## 3D Mathematical Morphology

Various algorithms for 3D Mathematical Morphology, as part of the 3D ImageJ Suite.

## Author

## Description

3D mathematical **operations** (erosion, dilation, …) are available in 3D Filters using minimum and maximum filters.

A 3D **Fill Holes** is available, works the same way as in 2D but will not fill holes if it is not closed in the Z dimension.

A 3D **Euclidean Distance Map** (also called *EDT*) is available that takes into account the calibration of the image stack. A 3D normalized distance map (called Eroded Volume Fraction, or **EVF**) is also available.

Left, raw image of a lymph node ((c) J. Groom, WEHI). Right, binary thresholded image.

Left, EDT image . Right, EVF image.

In the case of labelled objects (as count masks) a **Binary Close Labels** is available, that permits to perform closing on individual objects, hence avoiding objects to touch during the dilation operation.

Nuclear regions ((c) J. Ollion, MNHN) : raw image, segmented labelled image, close labels image.

## Download

For details go to the 3D ImageJ Suite.

## Citation

When using the *3D Mathematical Morphology* plugins 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). Sources are available freely.

## Changelog

- 30/03/2016 V3.74: bug fixed in EDT