ais.m quantifies parameters of axon initial segment (AIS) location & length in appropriately immuno-stained neuronal tissue (see Grubb & Burrone 2010 Nature 465:1070). Can also produce indices of how well a particular probe or protein is localised to the AIS.
ais_z3.m (with input from Tom Watkins) maintains most features of ais.m, but now takes in a single RGB tif file as input, can analyse up to 3 separate fluorescence channels, gives measures of AIS fluorescence intensity, and gives more accurate measures of position along the axon.

ais_auto.m (written by Dennis Kruijssen) allows for semi-automatic measurement of AIS length when label is very clean, and can be combined into batch analysis with batch_ais_auto.m .