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Various morphological and functional techniques for retina examination have been established in the recent years. Although many examination results are spatially resolved and can be mapped onto data originating from other modalities, usually only data from one modality is analyzed by a clinician at a time. This is mainly because there is no software available to the public that enables the registration of structure and function in the clinical setting. Therefore we developed an integrated mapping application that allows the registration and analysis of morphological data (fundus photography, optical coherence tomography, scanning laser ophthalmoscopy images, and GDx thickness profiles) and functional data (multifocal electroretinography, multifocal pattern electroretinography, perimetry, and microperimetry). To obtain quantitative data that can be used for clinical trials and statistical analyses, extraction routines for morphological parameters - such as retinal layer thicknesses and measures of the vascular network - have been integrated. Global, regional and point-specific data from registered modalities can be extracted and exported for statistical analyses. In this article we present the implementation and examples of use of the developed software.