There are several reasons why the reconstructed "volume" seems to be flat, but they all boil down to the volume's dimensions being very anisotropic. I.e., the reconstructed volume is very thin in the z dimensions (compared to the x and y dimensions) and this is the reason that you basically see a flat object. In order to fix this, please follow these steps:
- Make sure that the number of consecutive sections is large enough. The sections that are loaded into the reconstruction wizard should
- cover the structures that you are interested in
- at a resolution that matches the size of the details you want to see. (Voloom should be able to handle really large numbers of sections, up to several hundreds.)
- Double-check whether you are using the correct thickness and spacings values in step one of the reconstruction wizard. The thickness always has to be entered manually and the spacing values should be checked for .tif and .jpg images that don't store these values properly. See also the "Reconstructing 3D Volumes From Serial Sections" tutorial video (up to 1:48).
- Once you obtained a reconstruction, please try to zoom into the data set by holding down the Ctrl key and using your mouse wheel. See also our "Working With Reconstruction Results" tutorial video for how to navigate in reconstructed volumes.