A method for data storage includes storing data in a group of analog memory cells by writing into the memory cells in the group respective storage values, which program each of the analog memory cells to a respective programming state selected from a predefined set of programming states, including at least first and second programming states, which are applied respectively to first and second subsets of the memory cells, whereby the storage values held in the memory cells in the first and second subsets are distributed in accordance with respective first and second distributions. A first median of the first distribution is estimated, and a read threshold, which differentiates between the first and second programming states, is calculated based on the estimated first median. The data is retrieved from the analog memory cells in the group by reading the storage values using the calculated read threshold.