Fiji: an open-source platform for biological-image analysis

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

[1]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[2]  A. Turing,et al.  The chemical basis of morphogenesis. 1953. , 1990, Bulletin of mathematical biology.

[3]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[4]  Alex M. Andrew,et al.  Level Set Methods and Fast Marching Methods: Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science (2nd edition) , 2000 .

[5]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[6]  Jiri Matas,et al.  Robust wide-baseline stereo from maximally stable extremal regions , 2004, Image Vis. Comput..

[7]  Michael D. Abràmoff,et al.  Image processing with ImageJ , 2004 .

[8]  Demetri Terzopoulos,et al.  Snakes: Active contour models , 2004, International Journal of Computer Vision.

[9]  R. Waterston,et al.  Automated cell lineage tracing in Caenorhabditis elegans. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Anne E Carpenter,et al.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes , 2006, Genome Biology.

[11]  Carlos Ortiz-de-Solorzano,et al.  Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization , 2006, CVAMIA.

[12]  Scott E. Fraser,et al.  Imaging in Systems Biology , 2007, Cell.

[13]  Thorsten Meinl,et al.  KNIME: The Konstanz Information Miner , 2007, GfKl.

[14]  Charless C. Fowlkes,et al.  A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm , 2008, Cell.

[15]  Hanchuan Peng,et al.  Bioimage informatics: a new area of engineering biology , 2008, Bioinform..

[16]  Philipp J. Keller,et al.  Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy , 2008, Science.

[17]  Thomas J. Nicholas,et al.  Automated analysis of embryonic gene expression with cellular resolution in C. elegans , 2008, Nature Methods.

[18]  D. Mastronarde,et al.  A Computational Framework for Ultrastructural Mapping of Neural Circuitry , 2009, PLoS biology.

[19]  Ian H. Witten,et al.  The WEKA data mining software: an update , 2009, SKDD.

[20]  E. Myers,et al.  A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses , 2009, Nature Methods.

[21]  Stephan Saalfeld,et al.  Globally optimal stitching of tiled 3D microscopic image acquisitions , 2009, Bioinform..

[22]  Kevin W. Eliceiri,et al.  Open source bioimage informatics for cell biology , 2009, Trends in cell biology.

[23]  R. Durbin,et al.  Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes , 2010, Nature.

[24]  G. Malandain,et al.  Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution , 2010, Nature Methods.

[25]  Benjamin Schmid,et al.  A high-level 3D visualization API for Java and ImageJ , 2010, BMC Bioinformatics.

[26]  Nico Stuurman,et al.  Computer Control of Microscopes Using µManager , 2010, Current protocols in molecular biology.

[27]  A. Cardona,et al.  An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy , 2010, PLoS biology.

[28]  Aabid Shariff,et al.  Automated Image Analysis for High-Content Screening and Analysis , 2010, Journal of biomolecular screening.

[29]  Y. Kalaidzidis,et al.  Systems survey of endocytosis by multiparametric image analysis , 2010, Nature.

[30]  Stephan Saalfeld,et al.  Software for bead-based registration of selective plane illumination microscopy data , 2010, Nature Methods.

[31]  Hanchuan Peng,et al.  V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets , 2010, Nature Biotechnology.

[32]  Joachim M. Buhmann,et al.  Geometrical Consistent 3D Tracing of Neuronal Processes in ssTEM Data , 2010, MICCAI.

[33]  Johannes E. Schindelin,et al.  Identifying Neuronal Lineages of Drosophila by Sequence Analysis of Axon Tracts , 2010, The Journal of Neuroscience.

[34]  Stephan Saalfeld,et al.  As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets , 2010, Bioinform..

[35]  Joachim M Buhmann,et al.  Fully automatic stitching and distortion correction of transmission electron microscope images. , 2010, Journal of structural biology.

[36]  Jean-Christophe Olivo-Marin,et al.  ICY: A new open-source community image processing software , 2011, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro.

[37]  Arthur W. Wetzel,et al.  Network anatomy and in vivo physiology of visual cortical neurons , 2011, Nature.

[38]  Julie H. Simpson,et al.  BrainAligner: 3D Registration Atlases of Drosophila Brains , 2011, Nature Methods.

[39]  Maurizio Vichi,et al.  Studies in Classification Data Analysis and knowledge Organization , 2011 .

[40]  J. Douglas Armstrong,et al.  Bioinformatics Applications Note Systems Biology Simple Neurite Tracer: Open Source Software for Reconstruction, Visualization and Analysis of Neuronal Processes , 2022 .

[41]  Matthijs C. Dorst.  Distinctive Image Features from Scale-Invariant Keypoints , 2011 .

[42]  Johannes E. Schindelin,et al.  TrakEM2 Software for Neural Circuit Reconstruction , 2012, PloS one.

[43]  A. Cardona,et al.  Elastic volume reconstruction from series of ultra-thin microscopy sections , 2012, Nature Methods.