Extract X, Y, Z Locations from AreaList

[Ethan Glasserman]

Hey, I am a student working in a Neuroscience lab at Harvard this summer and looking for a way to get the locations of cell bodies and synapses that we have identified using Trak EM 2.

The cell bodies were painted over using area lists, and we used connectors to link a bouton to the cell body. Our goal is to have a list of coordinates for the cell bodies, and one for the synapses. I get how the basics of scripting for Trak EM 2 work, but there were no examples for getting locations from Area Lists, and I'm a little lost.

Thanks,
Ethan

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Peter Mc]

Hi Ethan;

Neuroscience lab at Harvard...cool!.
Well I do not use Trak EM 2, but recently I asked about how to get the X,Y,Z coordinates from a ROI, so maybe could be useful for you;I don't know how the Area List work but probably you can get a ROI from the cell bodies or synapses directly.Here is the link http://imagej.1557.x6.nabble.com/Getting-coordinates-inside-a-ROI-td5003250.html#a5003325

I already have a piece of code working with these and getting the three spacial coordinates so hope can help you.