If those images are slices or something similar, maybe try reconstructing the structure with 3D Projection tool in ImageJ. This  tutorial explains it step by step:

http://iicxserve.jhu.edu/groups/integratedimagingcenteruserwiki/wiki/871ba/Create_and_align_a_3D_reconstruction.html

If those images are slices or something similar, maybe try reconstructing the structure with 3D Projection tool in ImageJ. This  tutorial explains it step by step:

http://iicxserve.jhu.edu/groups/integratedimagingcenteruserwiki/wiki/871ba/Create_and_align_a_3D_reconstruction.html

The University in Leuven offers a reconstruction webservice:

http://homes.esat.kuleuven.be/~visit3d/webservice/v2/index.php

http://www.123dapp.com/catch

123D Catch is probably your best option. If you want to have some control of the process, then move up to a solution like Agisoft Pro.

http://www.agisoft.ru

Or just use this one: http://ccwu.me/vsfm/

Cheers

Dear Abeera Tarik,

while dealing with 3-D image reconstruction you must remember the constraing deriving from the spatial sampling theorem. How far are the 2-D slices one from the other? How many pixels has your image: unfortunately there exist aliasing problems also in spatial sampling.

3dSlicer could be a solution

I transferred these 2D slices in 3D single Matrix.

Now how can i visualize this 3D matrix into a gray scale image?

If your data is a slice stack, you might want to try these:

http://fiji.sc/TrakEM2

http://sf.anu.edu.au/Vizlab/drishti/