A freeware java tool for spatial point analysis of neuronal structures.

Spatial point analysis is an analytical approach towards understanding patterns in the distribution of single points, such as synapses. To aid in this type of analysis of neuronal structures, a freeware tool, called PAJ, has been developed. This Java-based tool takes 3D Cartesian coordinates as input and performs a range of analyses to test for underlying patterns. In addition, Monte Carlo analysis is performed to compare experimental input with randomized input. This tool should be especially useful in determining whether neuronal structures are spatially patterned such that individual units interact with each other.