Dark grey is the new white.

Less than three weeks since the Rijksmuseum reopened to the public with gallery walls of shadowy grey, so too does its neighbour, the Van Gogh Museum. Following seven months of renovation, the 40-year-old building has been brought up to modern technical and environmental standards, and has ditched its unfashionably white walls.

Last time I was here, I viewed the paintings over the tops of dozens of heads. Today, I'm enjoying a personal tour, before the museum reopens with all guns blazing. In a move which should spread the crowds more thinly, all four floors of the building are filled with the results of a major eight-year research project into Van Gogh's working methods.

Van Gogh At Work sees not just the return of the gallery's own impressive permanent collection, but also significant loans from around the world. The National Gallery in London has been persuaded to part with its Sunflowers until September, which is nothing less than "a miracle", according to the exhibition's curator, Nienke Bakker.

"This research project is quite unique," says Bakker, "because we have been collaborating with institutions, chemists and new technologies."

The latest methods of analysis have turned up important findings. It's no secret that Van Gogh re-used his canvases, when he wasn't happy with his efforts, or had run out of materials, "but once you start to examine everything," says Bakker, "you realise he's done it much more often than we thought."

Bakker motions towards a landscape, Garden With Courting Couples. Through the adjacent microscope, you can view a tiny sample of paint taken from the painting. It's like a striated rock, layered with stripes of colour. Bakker identifies each layer of paint, showing that underneath the painting we see, hides another, unseen. X-rays and more recent forms of scanning (which don't involve the destructive extraction of such samples) show, in incredible detail, two bare-chested wrestlers lurking underneath a bright painting of a vase of flowers.

Microscopic analysis of pictures has thrown up other fascinating details – in one of his famous Bedroom paintings, tiny letters of newsprint have been found, where Van Gogh tried to dry it out with sheets of newspaper after a flood. And particles of sand have turned up in a rare early work on loan from a private collector, Net-Menders In The Dunes. "He painted it sitting in the dunes," explains Bakker, "and there was a lot of wind, and he's even rubbed the sand in - here in the path there's more sand than in the rest of the painting, so we think he used that to create a certain effect in the sandy path, which is quite modern."

Perhaps the most important discovery is Van Gogh's disappearing red. The artist made use of a relatively new pigment, Red Lake, unaware that it was badly unstable, and would quickly fade. Researchers identified its ingredients and reconstructed the paint, showing that within 10 years of exposure to light, "the colour was almost gone". Poor Van Gogh, who only painted for 10 years before his suicide, would never know.

Bakker demonstrates the problem in a painting of cabbages and onions. The edges sheltered from light are purple, but the rest of the background, originally that same hue, is now just blue. "And the same," she continues, "with this self portrait, where there was also red in the background, but now it has faded. So it's a completely different look, and that's quite an important discovery." Researchers have now moved on to Van Gogh's yellows; they wonder if there might be some colour change there too. Watch this space.

Van Gogh is loved the world over as the quintessential mad artist, spontaneous and instinctive, a lone genius in the wheat fields. But this exhibition shows us another side to him: the methodical learner, the theorist, the collaborator. "All the colours he chooses are well thought out," says Bakker. "He has a lot of knowledge about how colours react to each other, because he's read about it a lot, and because he practised in many still lifes."

Van Gogh spent a little time in conventional academies, but what he knew he learned from books, from copying prints (literally hundreds of them), from spending days in museums (including the Rijksmuseum when it opened the first time round), and from studying the works of his artist friends.

Included in the show are three portraits by his friends, which they rolled up and posted to him in Arles. "He's really setting himself a sort of study programme," says Bakker, "because he does it all on his own."

"Of course he had a wild character," she continues, "at one point he says 'I just let the brush go', but in order to achieve that, he's done many years of struggling to get there - and in that sense he knew exactly what he was doing, and where he was going."

Van Gogh At Work is at the Van Gogh Museum, Amsterdam, until January 13.