making multitudes of image‐analysis technology easily accessible to the scientific community.
Journal ArticleDOI
CellProfiler 3.0: Next-generation image processing for biology.
Claire McQuin,Allen Goodman,Vasiliy S. Chernyshev,Vasiliy S. Chernyshev,Lee Kamentsky,Beth A. Cimini,Kyle W. Karhohs,Minh Doan,Liya Ding,Susanne M. Rafelski,Derek Thirstrup,Winfried Wiegraebe,Shantanu Singh,Tim Becker,Juan C. Caicedo,Anne E. Carpenter +15 more
TL;DR: CellProfiler 3.0 is described, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional image stacks, increasingly common in biomedical research.
Journal ArticleDOI
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
Mark-Anthony Bray,Shantanu Singh,Han Han,Chadwick T. Davis,Blake Borgeson,Cathy L Hartland,Maria Kost-Alimova,Sigrun M. Gustafsdottir,Christopher C. Gibson,Anne E. Carpenter +9 more
TL;DR: This protocol describes the design and execution of experiments using Cell Painting, which is a morphological profiling assay that multiplexes six fluorescent dyes, imaged in five channels, to reveal eight broadly relevant cellular components or organelles.
References
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Journal ArticleDOI
NIH Image to ImageJ: 25 years of image analysis
TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Journal ArticleDOI
Fiji: an open-source platform for biological-image analysis
Johannes Schindelin,Ignacio Arganda-Carreras,Erwin Frise,Verena Kaynig,Mark Longair,Tobias Pietzsch,Stephan Preibisch,Curtis Rueden,Stephan Saalfeld,Benjamin Schmid,Jean-Yves Tinevez,Daniel J. White,Volker Hartenstein,Kevin W. Eliceiri,Pavel Tomancak,Albert Cardona +15 more
TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
Image processing with ImageJ
TL;DR: ImageJ is an open source Java-written program that is used for many imaging applications, including those that that span the gamut from skin analysis to neuroscience, and can read most of the widely used and significant formats used in biomedical images.
Journal ArticleDOI
Computer Visualization of Three-Dimensional Image Data Using IMOD
TL;DR: IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions and allows image data to be visualized by several different methods.
Journal ArticleDOI
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
Anne E. Carpenter,Thouis R. Jones,Michael R. Lamprecht,Colin Clarke,In Han Kang,Ola Friman,David A. Guertin,Joo Han Chang,Robert A. Lindquist,Jason Moffat,Polina Golland,David M. Sabatini +11 more
TL;DR: The first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler is described, which can address a variety of biological questions quantitatively.