In a stack, how can I make a different polygon in each slice and 'Save As' their XYZ coordinates?

Posted by imageJnoob on Apr 05, 2014; 10:16pm
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-tp5007218.html

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.

Can someone please help? If this tool does not exist, I am willing to pay a generous expert for his/her time to write me a plug-in.

Thanks very much!