Encoder signals
My scorbot has encoders on each axis.
They are described as phototransistors.
I have no info on them
They are powered by 5v with a 39 ohm resistor to limit current.
My signal is not a clean square wave as the manual says.
What could be the issue? 
Comments
Pictures
Data sheet
On the scope traces, where is zero volts? The photo was too close up.
The pulse rate is also very stable in that photo - At a little under 10 kHz. Disc is 20 lines per rev. So that's 500 revs per second or 30000 RPM. Sounds a tad too fast.
I'm guessing what you're seeing on the scope is just noise.
As #4 says, you may be miss-measuring these.
They are open collector photointerrupters, so need pullups to 5V. You should then see slow square waves of HLHL on the outputs as the disk spins manually.
They also may not like too much light intrusion.