With little fanfare, the Atwater Kent Museum closed for a major $5.9 million renovation in January 2009, saying it would reopen in fall 2010.

It remains closed, and officials say it probably won't reopen until June 2012, a year and a half late.

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A year is a long time for a museum to be closed. Two is an eternity. At three, they bring in the forensic unit to determine the identity of the body. Three and a half years?

"We have to get this place open," said the museum's new director and chief executive, Charles Croce, who signed on early this year. "We cannot continue to be out of the public eye."

Just this past week, the Atwater Kent did, in fact, reenter the public eye.

On Thursday, the Philadelphia Museum of Art announced it had purchased Charles Willson Peale's 1819 oil portrait of Yarrow Mamout, one of the nation's earliest and most significant formal portraits of a free African, from the Atwater Kent.

The sale, which Atwater Kent officials said was necessary to cover a $1.4 million construction loan, has thrown the museum's long-standing problems into sharp relief.

It is Philadelphia's charter-mandated history museum, leaning heavily on city subsidies that have declined steeply over time. The museum has been unable to sustain a broad fund-raising effort and has a minuscule endowment - less than $1 million.

The museum board of trustees is small, with several positions held by city officials who appear to view their roles as passive.

The result has been a brew of inadequate finances and fitful management - all amply on display thanks to Yarrow Mamout, a painting sold because the Atwater Kent embarked on an ambitious renovation project without adequate funding in hand or in the pipeline.

"A great city deserves a great history museum," said lawyer and trustee David Rasner, named to the board in 1993 by Mayor Ed Rendell to get a handle on the Atwater Kent. "I believe this place can become that, with a lot of hard work. Not all the steps are in a straight line. There have been zigs and zags, maybe some errors made, mistakes in judgment. But it now is an institution of significance. Will it have vitality? That remains to be seen."

The museum's vast collection certainly has some intriguing art and artifacts - everything from the famous wampum belt given by Native Americans to William Penn to 19th-century trading cards, industrial tools, Atwater Kent radios, and a Jimmy Rollins 2008 Phillies jersey.

Taken together, it represents three centuries of Philadelphia's material culture, high-, low- and middlebrow. But since opening in 1941 as a quasi-city agency, it has rarely achieved visibility - except during times of stress.

Gary Steuer, the city's chief cultural officer, says he has worked to assume responsibility within the city bureaucracy for the museum's expenditures and progress.

"I can say I am extremely concerned about the health and future of the Atwater Kent," Steuer said. "I'm concerned about the fact that millions have been invested in a facility that is still not open to the public."

Since it closed in January 2009, it has a new name - the Philadelphia History Museum at the Atwater Kent - so people will know what it is. It has a new climate-control system for its historic 1826 building on Seventh Street just south of Market. That's so exhibits can be mounted without fear of damage from extremes of temperature and humidity.

It finally has an exhibit plan for the new interior, which officials believe will draw visitors. It has a new maintenance and storage facility in East Falls, leased to hold a collection of 110,000 artifacts and artworks. The collection is now securely in one place.

But the museum also has a lot fewer artworks than it did a few years ago, the result of a string of controversial sales undertaken to cover debt and fund the renovation that purportedly guarantees the health and welfare of those very artworks.

Yarrow Mamout is only the most recent sale. Thousands of artifacts have now gone to market to raise money, free storage space, and focus the collection on items deemed of relevance to Philadelphia. Since 2003, the museum has sold between 5,000 and 6,000 items, according to officials, more than half since 2007.

Truly big-ticket art sales began in December 2009 with the sale of a Raphaelle Peale still life for $700,000. Though the price of Yarrow Mamout has not been disclosed, knowledgeable speculation puts it in the $1.5 million-plus range.

Croce said that half the renovation has been funded by sales from the collection - about $3.1 million. The other half came largely from city, state, and federal grants.

While he was not involved in the original decisions to sell, Croce said the deaccessioned pieces  were deemed to have little or no relevance to the city. Other jettisoned works were judged to be duplicates, in poor condition, or not of museum quality.

Both the Peale still life and Yarrow Mamout were acquired from the Historical Society of Pennsylvania, which gave virtually all its collection of 10,000 artworks and artifacts to the Atwater Kent a decade ago. The society receives half the proceeds of sales of its former collection.

 Croce argues that the Atwater Kent had little choice but to sell the two paintings. Lacking money to complete its $5.9 million renovation and suffering under a large bank loan, selling a few works was a wise, if painful, decision, he said. Debt owed will soon be debt repaid.

"I think the toughest thing in the world is to come into any [closed] institution and inherit what amounts to $2.4 million of debt. How do you operate? Where's your revenue stream? When are you going to reopen? All of those things. The first order of business was to eliminate this debt, and we are almost there."

Not everyone agrees this is an ironclad argument.

Derek Dreher, head of the Rosenbach Museum and Library, without specifically commenting on the Atwater Kent, notes that using money from collection sales to fund building construction, aside from any ethical considerations, often simply kicks problems down the road.

"If the problem is bad management, a quick infusion of cash will solve the problem, but only for the short term," he said, adding that one of the real dangers is that the public, and potential donors, may not greet such sales with warmth.

"You're faced with a real loss of trust," Dreher said.

Ford Bell, head of the American Association of Museums, a Washington-based service organization, noted that his organization's ethical code allows sales only if funds are then used for acquisitions or direct care of collections.

"A building that may lead to damaged objects - that in itself is unethical," he pointed out, but added that a "museum should not be using the collection to fund deferred maintenance."

Since the Philadelphia fiscal crisis of the late 1980s and early 1990s, the Atwater Kent repeatedly has faced funding cuts, potential closure, staff reductions, and a revolving door in top management.

Radio pioneer Atwater Kent bought the museum building (first home of the Franklin Institute) in 1938 and gave it to the city, which owns it. But what is the museum? A city department? A private nonprofit? Who exercises ultimate responsibility?

When Croce took the reins in January, he was surprised by what he faced.

"We had no strategic plan," he said. "We had no fund-raising case study. We had no interpretive master plan for the exhibitions. We have all three of those now."

Croce began the museum's first systematic corporate fund-raising effort, which has borne fruit with a gift from Dow Chemical to help renovate the museum's rear garden. When completed, it may produce event income.

When Steuer took a closer look at the museum earlier this year, when the museum was scheduled to open this fall, he was surprised to find there was no funding for exhibition installation.

Since then the museum has found a donor to help defray installation costs, but the lack of earlier fund-raising pushed the opening deep into 2012. Facing that, Croce has decided to open the front galleries of the building, probably in November, to lend some life to the dark facility.

Acknowledging that he needs fund-raising help, he also is implementing a plan to expand the board of trustees over the next 18 months.

"I can't do it alone," he said. "To go to a corporation, to set up a meeting with Peco, you do need some influence on your board, and you need some affluence. I'm confident that a stronger board, a strengthened board, a larger board with entrée to the corporate sector is going to be very important here."

An active board is essential, he said, not only in the move toward financial stability but to establish the Atwater Kent's public credibility.

Museum officials believe the city's annual operating subsidies have stabilized at $240,000, about 25 percent of the museum's budget. But that's only a part of the funding problem.

"What guarantees does anyone have, does the city have, do you have . . . that every time there's a debt [we won't] go into the vault?" Croce asked. "I wouldn't permit that. We have to raise money in other ways."

Contact culture writer Stephan Salisbury at 215-854-5594, ssalisbury@phillynews.com, or @SPSalisbury on Twitter.