A knife slices through the skin of your right arm, causing blood to spurt and exposing the muscles, blood vessels and finally the bone. Andreas Vesalius (1514-1564), the founder of anatomy, is operating on your arm in a video projection in the rejuvenated Rijksmuseum Boerhaave.

Its doors opened again in December, when it was also announced that, after dedicating twelve years to the museum, its director, Dirk van Delft (1951), would be succeeded in April by Amito Haarhuis (1967).

"I retired officially in June", Van Delft explains, "but the reopening was postponed for six months. I would have sunk into a terrible depression if I had been forced to leave just before we were finished but, luckily, I could stay on for a bit."

The museum is now divided into five themes. "Before, the display was chronological: from the oldest book of plants, which dates from 1485, to an intricate microscope built in 1986. Most people flaked out before the end – by the time they reached 1857, they would be wondering where the café was. It didn’t help that its science was not very inspiring, being composed mainly of grey cabinets and data. In addition, the objects from the last century were displayed in a kind of depot, with very little cohesion and all piled together. Now the collection is of flesh and blood; after all, it should tell people about the scientists and their patients."

The courtyard had already been done up in 2014 and now includes a water playground. The anatomical theatre, located at the beginning of the museum’s route, came to life when video projections were introduced in 2015. Now, it’s followed by the Golden-Age theme. "In that era, our perception of the world changed as the sun replaced the earth as the centre of the universe", Van Delft explains. In the unlit hall, the eye is caught by the Leiden Sphaera, "the oldest heliocentric planetarium in the world. Many visitors wonder whether it was already in the collection. Well, it was, just planted in a corner, without a context of any sort. A science journalist once pointed out to us that the zodiac had been fixed on back to front. The planetarium was damaged during a bombing raid in the Second World War and it must have been restored, because the sequence is correct on older photographs. We decided to leave it as it is."

The Golden-Age halls still house the book of plants from 1485. "The focus here is on exploration, of the world by explorers, but also with microscopes." You can look down Antoni van Leeuwenhoek’s microscopes, next to sketches of his discoveries, magnified many times on glass plates. "He was the first to see a sperm cell", Van Delft points out. "Curiosity has no limits."

There are plenty of extras in the museum as well as the original objects: interactive information kiosks, experiments and games. The Sickness-and-Health theme begins with a screen where your own body teaches you about narcotics and X-rays. The skeleton opposite you moves with you, as if you are standing in front of a mirror. "Imagine, we have whole families dancing in front of it," Van Delft smiles.

His favourite room is just beyond: large and white, with hospital beds as display windows. Projections on the walls show nuns from a bygone era in large coifs bending over real patients. This room also contains the big iron lung. "Initially, it was displayed among objects that had nothing to do with it – it was slightly patronising: I’m an iron lung and I don’t care if you don’t understand." Now, its large, white cover shows a video of how a young polio sufferer who cannot breathe independently is lifted into an apparatus such as this one. You can listen to a sound fragment too. "An older lady recalls how, when she was four, she had to spend months in one of these. For her, the worst thing was when they burnt her doll because it might contain the virus." Next to the iron lung – and about the size of a handbag – is a modern device. "You carry it about with you nowadays, instead of spending months in one of those."

So, in fact the collection doesn’t end with that intricate microscope from the eighties. "No, actually, it goes much further", Van Delft enthuses. "We’ve introduced tomorrow’s science to the museum with a number of joint projects." One example is the Extreme Ultra Violet mirror, manufactured by chip producers ASML, and a qubit from QuTech at the Delft University of Technology, which are exhibited in the technology room, opposite the X8, a gigantic computer from the sixties.

However, the darker aspects of science are no less important. The museum has room for failures. The theme room Mighty Collections contains human skulls and monochrome portraits in addition to eighteenth and nineteenth series of shells and birds’ skulls. "In the nineteenth century, people would pick up skulls from battlefields. They looked for links between the soldiers’ origins, revealed by their uniforms, and characteristics of their skulls. Very soon after that, the criminologist Cesare Lombroso tried to determine whether you were a crook or a tramp by your physical features, while later still, in the Third Reich, those ideals went completely off the rails."

The last theme is Big Questions. Top-ranking scientists explain how they were inspired by their famous predecessors. One of them, physicist Erik Verlinde tells us about Albert Einstein, who was appointed endowed professor at Leiden in the nineteen-twenties. "And of course, we have Einstein’s fountain pen and a telegram he sent", says Van Delft. One display window is dedicated to Dutch Nobel Prize winners and includes the box of bricks physicist Gerard 't Hooft played with as a child. "But we also have notes he used for his Nobel-Prize research and clogs belonging to Ben Feringa, which he wore as a three-year-old on his first exploration round his parents’ farm, long before he went on to win the Nobel Prize for chemistry in 2016.

The room for temporary exhibitions is still under construction, but Frankenstein: The path to a new human is to open here on 16 March.

Rijksmuseum Boerhaave

Open from Tuesday to Sunday, €12.50; free admittance on presentation of a student card.

Back in 2011, Rijksmuseum Boerhaave was threatened by closure following cuts in the national budget for culture. "Brilliant, it was brilliant!", Dirk van Delft recalls. "In hindsight, and even at the time, it was an invigorating and chaotic time, which I really enjoyed. We didn’t take it lying down, whimpering that it was a scandal! Of course, we whimpered, but we gave it everything we had, too. Businesses, private individuals and Friends of the Museum all supported us, en masse. And once we reached achieved some great improvements, we didn’t relax. The water playground, the treasure island and the anatomical theatre were all planned in those years."

He regards the renovation as the finishing stage. "Of course, it’s never finished, but we truly have progressed." He will remain involved as a Friend of the Museum. "I was already a Friend; I have always dutifully paid my membership, but I don’t want to get under the new director’s feet."

Moreover, he will stay at Leiden University as an endowed professor. "I have some PhD students, so that I’ll still do that, and I have a zero-hour appointment, which means I can certainly do research. My PhD dissertation was a biography of Heike Kamerlingh Onnes. Writing is my favourite occupation, preferably in a way that appeals to more people than just the 23 colleagues involved in my work. I just must write, even during the whole to-do with the reopening, otherwise I’ll suffocate. Luckily, I don’t need much sleep."