Help with 3D views

[Pedro J CamelloDr Pedro J Camello]

Hi all,
I want to compare z stacks of cells showing irregular fluorescent
structures (from spots to rod-like and some irregular masses). Of course,
there is some cytosolic background between these structures. I need a
proper 3D visualization and a volume measurement (pixels are calibrated
from the confocal used to get the images).

Though I´ve visited the listserver I have three questions for experienced
users:

1) what is the best/less subjective method to make threshold of the entire
stack? (I need it before 3D project)

2) should I perform a deconvolution before 3D buildings? If so, would a
blind method suffice?

3) has anybody compared MeasureStack (Bob Dougherty) with other available
plugins?

Thanks

Pedro

--
Dr Pedro J Camello
Dpt Physiology
Faculty of Veterinary Sciences
University of Extremadura
10071 Caceres
Spain
Ph: 927257100 Extension 1321
Fax:[phone]

[Aaron Johnson-9]

Pedro,

I'm also measuring structures in 3D confocal stacks.  I've been using the
Voxel Counter plugin (http://rsb.info.nih.gov/ij/plugins/voxel-counter.html)
to do my volume measurements and the numbers have had good agreement with
other (more expensive) methods.  

As far as thresholoding, that is an issue I haven't quite come to terms
with.  I've tried using my eye and have had pretty good interrater
reliability.  But, like you, I'd like to have a less subjective and more
automated method.  I'm in the process of trying to figure out how to write a
plugin to automatically set the top of the threshold to the max intensity in
the stack and the bottom threshold to 10% of the max, but I'm pretty new to
ImageJ and to programming.

I'd be very interested on input from the more experienced list members out
there.

Aaron

---
Aaron Johnson
Doctoral Student
University of Wisconsin - Madison