First reconstructed slice during microtomography experiment

On GANYMEDES PC workstation:

Open an xterm window (right button click and click on 'Xterm')

ganymedes:~ % ssh -X mdxxx@coral
coralX% octave

To reconstruct one slice (reconstruction with pyHST):

Once at the beginning:
> fastsetup
Setup of global parameters for fasttomo
Reconstruct always biggest possible slice? :[y]
Select slice to be reconstructed graphically? :[y]
Method to find rotation axis position: [g]lobal, [a]ccurate, [h]ighlow, [m]anual? :[g]
Automatically execute calculation refHST files? :[y]
Selection volume: [t]otal,[m]anual,[g]raphics? :[total]
Move axis to the center? :[y]
Correct for spikes? :[y]
Threshold for spikes removal :[0.04]
Put acquisition in database tomoDB? :[y]

To reconstruct a single slice, use "fasttomo" macro.
It is also a program which prepares files for the future whole volume reconstruction.
Go in the sample directory:
> cd sample_dir
> fasttomo
name of directory:
A new figure appears with projection at 0º (flatfield done):
Indicate layer to be reconstructed
Choose a line in the sample
The reconstructed slice will appear in a new figure (in a logarithm grey level scale)


Now, see this page: To reconstruct the whole volume