Oscilloscope measuring of PMT in photon counting mode

The problem is that you are using a MEMS digital accelerometer, and what you are reading is the SCK (serial clock) pin of the serial interface. In order to function, that sensor needs to be interfaced with a microcontroller, that sets it for the sampling frequency, the range and so forth.

So you don't have to expect a square wave with 100Hz frequency, but a fast (depending on the bus bitrate) spike, corresponding to a transmission. Expanding the spike, if the scope is fast enough, you should then see the clock square wave inside the spike.

Moreover, if you don't set the SPI interface correctly, the uC will not generate the clock (the sensor operates in slave mode), and you won't read any value.

If you want to see a 100Hz signal, you could probe the Int pin, which sends an interrupt to the microcontroller every time a measure is available. Then, if you handle the interrupt from the microcontroller properly, you wil see the pulse corresponding to the transmission every 10 ms (100Hz).

But make sure that you're not using motion detection; in that case, only when an acceleration is measured, it will generate the interrupt.

To read the data at the SPI port, the simplest thing is to configure the communication with the sensor; otherwise, it won't send data at all. Then, check if the microcontroller is getting the interrupts and if it's reading the data the sensor gives; you can use a timer to add a timestamp to values and check the frequency they come.

(still WIP)

Depending on the oscilloscope you have (handheld vs. desktop with mains supply), the shield (reference) of your probe will be connected to the chassis ground of the scope. If you have a scope with mains supply, this will be protective earth (PE). If you connect a circuit that is also connected to PE to the reference at a place that is not Ground, current will flow through the shield of your probe and might damage the circuit or the scope.

Additionally, most Scopes are build with RF signals in mind, which require a reference signal close by for signal integrity. That's why you cannot treat them like a simple multimeter.

A handheld scope is easier to use similar to a multimeter, as it does not have a connection to PE. But even then, for high frequencies > 100kHz, you will most likely end up using it in a similar way and connecting the reference to a GND point on your PCB close to the point where you connect to your signal.

If you want to measure the difference between two points on your circuit, use two probes: Connect the reference of each to a GND point close to the probe point. Then on your scope, you can use the math function to view the difference between the two channels, which will give you the same result as if you had measured with a floating probe between the two probe points.