SLIX: A Python package for fully automated evaluation of Scattered Light Imaging measurements on brain tissue

SLIX (Scattered Light Imaging ToolboX) is an open-source Python package that allows a fully automated evaluation of Scattered Light Imaging (SLI) measurements. During an SLI measurement, histological brain sections are illuminated from different angles and the transmitted light is measured under normal incidence, yielding characteristic light intensity profiles which provide crucial information such as the directions of crossing nerve fibers in each measured image pixel. SLIX transforms the SLI raw data to human-readable parameter maps that can be used for further analysis and interpreted by researchers. SLIX contains various functions to visualize the resulting parameter maps, e.g. as colored vector maps. The resulting fiber direction maps can be stored as angles or as unit vectors, which could be used as input for streamline tractography algorithms.