Unsupervised quantification of tissue immunofluorescence in animal models of multiple sclerosis - instructions for use.

•Analysis of EAE immunofluorescence is inconsistent in methods and results, no unbiased methods.•We provide open-source work-flow for fully automatic analysis of spinal cord sections in EAE.•Results differ between EAE models and disease stages but not between spinal cord regions.•Intensity-based results do not fully reflect the information content given by immunofluorescence.