NASA's Juno probe flew by the spot Monday, passing within 5,600 miles of the planets surface to photograph it up close.
"Now we are finally going to see what this storm looks like, up close and personal". But recent studies suggest the Great Red Spot is shrinking.
While it is unclear what has kept the storm going for the best part of four centuries, scientists believe that it is essentially re-powering itself thanks to the energy created from the heat.
"For hundreds of years scientists have been observing, wondering and theorizing about Jupiter's Great Red Spot", said Scott Bolton, Juno principal investigator from the Southwest Research Institute in San Antonio. All the photos were then compiled by several citizen scientists, who were then able to put forward enhanced-color imagery of the spot.
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It then took 11min and 33s for Juno to cover another 39,771km to pass directly above the crimson cloud tops of the Great Red Spot.
The Great Red Spot is wider than the Earth and the storm within it may have been raging for more than 350 years.
All of Juno's science instruments and the spacecraft's JunoCam were operating during the flyby, collecting data that are now being returned to Earth.
So far, Juno has discovered the largest planet-Jupiter-is a "turbulent world, with an intriguingly complex interior structure, energetic polar aurora, and huge polar cyclones".
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Juno's next rendezvous with Jupiter will take place on September 1.
The spacecraft was about 6,130 miles (9,866 kilometers) from Jupiter's clouds, NASA says.
The close fly-by was completed during Juno's sixth scientific orbit of the solar system's biggest planet.
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