In the times of the Bet haMiqdash (Temple of Jerusalem), during the second day of Pesah, an offering was presented in the altar of the Temple which consisted of one 'omer of barley-flour, signaling that from that moment the Jews were allowed to consume from the new grain harvest (hadash). 'omer is a Biblical unit of measurement, approximately one gallon, and by extension it became the name of that offering ( מנחת העומר).
The offering of the 'omer at the beginning of Pesah also initiates a period of seven weeks, or forty-nine days, from Pesah until the holiday of Shabu'ot (Lev. 23:15-16).
Sefirat ha'omer is the Mitzva of counting these 49 days. Thus, the Holiday of Pesah, our physical or political freedom, is connected with Shabu'ot, when we achieve our mental, spiritual and cultural freedom by receiving the Tora.
In a sense, this period of 49 days is a kind of a very long Hol-haMoed, an extension of Pesah, reaching out to Shabu'ot. Our Rabbis explained that unlike physical freedom, mental freedom does not happen overnight. It is a long process of deprograming. In the case of the people of Israel it consisted, among other things, of getting rid of all the habits of a slave-mentality and learning to take charge of their own lives. They also had to recognize and leave behind the pagan and immoral practices of the idol-worshipping Egyptian society (tum-a), which were obviously incompatible with the values of our Tora.
In Pesah we celebrate that we got out of Egypt. And during the days of 'omer we had to get Egypt out of our system and minds, in preparation for receiving the Tora and establishing a covenant (berit) with HaShem at Mount Sinai.
The counting of the Omer takes place at night and it is preceded by the blessing: ... asher qiddeshanu bemitsvotav vetsivanu 'al sefirat ha'omer. Then we proceed to count the days and the weeks. Today, for example, is the ninth day of the 'omer, that is: one week and two days from the 'omer.
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