Immunofluorescence is the gold standard technique to determine the level and spatial distribution of fluorescent-tagged molecules. However, quantitative analysis of fluorescence microscopy images faces crucial challenges such as morphologic variability within cells. In this work, we developed an analytical strategy to deal with cell shape and size variability that is based on an elastic geometric alignment algorithm. Firstly, synthetic images mimicking cell populations with morphological variability were used to test and optimize the algorithm, under controlled conditions. We have computed expression profiles specifically assessing cell-cell interactions (IN profiles) and profiles focusing on the distribution of a marker throughout the intracellular space of single cells (RD profiles). To experimentally validate our analytical pipeline, we have used real images of cell cultures stained for E-cadherin, tubulin and a mitochondria dye, selected as prototypes of membrane, cytoplasmic and organelle-specific markers. The results demonstrated that our algorithm is able to generate a detailed quantitative report and a faithful representation of a large panel of molecules, distributed in distinct cellular compartments, independently of cell's morphological features. This is a simple end-user method that can be widely explored in research and diagnostic labs to unravel protein regulation mechanisms or identify protein expression patterns associated with disease.