A method includes programming a group of analog memory cells by writing respective analog values into the memory cells in the group. After programming the group, the analog values are read from the memory cells in the group using a set of read thresholds so as to produce readout results. Respective optimal positions for the read thresholds in the set are identified based on the readout results. A noise level in the readout results is estimated based on the identified optimal positions of the read thresholds.