Deviations from the common distribution of proteins within cells are linked to aging and diseases. Analysis tools to determine quantitative changes in the spatial distribution of components inside cells are not well developed. To this end, we built the open-source automated analysis platform Cell Detection and Analysis of Intensity Lounge (CellDetail) together with a graphical user interface (GUI). The algorithm within CellDetail generates a physics-based, quantitative determination of spatial distributions of multiple proteins within a single cell. For example, CellDetail transforms previously reported binary changes (polar/apolar) in the intracellular distribution of the polarity proteins Cdc42 and Tubulin in young and aged hematopoietic stem cells (HSCs) into quantitative changes within the polarity space. Thirteen distinct Septin proteins form networks within cells that are critical for cell compartmentalization and maintenance of polarity. Changes in the structure of the Septin network within HSCs might therefore be linked to changes in polarity in aged HSCs. An immunofluorescence approach that identified 6 individual Septins within a single HSC was analyzed with CellDetail and revealed a critically reduced level of organization of this Septin network within aged HSCs. CellDetail thus provides complex 3D cell image analyses which allows for a quantitative determination of the spatial distributions of proteins and protein networks in single cells.