Truth is truth, whether we believe it or not.
"You shall count for yourselves -- from the day after the Shabbat, from the day when you bring the Omer of the waving -- seven Shabbats, they shall be complete. Until the day after the seventh sabbath you shall count, fifty days..."
"You shall count for yourselves seven weeks, from when the sickle is first put to the standing crop shall you begin counting seven weeks. Then you will observe the Festival of Shavu'ot for the L-RD, your G-d."
The purpose of this counting was to give clear direction to the future agricultural society of Israel as to how and when the moed (Holy Festival) of Shavuot (Pentecost) of HaShem was to be kept in relationship to the Pesach/Passover. During second Temple times, the P'rushim (Pharisees) and the Tz'dukim (Sadducees) disagreed on the dating of the beginning of the counting. The P'rushim insisted that the Shabbat referred to, was the High Shabbat of Pesach, whereas the Tz'dukim believed it was the weekly Shabbat of Pesach. Following the destruction of the Temple in 70 AD the P'rushim sect became the reformers of Judaism, taking it from its Temple reliant observances into a rabbinical halakhic form that in turn affected the liturgy of Judaism and also its common observances. Therefore, today we begin the count on the day following the High Shabbat of Pesach. However, as Messianic Jews we see that the resurrection day of our Messiah corresponds--if ironically--with the Tz'dukim view. This is ironic because the Tz'dukim did not believe in the resurrection of the dead. A poignant reminder that truth is truth, whether we believe it or not.
An omer is a unit of measure. On the second day of Passover, in the days of the Temple, an omer of barley was cut down and brought to the Temple as an offering. This grain offering was referred to as the Omer. Every night, from the second night of Pesach/Passover to the night before Shavu'ot/Pentecost, we recite a blessing and state the count of the omer in both weeks and days. So on the 13th day, you would say, "Today is thirteen days, which is 1 week and 6 days of the Omer."
Follow this link for the Brakhot shel Omer (Blessings of the Omer): http://www.chabad.org/holidays/sefirah/omer-calendar.htm
This time of counting and expectant waiting is of additional importance to the follower of Yeshua because as well as the celebration of the harvest at Shavuot and the delight in the remembrance of the giving of the Torah at Sinai, we also anticipate the remembrance of the giving of the Spirit of the living Word, the pouring out of the Ruach Ha-Kodesh (Holy Spirit) upon and within the disciples of Messiah. We count with hopeful and expectant hearts as we continue to pray for that day--spoken of by Shaul in Romans 11--when all Israel (ethnic/empirical) will be saved.