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Created a short GND return path for the oscilloscope probe (as opposed to the alligator clips) by using a piece of 22AWG solid core wire and twisting it around the barrel of the scope probe:
In order to make use of this, I had to provide a resistive element which also had a low inductance - which a current sense resistor is great for! In this case, I used one from a cheap 4S BMS that I got off Aliexpress a long time ago (the BMS itself is terrible). I would expect probably a 5% tolerance or so on the resistor given how cheap the module was.
And we got some much better results:
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My firmware knowledge if very limited at the moment, so I will wait until I learn to generate a clock pulse or just jump straight to the AFE validation and hope it works.
Testing out the AFEs - we got them working, so isoSPI seems to work well!