The rules
Musical instruments are exempt from the oversized baggage rule, but must still fit within 250 cm and 30 kg.
Small cases fit overhead. Larger cases like cellos are often easier with an extra seat or a last row seat.
With a Japan Rail Pass, seats with an oversized baggage area are included at no extra cost. Book them by scanning the QR code on your pass at a Shinkansen ticket machine or at any staffed JR desk. Get your Japan Rail Pass