Thanks to the magic of dissection, we have a pretty good idea of the changes that occur when a caterpillar spins its chrysalis and enters its metamorphosis -- the developmental stage that sees it move from the juvenile larval stage to the gorgeous adult life of a butterfly.
However, as you might have already guessed, dissection destroys the specimen, meaning that researchers are unable to follow the full development of a creature. We do know that the caterpillar will use enzymes to break down some of its proteins to reform; Scientific American called this a cocoon full of "caterpillar soup." However, scientists have performed research revealing that while some breakdown occurs, the idea of caterpillar soup is mostly wrong (but still gross).
Using micro-computed tomography, or micro-CT scanning, which uses X-ray imaging to re-create 3D cross-sections of the scanned object, Tristan Rowe and Russell Garwood from the U.K's University of Manchester and Thomas Simonsen from London's Natural History Museum have discovered exactly what happens to a painted lady butterfly inside the chrysalis.
Although a lot of rearranging occurs, some things remain. The insect's guts change shape, shrinking down into the butterfly's smaller body, but never disappear entirely. Meanwhile, the tracheal system gets bigger and reattaches itself to a different set of openings. However, a number of tissues, such as the muscles and central nervous system, are invisible to the scan and could not be studied. Although ionizing radiation would give these tissues the necessary contrast, it destroys tissue in the process and is not a good solution.
Overall, the technique will not revolutionize what we know about insect metamorphosis in any significant way, but it does make for a fascinating glimpse into something usually hidden from human eyes.
The full research paper, "Metamorphosis revealed: time-lapse three-dimensional imaging inside a living chrysalis," can be read for free in the Journal of the Royal Society.