California-based mega-retailer Amoeba Music, the last big record store on the block, has moved into the digital age with both feet, with its inauguration of a revamped website. And possibly the most intriguing element of that site, and a direct reflection of Amoeba’s dig-deeper philosophy, is the so-called Vinyl Vaults section — thousands of rare and out-of-print LPs, 78s and 45s that flow through the company’s three outlets in any given week — now available for sale via download.

“We’ve been digitizing a lot,” says Jim Henderson, who owns Amoeba along with partners Marc Weinstein, Karen Pearson and Dave Prinz. “What you see now is the lost-between-the-cracks, underappreciated, undervalued (music) from dead labels, (obscure) artists, stuff that we really stand behind. It’s mostly in the rock genre, with a lot of jazz, a lot of blues, some country, some spoken word. There are some oddities for sure.”

Many of the LPs have been getting remastering upgrades from the original vinyl and shellac sources. Currently, there are only about 1,000 titles for sale, but Amoeba is adding 10 or 15 more every day.

Some Vinyl Vaults artists are readily familiar, and in some cases Amoeba’s source material emanates from its owners’ own collections. Some of Prinz’s rare Louis Armstrong 78s were digitized and are being sold as downloads, while Weinstein’s prized collection of 144 Sun Ra albums has also been ripped.

Some Vinyl Vaults artists have proven so elusive that even diligent detective work could not track them down. Henderson points to an unknown ’70s country artist known only as C.J., whose album “My Lady’s Eyes” is for sale on the site.

“We couldn’t find C.J.; we couldn’t find a label that put the record out,” Henderson says. “But it’s a compelling piece, (so) we said, ‘This should be up.’ ”

Weinstein adds that if a sale is made, the money goes into an escrow account. “If (someone says), ‘That’s mine,’ well, OK, we can either take it down or we’ll sell it, and you’ve got this nice (digital) master. We’ll sell it, we’ll promote it; let’s sign a contract.”

The retooled http://www.amoeba.com — which has been selling CDs, vinyl LPs, DVDs, accessories, tchotchkes and collectibles for 18 months, and shipping them (at no charge) to customers around the world — launched in beta form on Oct. 2.

The site now offers a range of digital downloads, that includes not only the Vinyl Vaults collection, but also curatorial data that features 4,500 artist bios and 6,500 record reviews.

The entirely inhouse undertaking has taken six years, at a cost estimated by the Amoeba partners of around $11 million. The project employed some 200 people.

Amoeba is selling its Vinyl Vaults material, which can be heard in streaming samples on the site, http://www.amoeba.com, in three pricing tiers, reflecting the audio quality of the tracks: 78¢ per track for MP3s, 80¢ for Lossless M4As and $1.50 for WAVs.

No matter which format is preferred, the older tracks have undergone extensive sonic cleaning and remastering that eliminates the noise that plagues 78 rpm records. “There’s percussion and stuff that you wouldn’t be able to hear on a 78,” Weinstein says. “We have one particular engineer who really figured out how to deal with the inconsistencies, static, to really root out all the sound without losing it.”

When the Amoeba site finally went live selling downloads last fall, the product was strictly independent; the offerings currently comprise 600,000 tracks from indie imprints, licensed from such distributors and labels as Redeye, Beggars Group, Virtual, Warp, Alligator and Naxos. Many others figure to get involved after Amoeba lands major-label licensing.

“We do not have a major-label deal,” Henderson says. “We’re hoping to start talking with the majors again in the spring. We had conversations last summer with two of(them), and it was very positive. The only reason we’re not live with the majors is that we can’t quite handle ingesting it, and doing all the levels of reporting that they ask.”

In business for 22 years, Amoeba has 500 employees and operates the three largest full-catalog record stores in the country: Its original 10,000-square-foot Berkeley shop got the ball rolling in 1991; a 19,000-square-foot location in San Francisco’s Haight district opened in 1997 in a converted bowling alley; and its two-story, 28,000-square-foot flagship store in Hollywood opened in November 2001.

Despite declining sales that reflect an industry-wide downturn — Amoeba’s numbers were flat in 2012 compared with the previous year — the company has remained a Mecca for music consumers, even as a decade-long crash claimed such deep-catalog chain competitors as Tower Records and Virgin Megastores.

“I don’t think any of us, years ago, would have thought that every record store would be gone,” Pearson says. “Realizing that a hard copy (of a record) was ultimately going to disappear, I think that changed how we were looking at the website.”

The development of a bigger online presence came at great cost, notes Weinstein: “Every bit of profit we’ve had for the past few years has gone into trying to build this thing, to get to where we’re at now.”

Reflecting Amoeba’s curatorial bent, efforts began early on to develop informational content for the site. After first mulling the possibility of licensing of All Music Guide’s enormous database of artist biographies and reviews, the retailer decided to create its own. Pearson notes that every artist on the website has his or her own page, with information aimed at simulating the experience of talking to somebody in the store.

But while Amoeba has entered the brave new world of digital retailing, the company is by no means contemplating an exit from the sale of physical product. In fact, the partners view their Web agenda as an adjunct to the company’s traditional business.

“Our goal is to have a website that helps prop the stores up,” Henderson says. “We view it as a very cyclical relationship, and a logical next step for us.”

Henderson says he feels the site could be a profit center if Amoeba can get the majors onboard and Vinyl Vaults becomes popular. Weinstein sees the site as a magnet for audiophiles.

“We would love to be as comprehensive as we think every record geek would want us to be,” he says, “so that there’s a place to go to see the depth of everybody’s catalog, to learn more about them and to exchange information with other collectors.”