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Pascal Cotte said he has spent more than 10 years using the technology to analyse the painting.
He claims the earlier portrait lies hidden underneath the surface of Leonardo's most celebrated artwork.
A reconstruction shows another image of a sitter looking off to the side.
The Louvre Museum has declined to comment on his claims because it "was not part of the scientific team".
Instead of the famous, direct gaze of the painting which hangs in the Louvre Museum in Paris, the image of the sitter also shows no trace of her enigmatic smile, which has intrigued art lovers for more than 500 years.
But Mr Cotte's claims are controversial and have divided opinion among Leonardo experts.
Cotte, founder of Lumiere Technology, scanned the painting with a 240-megapixel Multi-spectral Imaging Camera he invented, which uses 13 wavelengths from ultraviolet light to infrared. The resulting images peel away centuries of varnish and other alterations, shedding light on how the artist brought the painted figure to life and how she appeared to da Vinci and his contemporaries.
"The face of Mona Lisa appears slightly wider and the smile is different and the eyes are different," Cotte said. "The smile is more accentuated I would say."
"If you look at the left hand you see the first position of the finger, and he changed his mind for another position," Cotte said. "Even Leonardo da Vinci had hesitation."
Other revelations include:
- Lace on Mona Lisa's dress
- The transparency of the veil shows da Vinci first painted a landscape and then used transparency techniques to paint the veil atop it.
- A change in the position of the left index and middle finger.
- The elbow was repaired from damage due to a rock thrown at the painting in 1956.
- The blanket covering Mona Lisa's knees also covers her stomach.
- The left finger was not completely finished.
- A blotch mark on the corner of the eye and chin are varnish accidents, countering claims that Mona Lisa was sick.
- And the Mona Lisa was painted on uncut poplar board, contrary to speculations.