Many thanks in advance for help: I am working with an LSM image from a Zeiss LSM 700 Confocal Microscope (101.61x101.61 um, 1024x1024). I am looking to collect the XY coordinates of a line segment ROI (I take the XY coordinates to be the midpoint of the line segment). I have gone to *Analyze > Set Measurements > Invert Y Coordinates* to make the origin of the image the lower left corner. When I measure ellipses, rectangles and points, the XY coordinates are given with respect to the lower left corner. However, when I use the line tool, the XY coordinates are given with respect to the upper left corner (the default where the upper left corner is taken to be (0,0)). Is there a way to get the lineâ€™s coordinates with respect to the lower left corner? Huge thanks again, cheers.

Hello!

You can save the xy co-ordinates of your line selection (segmented line/straight line). First make your selection then File>SaveAs>XY Coordinates. Not sure if this helps your case though

The latest ImageJ daily build (1.51d1) fixes a bug that caused the Measure command to ignore the â€śInvert Y coordinates settingâ€ť in Analyze>Set Measurements when measuring the centroid of stright line selections.

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