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I'm working on a project, where I will have 2 red light beams, where one will be constantly turned on while the other will be turned on and off continuously with frequency about 100 hz. I need to detect, on which side is the blinking beam and show it on the output (something such as if the blinking beam is on the left, turn green LED on; if it's on the right side, turn on the red LED). Each beam is big as 3mm circle.

I bought 3pcs (in case if I burn 2 of them :D) of Toshiba TCD1304 sensors(datasheet), which have 3684 elements in a row. I want to connect the sensor with Arduino, but I really don't know how I would even start this project. I've found some schematics, but it's either for some other model or is for different kind of a project(reading different colors over the field). Either way, none of them is useful for me.

It will look something like that at the end (the blue circle will be also red, but it's striped to show, it's the blinking one). enter image description here

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The TCD1304's minimum OS-datarate is 200 kHz. Quite a lot more than what the arduino is capable of. You should look to faster processors or to a different sensor. The TSL1401 seems to be popular with the arduino-community.

If you /need/ the TCD1304, then an arduino due will probably be able to do it, but I'm guessing you'll have to drop the arduino-IDE to achieve the full speed of the ADC.

Here's how I've done it with a STM32F4 processor: https://tcd1304.wordpress.com/

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