Image-based multiplexed in situ RNA detection makes it possible to map the spatial gene expression of hundreds to thousands of genes in parallel, and thus discern at the same time a large numbers of different cell types to better understand tissue development, heterogeneity, and disease. Fluorescent signals are detected over multiple fluorescent channels and imaging rounds and decoded in order to identify RNA molecules in their morphological context. Here we present a graph-based decoding approach that models the decoding process as a network flow problem jointly optimizing observation likelihoods and distances of signal detections, thus achieving robustness with respect to noise and spatial jitter of the fluorescent signals. We evaluated our method on synthetic data generated at different experimental conditions, and on real data of in situ RNA sequencing, comparing results with respect to alternative and gold standard image decoding pipelines.