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The mouse used in Mousehunt, the mouse is shown extra ordinarily clever. Was that a real mouse used in that movie or another computer created bug? Whatever it is, it seemed very real!

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up vote 5 down vote accepted

From Cinema Review:

It is actually an ensemble performance delivered by a combination of real mice, an animatronic mouse and a computer-generated (CGI) mouse.

Animal trainer Boone Narr trained ...

... 60 mice to perform the complex stunts and tricks they would have to perform in the film.

Grouped in teams of four or five, the mice had to be taught to do basic running and climbing stunts, as well as more intricate actions, including climbing into a sardine can bed beneath a tissue paper comforter.

The mice became so beloved that many of the "Mouse Hunt" cast and crew adopted them after shooting was completed.

The visual effects company Rhythm & Hues was responsible for the computer generated mouse.

According to Rhythm & Hues' visual effects supervisor Charles Gibson:

  • "The goal with 'Mouse Hunt's' visual effects was to make people believe we had the world's most amazing trained mouse, and never a CGI creation."

The animatronic mouse came from Stan Winston Studios.

VFX HQ has an article about the CG mouse.

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I must say they were successful in showing it was a real mouse indeed! – Mistu4u Dec 19 '12 at 15:54

From what I recall, I think it's a mix of real life and cgi, depending on the scene you're watching. In a good portion of the movie I believe they used a train mouse, and for the more complex scenes (liek when the mouse was knocked out if I remember correctly) they used cgi.

This is all based on my memory though so I have to references for you.

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