Re: In a stack, how can I make a different polygon in each slice and 'Save As' their XYZ coordinates?
Posted by
Rasband, Wayne (NIH/NIMH) [E] on
Apr 06, 2014; 2:09am
URL: http://imagej.273.s1.nabble.com/In-a-stack-how-can-I-make-a-different-polygon-in-each-slice-and-Save-As-their-XYZ-coordinates-tp5007218p5007220.html
On Apr 5, 2014, at 6:16 PM, imageJnoob wrote:
> Hi, I am very new to ImageJ here. I am hoping that someone here can point me
> to a polygon/contouring tool that I have been unable to find from searching.
> I apologize if I missed it.
>
> My project is centered around mapping out anatomy from CT and MRI scans. I
> am working with stacks of DICOM images of Knee MRI's, Chest CT's, etc. I
> need to be able to outline and save the X-Y-Z coordinates of each bone,
> muscle, artery, vein and nerve in each stack.
>
> The native polygon tool draws out the same polygon for every slice of the
> stack. This of course doesn't work for me because the shape of each anatomic
> part changes throughout the stack. I need to be able to draw a separate
> polygon for each slice as I trace out a femur, for example, then 'Save As'
> their X-Y-Z coordinates with the Z coordinate representing the slice number.
> It is much too tedious with the native polygon tool to 'Save As' XY
> coordinates for every slice.
After drawing a polygon, save it in the overlay by pressing "b" (Image>Overlay>Add Selection). All polygons in the overlay will be saved when the image is saved in TIFF format. Activate a polygon in the overlay by long clicking on it. Remove a polygon from the overlay by activating it and pressing the delete key. Use the Image>Overlay>List Elements command to get a list of polygons in the overlay. The "Pos" column in the list shows the slice associated with each polygon.
-wayne
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