This issue has been there forever, as far as I know. Part of it is because the origin for the XY graph is at the lower left, while the origin of the image display is upper left. You can do a partial fix by flipping the Y axis on the intensity graph (Enter 0 as the top limit). It still requires transposing the array, though. Does the intensity graph have an option that can be checked to transpose the array like the line graph does?
Yes Bruce the Intensity Graph does have a Transpose property available both as a R-Click popup setting as well as a property node.
Additionally, the Y axis can be flipped using its Flipped property node thus avoiding the need to manually enter 0 for the Y axis upper limit. So this will avoid the need to reorient the image using code.
However, the 2D data array orientation will still be the same and perhaps not correct for further processing.
Curiously, that Flipped property is called Inverted when accessed using R-Click popup Properties option. That Inverted property is not exposed in the R-Click popup settings for each individual axis but instead is under the popup Properties under the Scales tab. The Z axis also has an Inverted property which simply inverts the scale label limits and does not change the displayed data image.
Well, this resolves your display issue. For processing, you just need to remember the origin for an image is in the upper left corner, and figure out which array index corresponds to each image axis. Transpose if necessary before auto-indexing would be my only concern.