Removing the gaps exist between the stack images for 3d reconstruction

Hi,

i am working on 3d reconstruction of microstructure from 2d serial section images. i am facing a problem in stacking of these sections, when i stack these images and visualize then the visualization shows that there are gaps between the sections. when i insert two sections in each gap then the visualization shows quite good result, but that is not useful for me. i want to remove/minimize this gap so that the visualization looks like smooth from each direction. (i have the data set of the 3d stack of images as text file) can any one help me please

Thanks

[Sean de Wolski]

Could you show us a screen shot of the images and the discrepancy between them and what you expect?

[Asadullah]

Dear Sean de Wolski, the screenshot of the process can be found here http://www.sendspace.com/file/5ibrvn

Thanks for your help

Answer 1

[Walter Roberson]

You need interpolation or "inbetweening"

[Asadullah]

Dear Walter Roberson, I have tried the interpolation by adding two sections in each gap then the visualization shows quite good result, but that is not useful for me. My aim is not to just visualize it, i want to do further characterization on the basis of these data. As adding sections inbetween the gaps by interpolation creates biasness in the final data, i want to do characterization on actual real data. so please can you help me to minimize/remove these gaps between the sections without inserting additional sections in gaps by interpolation. Is there any other way without using interpolation?

Thanks

[Walter Roberson]

Give the images all the same Z coordinate and the gaps will be gone.

[Asadullah]

Dear Walter Roberson, Thanks for your useful comments. i got solved this problem. Now i want to apply a 3d euclidean distance function and 3d watershed segmentation algorithm on this 3d stack of images, i have no experience to apply these. Do you have any idea to guide me please, i have this stack of images in form of a text file.

[Isee You]

please i try do the same thing you do but i cant i search a lot .

can you write down the code you use to stack the images in the at first

[Asadullah]

In MATLAB, i have used the cat() function to stack the images

[Jasmin]

Hello, I am doing same viz., 3D construction using 2D sequential jpeg images (stack of 20). I tried it using cat() command, but I am not getting output. How to view this?

Thanks in advance

[Walter Roberson]

Look in the File Exchange for vol3d v2