But these tools basically "translate" data into something we can input using one of our five senses.
Thus we are not limited by what we can
directly perceive. Maybe we can call it indirect perception, when our instruments measure xrays (or some other thing), and we then perceive the measurements.
Does that mean there could possibly be something else outside of our perception?
I'll take that as meaning indirect perception. That is, it includes what we can somehow measure.
If there is anything that affects us then, at least in principle, we could use its affects on us as a way of measuring it. Thus we can deal with whatever affects us, whether directly or indirectly.
Can there be something which does not affect us even indirectly? That's certainly a possibility. But I don't see any reason to lose sleep over that possibility.