Barnes & Noble announced today that its popular nook eBook Reader is back in stock online at nook.com and it will be rolling out in the majority of Barnes & Noble brick and mortar stores beginning mid-week.

Barnes & Noble quickly sold out of nook stock online over the holidays due to customer demand. The company said it ramped up production and is shipping stock to the majority of its stores beginning this week.

Nook users are also getting an improved version of the device’s software. B&N today rolled out an automatic over the air (OTA) update for all nooks. The OTA is version 1.2 of the device’s operating software and does not require any action from nook customers.

The new version of the operating software could be a big draw for potential customers. While reviewers were generally pleased with the device’s hardware, the software for the device was panned as mediocre.

The nook offers 3G wireless connectivity from AT&T, as well as Wi-Fi access, and currently sells for $259.