Five thousand metres above the most biodiverse corner of the Amazon, tropical ecologist Greg Asner and his team see a kaleidoscope of colours among a mass of green.

Huddled in a twin-engine Dornier 228 aeroplane called the Carnegie Airborne Observatory, the scientists are capturing multicoloured images of the Peruvian rainforest canopy that verge on the psychedelic.

Inside the plane, a machine known as a Lidar (Light Detection and Ranging) bounces a laser beam off the forest canopy 400,000 times per second – the result is a three-dimensional map of the forest showing unprecedented detail.

In addition, a spectrometre, kept at a temperature of -131C (-204F), measures the biodiversity of the jungle in vivid colours by registering the chemical and optical properties of the forest canopy. The team can scan 360 sq km each hour.

"The technology that we have here gives us a first-ever look at the Amazon in its full three-dimensional detail, over very large regions," said Asner, who is conducting the research for the department of Ecology at the Carnegie Institution for Science, based at Stanford University, California.

"[It's] the critical information that's missing for managing these systems, for conserving them and for developing policy to better utilise the Amazon basin as a resource, while still protecting what it has in terms of its biological diversity."

As well as measuring how the forest ecosystem is responding to the 2010 Amazon drought – the worst ever recorded – the technology accurately monitors deforestation and degradation, and has revealed unexpectedly high levels of biodiversity in high forest on the Andean rim of the Amazon basin.

The data could prove critical to the United Nation's Redd (Reducing Emissions from Deforestation and Forest Degradation) initiative, which will be the biggest future source of funding to protect the planet's tropical forest.

The programme is designed to compensate tropical countries for reducing deforestation and forest degradation.

"Redd cannot exist without scientifically monitored data on carbon stock," said Asner, who may have invented the most efficient way of measuring it to date.

Daniel Nepstad, director and president of the international programme at the Brazil-based Amazon Environmental Research Institute (Ipam), and a leading expert on Redd programmes, described Asner as in "a league of his own in resolving the technical challenges that must be overcome for Redd to realise its potential."

Having scanned some of the Peruvian Amazon's most inaccessible places, Asner says the region has one of the "most incredible portfolios of biodiversity". But Asner said his initial research showed a radical increase of illicit alluvial gold mining in Peru's Amazon region of Madre de Dios since it was last mapped in 2009, making it the region's primary cause of deforestation – an area estimated to exceed 100 sq km.

• Get the Guardian's environment news on your iPhone with our new app. You can also join us on Twitter, Facebook and Google+