[vulgarshudder]

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Tokyo National Museum
Advertising Museum Tokyo
Mitsuo Aida Museum
Edo Tokyo Museum
O Art Museum
Hara Museum
Mori Art Museum
National Museum of Western Art
Paper Museum
Setagaya Art Museum
Tabacco and Salt Museum
Tokyo Fuji Art Museum
Tokyo National Museum of Modern Art
Tokyo Metropolitan Art Museum
Tokyo Metropolitan Teien Art Museum
Tokyo Station Gallery
The University Art Museum, Tokyo National University of Fine Arts and Music
Mitaka Ghibli Museum
Nezu Institute of Fine Art
The Bunkamura Museum of Art
Bridgestone Museum of Art
Matsuoka Museum of Art
Science Museum Tokyo
National Science Museum
Transportation Museum
The Ueno Royal Museum
Sompo Japan Museum of Art

Oh and the awesome yashukan museum behind the yasukuni shrine about the kamikazi soldiers - which includes a kamikazi one man submarine.