Fig. 3.

The presented Bayesian model is an accurate estimator of gene expression. We simulated MERFISH data under protocol version 1 (MHD4 codebook) and protocol version 2 (MHD2v2 codebook). (a) Prediction error as violin plots for different mean expressions using posterior estimates (maximum a posterior probability, right violin half) and raw counts (left violin half) with MHD4 encoding. (b) Predicted versus true gene expression using posterior estimates (c) and raw counts with MHD4 encoding. Data is shown in hexagonal bins with intensities corresponding to bin counts (i.e. a 2D histogram). (d, e, f) Corresponding results for MHD2v2 encoding