Why do we count the Omer

Counting of the Omer (Hebrew: ספירת העומר, Sefirat HaOmer, sometimes abbreviated as Sefira or the Omer) is a verbal counting of each of the forty-nine days between the moedim of Passover and Shavuot.

It is noted specifically by the following blessing, which we are to recite in order to count the days leading up to Shavuot:

Baruch atah YHVH Elohenu melech haolam asher kideshanu b'mitzvotav
vetzivanu al sefirat haomer.

Blessed are You, Lord our God, King of the Universe, who has
sanctified us with His commandments, and commanded us concerning the
counting of the Omer.

Today is the 21st day of 50 of counting the Omer.  Shabbat Shalom.

This mitzvah ("commandment") derives from the Torah commandment to count forty-nine days beginning from the day on which the Omer, a sacrifice containing an omer-measure of barley, was offered in the Temple in Jerusalem, up until the day before an offering of wheat was brought to the Temple on Shavuot. The Counting of the Omer begins on the second day of Passover (the 16th of Nisan) for Rabbinic Jews (Orthodox, Conservative, Reform), and after the weekly Shabbat during Passover for Karaite Jews, and ends the day before the holiday of Shavuot, the 'fiftieth day.'

An omer is a unit of measure which respresent one sheaf of grain and is the same amount of manna gathered daily for each person by the nation of Israel while there were in the wilderness.

The idea of counting each day represents spiritual preparation and anticipation for the giving of the Torah which was given by God on Mount Sinai at the beginning of the month of Sivan, around the same time as the holiday of Shavuot. The Sefer HaChinuch (published anonymously in 13th century Spain) states that the Hebrew people were only freed from Egypt at Passover in order to receive the Torah at Sinai, an event which is now celebrated on Shavuot, and to fulfill its laws. Thus the Counting of the Omer demonstrates how much a Hebrew desires to accept the Torah in his own life.

The scripture for this commandment is derived from Leviticus 23:15-16

15 And you shall number to you from the next day after the Sabbath, from the day you bring in the omer of the wave offering; they shall be seven complete Sabbaths;
16 to the next day after the seveth Sabbath, you shall number fifty days; and you shall bring near a new food offering to YHVH;

This is directly related to the Jubilee from Leviticus 25:8-13

8 And you shall number to yourself seven Sabbaths of years, seven years times seven, and all the days of the seven Sabbaths of years shall be to you forty nine years.
9 And you shall let a ram's horn resound, a signal in the seventh month, in the 10th of the month; in the day of atonement, let a ram's horn pass throughout all your land;
10 and you shall make the fiftieth year holy, one year.  And you shall proclaim liberty in the land to those living in it; He shall be a jubilee to you.  And you shall return every man to his possession; yea, you shall turn back to his family.
11 It is a jubilee year, the fiftieth year; it is to you.  You shall not sow, nor reap that which grows of itself, nor gather from the unkempt vines;
12 for it is a jubilee, it is holy to you; you shall eat its increase out of the field.
In the year of jubilee you shall return each one to his possession.
13 In the year of jubilee you shall return each one to his possession.

Counting the omer also represents the unification and completion of both Salvation and Sancitification.  YHVH rescued the people of Israel from Egypt (Salvation), led them through the Red Sea (Baptism) and gave them the Torah on Mount Sinai (Sanctification).