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3D ImageJ Suite

This suite provides plugins to enhance 3D capabilities of ImageJ. Updated content will be available in Framagit.

Presentation

The pdf of the NEUBIAS academy presentation “Introduction to 3D Analysis with 3D ImageJ suite” is available: NEUBIAS_3DSuite.pdf.

The QAs are available on the Image.sc forum.

The associated project for automation is available in TAPAS.

Author

Thomas Boudier , Sorbonne University, Paris, France.

With many contributions from J. Ollion, Laboratoire Jean Perrin, Paris, France.

Citation

If you use the 3D suite for your publication please cite:

Ollion, J., Cochennec, J., Loll, F., Escudé, C., & Boudier, T. (2013). TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. Bioinformatics, 29(14), 1840–1841. doi:10.1093/bioinformatics/btt276

License

GPL distribution (see license).

  1. GNU Lesser General Public License
    The GNU Lesser General Public License (LGPL) is a free, open source license for software and other kinds of works.
  2. Why Closed-Source Is Wrong
    This page has a few war stories about having to fight with developing software where you should not need to fight.
  3. GNU General Public License
    The GNU General Public License (GPL) is a free, open source license for software and other kinds of works.
  4. Apache Software License
    The Apache License is a permissive free software license, imposing minimal restrictions on the redistribution of covered software.
  5. Detect Information Loss
    How to detect various forms of information loss in images
  6. Eclipse Public License
    The Eclipse Public License (EPL) is a free, open source software license.
  7. Color Image Processing
    Images with color come in three different forms: pseudo-color, 24-bit RGB image, or color composite image.
  8. Why Open Source?
    This page highlights the benefits of open source software.
  9. BIG Licensing
    Components distributed via the BIG-EPFL update site were developed by the Biomedical Imaging Group (BIG) at the École Polytechnique Fédérale de Lausanne (EPFL).
  10. Public Domain
    Software in the public domain disclaims all copyright interest, being freely available to everyone for any purpose, with no attribution or acknowledgement required.
  11. Deconvolution
    corrects the systematic error of blur (loss of contrast in smaller features) in optical systems such as fluorescence microscopy images.
  12. Visualization
    is a set of techniques for graphically illustrating scientific data, enabling scientists to better understand, illustrate, and glean insight from their data.
  13. BSD Licenses
    BSD licenses are a family of permissive free software licenses, imposing minimal restrictions on the redistribution of covered software.
  14. Voxelization
    Voxelization is the process of converting a data structures that store geometric information in a continuous domain (such as a 3D triangular mesh) into a rasterized image (a discrete grid).
  15. MIT License
    The MIT License is a permissive free software license, imposing minimal restrictions on the redistribution of covered software.
  16. Licensing
    This page describes the legal structure of ImageJ and SciJava projects.