displaying a 3D dataset

Ive been struggling to display a 3D array composed of 2D images of size m*m in a set of n. For this current example, a hydrophone scanning system, he distances between the elements are 100um while there is 1mm between each scans. hydrophone_data 12x91x91 794976 double array

Its not really just for this one set though, for example, i want to demonstrate lesion sizes created by a surgical device treatment by taking images in 2D cross section and then putting them back in 3D. I figured there was a way to take a theshold and show the volume in 3D.

Ive tried the slice command without luck. It seems to be for 2D slides through a volume though anyway but the images seem 2D. The surf function seems to be mostly for surfaces. Plot3D is not doing the trick either.

If anyone is interested Ive uploaded a set of 2D scans of hydrophone data I would like to put in 3D. There should be a focal point at around the 10th image in the set. http://www.engr.uconn.edu/~jmacione/temp/hydrophone%203D%20scan.zip

I was thinking it would come out to something like this when put in 3D (although I think this just 2D surface plot).
http://www.mathworks.com/help/matlab/learn_matlab/surf_light.gif

Ive tried Imagej too but it dosent really have the ability to make up for the skips in the step size i did while scanning and are pretty poor quality. Any help is appreciated.

Answer 1

[Doug Hull]

This looks like a job for sliceomatic

Just put your images into a 3-d matrix and feed to sliceomatic.

Answer 2

[jim]

hi Doug

thanks for the answer. I did see slice-o-matic before but gave it a second evalution and it does look very promising.

I dont see how to change the distance between the image planes though. If each image plane is represented by pixels which are 100*100um2 and then then images planes are 1mm apart, i need need a way to repsent this in the sliceomatic. I didnt see anything in the help files about this. So for example, in this image, each of the planes look like they are 100um apart rather than 1mma nd you cant see the focus which is squished between the image planes. http://www.engr.uconn.edu/~jmacione/temp/Untitled.png

Also, Is there a way to rotate the rendered image to get a different view of it? There didnt seem to be a lot of literature on this sliceomatic other than in the .m file itself.

Why dosent matlab have an some awesome to use program for this?