Designed Macros for ImageJ software to click and pick the pixel y/x coordinates, collect them into "Results" table, measure distance and scale, manage order and mark the points.
On each click into an image, the x, y coordinates of the point are written into the "Results" window. The point can be also marked in the image (destructively). This tool can handle scaled images (also with nontrivial pixel aspect ratio). Double click on the tool icon to display the options dialog box. The "Invert Y" option in Analyze>Set Measurements is supported.