Fiji / ImageJ coordinates start point

Dear colleagues,

ImageJ’s origin of coordinates is in the upper left corner of an image. Is there any chance to set the origin in the bottom left corner?

Best regards,

Hello Felix -

The convention in image processing that y values increase
from top to bottom can seem counter-intuitive for those of us
who come from a background of working with x-y plots where
y values increase from bottom to top. However, as least as
far as I have seen, the zero-at-the-top convention is completely
standard across image processing.

Hypothetically, the convention could be switched in ImageJ.
I fear, however, that:

  1. This would be unhelpfully confusing, given the established
    image-processing convention, even if offered as an option.

  2. The code modification would likely be error prone, as this
    convention is probably tacitly baked into the code base all
    over the place.

Is there any chance that as a work-around for your use case you
could first flip your image:

Image > Transform > Flip Vertically

perform your processing in your preferred coordinate system,
and then flip back?

Thanks, mm

Enable “Invert Y coordinates” in the Analyze>Set Measurements dialog box.

Thank you for your reply, mountain_man. To be honest I am not sure about flipping vertically and since there is another built-in tool (see Wayne’s message) I would go therefore. However you showed a good work-around.

Dear Wayne,
thank you very much for your reply and showing me the proper tool.

If I save the XY coordinates they appear not inversed. Is there a work-around to get these inverted, too?

Best regards,