3/9/2024 0 Comments Imagej Fiji h9p fijiDouglas for a hackathon at Institute of Neuroinformatics in Zurich, F. Baines for hackathons at Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, R. Rasband for developing ImageJ and helping thousands of scientists, those who contributed to the Fiji movement by financing and organizing the hackathons, namely G.M. in Current Protocols in Molecular Biology (John Wiley & Sons, Inc., 2010). Computer control of microscopes using μManager. Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes. Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. Geometrical consistent 3D tracing of neuronal processes in ssTEM data. The WEKA data mining software: an update. Level Set Methods and Fast Marching Methods: Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science (Cambridge University Press, 1999). Distinctive image features from scale-invariant keypoints. in Lecture Notes in Computer Science 4241, 85–95 (Springer, 2006). Consistent and elastic registration of histological sections using vector-spline regularization. Nature Methods advance online publication, doi:10.1038/nmeth.2072 (10 June 2012).Īrganda-Carreras, I. Elastic volume reconstruction from series of ultrathin microscopy sections. Fully automatic stitching and distortion correction of transmission electron microscope images. Network anatomy and in vivo physiology of visual cortical neurons. An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy. Globally optimal stitching of tiled 3D microscopic image acquisitions. in Handbook of Computer Vision and Applications Vol. The ITK Software Guide (Kitware Inc., 2005). Robust wide baseline stereo from maximally stable extremal regions. Software for bead-based registration of selective plane illumination microscopy data. Preibisch, S., Saalfeld, S., Schindelin, J. A high-level 3D visualization API for Java and ImageJ. Schmid, B., Schindelin, J., Cardona, A., Longair, M. TrakEM2 software for neural circuit reconstruction. in Studies in Classification, Data Analysis, and Knowledge Organization (GfKL 2007) 319–326 (Springer, 2007).Ĭardona, A. ICY: a new open-source community image processing software in. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Peng, H., Ruan, Z., Long, F., Simpson, J.H. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Bioimage informatics: a new area of engineering biology. Open source bioimage informatics for cell biology. BrainAligner: 3D registration atlases of Drosophila brains. elegans and its application to single-cell analyses. Automated cell lineage tracing in Caenorhabditis elegans. Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution. Automated analysis of embryonic gene expression with cellular resolution in C. As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Saalfeld, S., Cardona, A., Hartenstein, V. A computational framework for ultrastructural mapping of neural circuitry. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Keller, P.J., Schmidt, A.D., Wittbrodt, J. Automated image analysis for high-content screening and analysis. Shariff, A., Kangas, J., Coelho, L.P., Quinn, S. Systems survey of endocytosis by multiparametric image analysis. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Rueden, C., Dietz, C., Horn, M., Schindelin, J., Northan, B., Berthold, M. To add a tool to this list, add the doi: for The following table lists all citable software packages, plugins, etc.,ĭocumented on the site. ImageJ Ops Rueden, C., Dietz, C., Horn, M., Schindelin, J., Northan, B., Berthold, M.
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