I'm going to call this the CRT/Newspaper theory of EPMA scanning.
When we acquire a beam scan on an EPMA instrument it makes sense that we start in the upper left of the scan area and scan horizontally from left to right stepping down for each scan line until we end in the lower right corner. Why? Because that is the way the first CRT (cathode ray tube) devices were designed to scan. But why were CRTs designed to scan this way? My thought is this is because when you're printing out characters to the screen (on the first output devices), you want to read it just as one would read a newspaper or book. Start in the upper left, scan to the right, and down one scan line at a time.
As for stage scanning, in the Cameca world the stage is scanned in exactly the same way. From upper left to lower right, just as we do for beam scans. There it should end.
But on JEOL instruments we start scanning in the upper right and scan down, then step horizontally from the right to the left, ending in the lower left. Now maybe JEOL had to scan their stage this way because Nippon Steel requested it as proposed by Takahashi. But why did Nippon Steel request that the stage be scanned this way? Again as previously stated, I propose it's because that's the way a Japanese newspaper in Kanji is read. Starting at the upper right and scanning down.
Now it's true that JEOL instruments use the same scanning convention for beam scans just as Cameca does, but that's only because that's the way CRTs are designed to scan. The first beam instruments could only scan the beam on a CRT. But once stage scanning became an option, the default way to think of doing this is the way we read our respective newspapers. Does anyone have a better theory?
By the way the first beam scanned instrument were developed by Ernst Ruska/Max Knoll/Manfred von Ardenne. See McMullan, D. (1988). "Von Ardenne and the scanning electron microscope". Proc Roy Microsc Soc. 23: 283–288
https://en.wikipedia.org/wiki/Scanning_electron_microscopeThat's my half baked theory of EPMA history for today!