3D Fast Filters

3D filtering using ellipsoidal neighbourhood, as part of the 3D ImageJ Suite.

Author

Thomas Boudier

Matthias Labschütz contributed a fast version for isotropic kernels (for min, max and mean filtering)

Description

The plugin 3D Fast Filters performs various filtering on image stacks. The kernel is ellipsoidal, you can then select three radii for X, Y, and Z. Note that the plugin uses parallel implementation, and a fast version using rolling ball algorithm is used for isotropic kernel (all three radii equal).

The filters mean, median, variance, min and max are implemented in ImageJ since version 1.47.

Available filters :

  • Mean and variance filtering

  • Minimum and maximum filtering (erosion and dilation for gray-level images)

  • Open and close

  • Local maxima

  • TopHat transform (to detect spots-like objects)

  • Sobel (simple edge detection)

  • Adaptive Nagao-like

3d-variance

3D variance

Download

For details go to 3D ImageJ Suite.

If you want faster version using GPU, please refer to CLIJ.

A Google Colab notebook is availabe to test the plugin without any installation and check the code.

Citation

When using the 3D Filters plugin for publication, please refer to :

J. Ollion, J. Cochennec, F. Loll, C. Escudé, T. Boudier. (2013) TANGO: A Generic Tool for High-throughput 3D Image Analysis for Studying Nuclear Organization. Bioinformatics 2013 Jul 15;29(14):1840-1. doi

License

GPL distribution (see license).

Changelog

  • 10/04/2017 : new timer for computing time
  • 28/05/2013 : new filters Open and Close
  • 22/10/2012 : bug fixed for filters3D with 32-bits images
  • 22/06/2011 : Parallelization updated

Known Bugs

  • ij1.47d : Bug in Color/Split, the resulting stacks have incorrect bitdepth