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Can I use the relativity formula $(\Delta s)^2 = (c \Delta t)^2 - (\Delta r)^2$ even when observers did not start at the same origin at $t=t'=0$? I know this is constant, but is it constant even if the other origins of observers were not the same at $t=t'=0$?

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Space-Time Interval: Suppose an observer measures two events as being separated in time by $\Delta t$ and a spatial distance $\Delta x$. Then the spacetime interval $(\Delta s)^2$ between the two events that are separated by a distance $\Delta x$ in space and by $\Delta ct =c\Delta t$ in the $ct$-coordinate is: $$(\Delta s)^2=(\Delta ct)^2-(\Delta x)^2$$

You can see not the absolute time but the time interval between two intervals is involved in the formula and So it doesn't matter whether or not $t=t'=0$ But both observers must measure the time interval between the same events.

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Choosing t0 == t'0 is a completely free choice, it says nothing about the physics (all that matters is that you can choose). Not doing it just makes the mathematics messier.

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