Territory scoring is used in Japanese and Korean rules, as well as in many other countries in the world and on many online go servers. At the end of play dead stones are removed from the board and added to the prisoners. Each player's score is the sum of her territory plus prisoners.
Whether they can be counted depends on the type/mode of rules. If disputes are played out with pass stones, points in seki can be counted (just like under area scoring). If group statuses are assigned by hypothetical play, sekis cannot contain territory (for stability reasons).
To determine the score with territory scoring Japanese Counting is used.
See also: area scoring