The current quest for brain-machine-interfaces is hindered by the need to find a reliable solution for truly chronic brain implants. One approach to tackle that problem is not only to use flexible, mechanically compliant micro recording probes, but to enhance their acceptance in the target tissue by biologization. In order to shed light on the best modifications, immunohistochemical staining of long term implants in rat brains provided thousands of images over a six month experimental phase. The current work explains the image processing method, how these images were analysed in the least ambiguous way to provide meaningful and statistically relevant results. Quantitative analysis of the images allowed for the comparison of changes within the image and comparison between different images.