I am trying to get the coordinates from a mouse click in the ImageJ canvas and then pass them to R. I have been reading these two sources, am I on the right direction? is there any example showing this feature?
you can use two available functions in Bio7 (Image-Methods dialog) to transfer point coordinates directly to R.
Without the ROI-Manager just press Shift and click some point selections. Transfer them with the "Points" action or use the ROI Manager with the "Selection" action. With the ROI-Manager multiple slices can be transferred, too. For both see: