CT_Recon is a user interface to Base_Recon.exe, a Windows based
executable for reconstructing 180 degree parallel-beam sinograms using
direct Fourier inversion(DFI).
Sinogram(Left), CT_Recon User interface(Center),
Reconstructed Slice(Right))
Description
Input sinograms are parallel-beam projected opacity (tau) values acquired at equally
spaced angles between 0 and 180 degrees of specimen rotation. Sinograms
of this type can be obtained either by experiment or by digitally
scanning test images with the parallel projector plugins described on
the Scan Simulators page.
Sinogram images have dimensions of length(cm) in the horizontal(x)
dimension and angle(theta) in the vertical(y) dimension. The DFI
algorithm first computes the 1D FT of each of the rows(angles) in the
sinogram. The f(r,theta) polar transforms are interpolated onto a 2D
Cartesian f(x,y) grid to form the 2D FT of the image. The output image
is computed from the inverse 2D FT of the interpolated transform. DFI
is inherently noisier than other reconstruction techniques and produces
significant artifacts if the input sinogram data does not cover the
full 0-180 degree angular range. However, it has a significant speed
advantage that makes it well suited for digital simulations.
Using CT_Recon non-modal dialog
Dialog Components
Data Source - The default data source is the active image or
image stack. You may select another sinogram using the Data Source
menu.
Refresh - Click if the Data Source list gets out of sync with
the displayed images.
Rotation Axis - The default axis of rotation is the mid-point
of the active image. Enter the actual value for your CT scan
Shift Axis - A scan's axis of rotation is not always exactly
centered on a pixel. Select a fractional shift and observe the
reconstruction for any improvement.The image data is shifted by
interpolation so some loss of resolution may occur.
Cartesian Cutoff - 1 is the Nyquist frequency. Lower values
reduce noise by blurring the image.
Cartesian Filter - The usual suspects to reduce noise with
minimal blurring. The cutoff is applied to the chosen filter.
Extension Width - Minimize artifacts arising from a portion of
the specimen rotating outside the field of view by pasting "wings"
onto the sinogram edges that decay smoothly from the edge attenuation
value to zero. Pick a shape that works best for your sinogram.
Extension Shape - Like Extension Width, pick a shape that
gives the best looking reconstruction. WARNING! Profile extended
reconstructed attenuations will most likely be incorrect.
Fix Severe Rings - Detector point defects can cause severe
ring artifacts. This option uses a 1D median on the sinogram rows to
try to suppress the artifact.
Beam Harden - Applies a second order beam hardening correction
to the sinogram attenuations τcorr = (1-W)(τobs)
+ (W)(τ2obs). The slider adjusts the weight between
the first and second order terms. Crude but effective on many
relatively homogeneous specimens. Reconstructions may require
rescaling to obtain correct linear attenuation values.
Use Scale Factor - Check this box and edit the default scale factor
when reconstructing 16-bit sinograms. The scale factor should be the
same as that used by your CT scanner. The plugin
projector scale factors are imported automatically..
Reconstruct Test Slice - Opens a "TestRecon"" reconstructed
image. Change a setting and click again to observe the result.
OK(reconstruct) - Creates a new image or image stack with the
final reconstruction(s)
Notes about Base_Recon.exe
It's old, original in 1997, unchanged since 2007
It uses FFTW to
do the FFTs and does not require input sinograms to be a power of 2 in
width.
It expects signed 16-bit sinograms as input, i.e.
absorbance*scaleConstant.
Both FFTW and Base_Recon.exe are written in native 'C' and may
not be compatible with your ImageJ environment.
It uses a command line interface for instructions and file IO
for data transfer.
The command line interface was programmed by a third party.
LazzyIzzi wrote the DFI code.
I still have the source codes for the reconstructions but the
Base_Recon command line UI codes have been lost.
The CT_Recon plugin communicates with Base_Recon.exe using the
command-line interface by creating temporary files in the ImageJ
"plugins"" folder.
Notes about CT_Recon plugin
It leverages an old reconstruction code. Better
implementations may be available.
It is unlikely to be updated because more recent
implementations are available from other sources.
32-bit sinograms are automatically scaled by 6000, i.e.
absorbance*6000.
The projector and reconstruction plugins allow for other scale
constants.
Auto-scaling 32-bit absorbances greater than τ=5.461
will cause ImageJ's unsigned 16-bit data to wrap when converted to
Base_Recon's signed 16-bit2. Use the same smaller scale
factor when projecting and reconstructing.
It is not suitable for fan-beam data.
The image list may get out of sync with the displayed images.
It leaves temporary files in your plugins directory. You may
delete them at any time.
Base_Recon.exe must be present in the plugins folder.
An absorbance greater than 5.46 are unlikely to be observable
in routine practice but can be easily produced in simulation.
Base_Recon uses signed 16-bit sinograms because negative
absorbances can occur in real CT scans due to noise and X-ray
scatter.
