Calculating distance with the Gal Map

Distance can be easily calculated with the diagram in the Galaxy Map but only for The X (?) axis.
I seen many post where explorers manage to calculate the distance for stars in the Y axis a.k.a verticall, most recently for the M67 expedition.
How you guys calculate those distances for vertical trip, specially while explorings the "top" and "bottom" of our galaxy?
 
You can estimate coordinates for all three axes from the galmap and then do exactly what you're doing on the horizontal plane.
 
Pythagoras' Theorem works in three dimensions, as well as 2.

Distance to Sol = sqrt (X^2 + Y^2 + Z^2).
 
Most of this is done by EDSM - https://www.edsm.net - which given the distances between an unknown system and at least four known systems (4 is the theoretical minimum, sometimes it takes more) can calculate the exact coordinates of the unknown system. From that, working out the distance from it to anywhere else is easy using the Pythagoras equation posted above. Tools such as EDDiscovery can help submit distance data to EDSM.

Since 2.1 came out, we've been able to get exact coordinates for any personally visited system out of the game logs, so that gives EDSM a lot of data to work with. Before that it was a much slower process.
 
As a fudge, if you have 'show navigation markers' selected in the last tab of the map, when you mouse over a particular system all other stars in range (with your current fuel/cargo load) will have a little orange semi circle appear above them. You can also select the various FSD boost levels and check with the displayed jump range. Won't give you an exact distance, but will let you know if you can make the jump.
 
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