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Purpose: The standard watershed algorithm in ImageJ is very usefull to separate connected, roughly circular structures. Nevertheless, it gets into trouble while separating irregular structures. The Irregular Watershed enables the user to separate also irregular shaped structures to a certain extend.
How to: In one dialog the user needs to specify the number of erosion cycles to be used for the separation algorithm. "0" prevents watershedding. Since increasing numbers use a decreasing size of selector for the separations to be skipped, a too high number might result in unwanted separation in the peripheral regions of the features. The separation only works in the 2D space at the moment and has its limitations when the connecting "bridges" between the features are too broad (as true for the normal watershed algorithm).