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I recently try to use Lidar Lite v3 with my Rpi 3, and it works with I2C communication. My wiring method is due to offical documentation. Wiring picture However, what I have learned before is that the gpio pin of RPI can only afford 3.3v working voltage. My Question is that shouldn't I add the resistor in my circuit to prevent from breaking out the pins of my RPI ?

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I assume your concern is that the SCL and SDA pins run at 5V because the device is powered with 5V.

Page 4 of the operation manual, under heading I2C interface paragraph 2

"The I2C bus operates internally at 3.3Vdc"

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