Re: adding real axes to pixel format, possible addition to ImageJ

Posted by Robert Dougherty on Jan 11, 2006; 6:22pm
URL: http://imagej.273.s1.nabble.com/adding-real-axes-to-pixel-format-possible-addition-to-ImageJ-tp3704097p3704102.html

The "Set Scale" feature would be slightly more useful to me if it included
the offset, since my images often represent contour maps that are defined in
a specific coordinate system.  The user interface for that could be to add
boxes for "x value of left side" and "y value of top", or something
equivalent.  (I can't find the z slice spacing input at the moment...).
With no input, the values would be zero, and the behavior would be the way
it is now.  Cropping and canvas size adjustments would need to change the
offsets.  If the offsets have not been deliberately set, then cropping,
etc., should probably not change them.  I'm not sure what to suggest for
that.  The new information would need to be stuffed into tiff files somehow.

Bob

Robert P. Dougherty, Ph.D.
President, OptiNav, Inc.
Phone [phone]
Fax [phone]
www.optinav.com
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Gabriel Landini
> Sent: Wednesday, January 11, 2006 1:45 AM
> To: [hidden email]
> Subject: Re: adding real axes to pixel format, possible addition to ImageJ
>
> On Tuesday 10 January 2006 22:54, John Carlson wrote:
> > What do you mean by calibrated image?  How do you do that in ImageJ?
>
> Image>Properties and then you put the value of the pixel size in your real
> units. You should have calculated beforehand what the calibration values
> should be.
> If you point to any pixels, you get the calibrated coordinates in the
> statusbar (instead of in pixels). This will be offset to 0,0, so you will
> only need to add/subtract any offset you need. The calibration is saved in
> the tiff format. You could store the offsets as metadata in the tiff tags
> and
> make a macro that reads them and converts to your chosen units in the
> statusbar or to a new window.
>
> > I would need to query the x and y coordinates for their values that were
> > obtained from the file format we are using.
>
> But the image is made of discrete units, so you will not be able to get
> more
> resolution than the image that holds the data. The coordinates would be
> transformed only.
>
> If such modification to the calibration was to be made, then one
> suggestion is
> to have a dialog that asks for the coordinates (in calibrated units) of
> the
> top left image pixel (0,0) and that one of the lower bottom pixel
> (getWidth()-1, getHeight()-1).
> As I said, you could incorporate these calculations in your own macro or
> plugin and store them as metadata.
>
> I hope it helps.
>
> Gabriel