3D Maxima Finder tutorial

Using same idea as the ImageJ Find Maxima function, the 3D Maxima Finder detects local maxima with high contrast. The 3D Maxima Finder plugin is part of the 3D ImageJ Suite.

Local maxima in a specified radius are computed and sorted by intensity. Starting from local maximum with highest intensity, a 3D flooding is performed, all connected pixels with values above the value of local maxima - noise value are marked as zone of the local maximum. All other local maxima from these zones are removed. The next local maximum is processed, this step is repeated until there are no more local maxima to process. The final image is created with local maxima, with their original intensity value.

Original image	Original local maxima
Local zones within noise tolerance	Final local maxima with high contrast

The main application of this method is of course objects (such as spots) detection and numbering. The local maxima detected can be used as seeds for the 3D Spots Segmentation plugin.