Forschungsneutronenquelle A freeware path to - isnr.de Technische ... A freeware path to neutron computed tomography Burkhard Schillinger Heinz Maier ... budget to build a tomography

ITMNR-8, Beijing, Sept 1-4, 2016

Technische Universität München Forschungsneutronenquelle

Heinz Maier-Leibnitz (FRMII)

1

A freeware path to

neutron computed

tomography

Burkhard Schillinger Heinz Maier-Leibnitz Zentrum

Technische Universität München, Germany

Aaron Craft Idaho National Lab,

Advanced Post-Irradiation Examination Department, USA




B.Schillinger 2

• Neutron computed tomography is now being introduced even at smaller and

older reactors.

• Operators are often faced with a Hen-and-Egg problem:

First, they have to show that they can do tomography before they can obtain a

budget to build a tomography system.

• Building a cheap system first, and using free software, will deliver first results to

support a grant application, and give invaluable experience to design a more

advanced system.




B.Schillinger 3

This talk presents

• a freeware path for

image processing through reconstruction to 3D images

• a cheap tomography controller and camera system to obtain first results

than can be used for a grant application.




B.Schillinger 4

The tomography data processing steps are

• Preprocessing of images:

Removal of gamma spots, subtraction of dark current,

normalizing to open beam

• Reconstruction:

Sorting projection data into sinograms, tomographic reconstruction

of image layers

• 3D Imaging:

Rendering 3D views of the stack of reconstructed layers




B.Schillinger 5

Professional software for tomographic reconstruction requires a stiff investment.

Octopus by InsideMatters for tomographic reconstruction

https://octopusimaging.eu/

and

VGStudio by VolumeGraphics for 3D rendering

http://www.volumegraphics.com/

have been established as a quasi-standard for high-end computed tomography;

Octopus has even started its development from neutron computed tomography, so it takes into account

several specific requirements for neutron measurements.






B.Schillinger 6

Professional software for tomographic reconstruction requires a stiff investment.

Octopus by InsideMatters for tomographic reconstruction


and

VGStudio by VolumeGraphics for 3D rendering


have been established as a quasi-standard for high-end computed tomography;

Octopus has even started its development from neutron computed tomography, so it takes into account

several specific requirements for neutron measurements.

Several packages are available on the web for free;

however, these have been developed for X-rays or synchrotron radiation and are not immediately useable

for neutron computed tomography.

Three reconstruction packages and three 3D-viewers have been identified and used even for Gigabyte

datasets.

We present the necessary additional preprocessing in ImageJ, some workarounds for bugs in the

software, and undocumented or badly documented parameters that need to be adapted for neutron

computed tomography.






B.Schillinger 7

General Image processing:

ImageJ from https://imagej.nih.gov/ij/

• Most important: X-ray packages expect a fully illuminated detector, black edges caused

by beam limiters are not permitted. These have to be cut off using ImageJ.

Load images together with open beam and dark frames to cut the same size.

• Run the despeckle noise filter to remove small gamma spots

• Save stack according to naming conventions of the reconstruction software, e.g. starting

at 0000 or at 0001, with specifix prefixes.

https://imagej.nih.gov/ij/






B.Schillinger 8

CT reconstruction with H-PITRE:

https://webint.ts.infn.it/en/research/exp/beats2/h-pitre-beta-version.html

H-Pitre is a reconstruction package developed by the Sychrotron ELETTRA in Trieste, Italy.

It runs on a NVIDIA Graphics card.

• H-PITRE was developed for attenuation and phase contrast measurements at synchrotrons, implying

low-contrast samples and parallel beam geometry.

For monochromatic parallel beams, 180 degree rotation is sufficient, but for polychromatic radiation

and large-contrast samples, a 360 degree scan would be helpful to reduce beam hardening artefacts,

however, this is not implemented in H-PITRE.

H-PITRE can read 8 and 16 bit integer and 32 bit float data in TIFF, PNG and BMP.

It requires a fixed naming and four digits numbering convention starting at 0001 with the names

tomo_0001, flat_0001, dark_0001.











B.Schillinger 9

screenshot of H-PITRE:




B.Schillinger 10

H-PITRE will do a dark frame and flat field correction, but the center of rotation must be found manually if it deviates from

the image center.

After converting all projections to sinograms, single slices can be reconstructed.

Small semicircles at edges are a sign for incorrect center of rotation; the correct value has to be found manually by trial and

error.

If the rotation axis is tilted, test slices must be reconstructed at top and bottom of the data set, and with the option ‘dynamic

rotation center’ set, the resulting values must be filled into the appropriate fields for ‘RoCenter’. For this, the reconstruction

range SinoSN(B-E) must be set to the same value for Begin and End to produce a single slice. The reconstructed stack is

saved as 16-bit TIFF.

H-PITRE runs very fast due to its use of the graphics board and produces accurate results on not-too-strong absorbing

samples, but has difficulties with beam hardening since only 180 degrees may be used as rotation range.

H-PITRE runs very fast due to its use of

the graphics board and produces accurate

results on not-too-strong absorbing

samples, but has difficulties with beam

hardening since only 180 degrees may be

used as rotation range.




B.Schillinger 11

CT reconstruction with N-RECON:

http://bruker-microct.com/products/downloads.htm

Bruker MicroCT sells distributed network licenses of NRECON, but provides a single-workstation license

for free, which comes as a server plus a single-client license.

With today’s PCs, this software is so fast that no network is required.

NRecon was designed to read the data from Bruker MicroCT scanning systems, but can also load 16 bit

TIFF images.

NRecon was developed for cone beam geometry, but assumes parallel beam geometry for any source-to-

detector distance greater than ten meters.

NRECON does not do dark image and flat field correction; this has to be done in ImageJ before

(subtract dark image from projections and open beam, divide projections by corrected open beam).

The resulting 32-bit float values must be scaled to 16-bit integer range and converted to 16-bit integer

type.







B.Schillinger 12

CT reconstruction with N-RECON:

On reading values produced by ImageJ, NRecon gives an error message declaring an invalid TIFF file.

ImageJ introduces a proprietory TIFF tag 50839 (0xc697) for its stack operations;

TIFF programming conventions state that unknown TIFF tags should simply be ignored,

but since NRecon was only produced for Bruker scanners, it ignores that rule and returns an error.

ImageJ provides no way to remove that tag; the simplest way is to read and write the TIFF files with the

very fast freeware ‘Advanced Batch Image Converter’, ABIC, from

https://sourceforge.net/projects/abic/?source=typ_redirect

which simply reads the TIFF files and writes them back with a new header without the proprietory tag.

ABIC requires the ending ‘tiff’, so all files must be renamed to ‘.tiff’ first, and after conversion back to ‘.tif’,

simply by command line ‘ren *.tif *.tiff’.

The very fast processing makes up for the inconvenience.

https://sourceforge.net/projects/abic/?source=typ_redirect




B.Schillinger 13

screenshot of N-RECON and its server:




B.Schillinger 14

screenshot of N-RECON and its server:

Nrecon requires a four-digit naming and numbering convention starting at zero like ‘name_0000.tif’, as well as a log file with

the same name without a number, called ‘name_.log’ that contains all parameters, including the option 180 or 360 degrees.

In the reconstruction window, the parameter ‘scales’ must be turned off, or scales will be written at the edges of the

reconstructed slices that prevent 3D rendering later on.

Output format must be set to ‘TIF(16)’, and in ‘Settings’, ’Misalignment compensation’ should be turned on to correct for a

tilted rotation axis.

In ‘Start’, this parameter can be tried out in ‘Fine tuning’.

There is also an option for beam hardening correction that only consists of a slider, which can only be used by trial and

error, since the algorithm may not be fit for neutrons, as the interaction process is very different.

NRecon is more tedious to use because of the

required preprocessing and image tag removing,

but gives more options than H-PITRE and allows

for a 360 degree scan, which helps to reduce

beam hardening artefacts for strongly absorbing

samples.




B.Schillinger 15

This information is provided by Author Anders Kaestner, because his brand new version

could not be tested yet:

CT reconstruction with MuhRec:

http://www.imagingscience.ch/muhrechome/index.html

• Was developed with three main goals

1) meeting the needs of neutron imaging reconstruction tasks supporting typical file formats,

artefact reduction

2) flexibility to add new processing features

3) To provide GUI to support the configuration

• Currently, only parallel beam is supported. Cone beam is under development.

• MuhRec can do the whole reconstruction chain from projection to reconstructed slices.

• Can be run in GUI mode or from the command line/scripting

• MuhRec is free of charge (no license needed anymore), 64-bit binaries can be downloaded for Windows,

MacOS, and Ubuntu.

• The open source release is under preparation.

http://imagingscience.ch/muhrechome/index.html




B.Schillinger 16

Details, ordered as they came to my mind (Add it if you like):

• Handles arbitrary scan angles <180 (with missing wedge errors), 180-360 with correct weighting

• Golden ratio angle sequence as hard coded option

• Meta data can be added to reconstructed slices

• Input file formats: fits, tiff (nexus will come)

• Output: tiff (8-, 16-bits, floating point)

• Copes with moderate truncation

• “Correct” attenuation coefficients – air is = 0 out side the sample, forward projection original projection

• Removes retake projection using a list (maybe more relevant for spallation sources)

• Performs dose correction

• Preprocessing modules

- Filtering

- Polynomial correction (beam hardening)

- Spot cleaning (different approaches, including an untested version of your gamma clean)

- Ring cleaning (different approaches)

• Processing order can be rearranged

• Multithreaded processing with high CPU utilization.

• GUI using Qt5

• Viewers to observe projections and reconstructed slices, the later in different orthogonal planes.




B.Schillinger 17

Data configuration

Finalizing reconstructed data




B.Schillinger 18

Spot cleaning Ring cleaning

Projection processing modules can be loaded dynamically, GUI helps to tune.




B.Schillinger 19

Viewing of 3D Data Slices with Bruker DataViewer:


Bruker DataViewer has the same TIFF problem as NRecon and requires removing of the tag in the

header;

alternatively, it can also read 16 bit PNG images, which ImageJ can also write – but ImageJ’s PNG routine

is much slower than the tag removal for TIFF files.

DataViewer can slice the reconstructed volume in three directions, and also display three slices together

in one 3D image.







B.Schillinger 20

screenshot of DataViewer: Single slicing in three direction windows




B.Schillinger 21

screenshot of DataViewer: Three combined slices in one 3D view




B.Schillinger 22

3D Rendering with Bruker CTVox:


Also Bruker CTVox has the same TIFF problem as NRecon and requires removing of the tag in the

header, or loading PNG files.

CTVox is very fast and allows manipulation of opacity and brightness.







B.Schillinger 23

screenshot of CTVox:




B.Schillinger 24

3D Rendering with Slicer:

http://www.slicer.org

Slicer has started its development in the time of ‘486 computers (then called Dicer) as a commercial

product and one of the first powerful 3D programs that could handle data sets larger than the main

memory.

It was taken over as a freeware research aid by the medical community,

with many extensions for treating medical data sets.

Slicer is very powerful, but very obviously a system used and always changed by professionals.

There is a Wiki documentation, but no manual with the beginner in mind –

usage is not always intuitive, and icons not obvious.

Therefore, some hard-to-find settings need to be mentioned here to get the beginner started.

http://www.slicer.org/




B.Schillinger 25

screenshot of Slicer:




B.Schillinger 26

3D Rendering with Slicer:

First, ‘Show text under icons in toolbar buttons’ should be activated in Edit/Application

settings/Appearance, which helps a lot to understand the somewhat cryptic icons.

If a stack of images is loaded with the standard command ‘load data’, the result will be all images overlaid

in the same position in 3D instead of a 3D volume, since Slicer seems to expect position information in

the TIFF headers.

To avoid this, ‘Show Options’ must be activated in ‘load data’.

Then, either a multiple layer TIFF file (as can be produced in ImageJ) can be loaded via ‘Choose File(s) to

add’ and ‘ignore orientation’ activated, or a stack of files can be loaded by selecting the first file in a set of

TIFFs via ‘Choose File(s) to add’ AND disabled ‘single file’ – this will cause the whole stack to be loaded

– AND ‘ignore orientation’ activated.

The stack of files will be loaded as a 3D volume, and slices in three directions will be displayed in three

separate windows. Size, rotation and thresholds can be varied with the three mouse buttons.

To start the actual 3D rendering, the module ‘Volume rendering’ must be loaded from ‘Modules’. There is a

tiny Eye symbol left of the active volume name that starts rendering. Fig. 6 shows a screenshot of Slicer

with a data set loaded and rendered.

Slicer is immensely powerful and offers a load of options and extension modules on the net, but has a

steep learning curve, and is not always overly intuitive to use.




B.Schillinger 27

Complete data processing with MuhRec:


MuhRec is free of charge, but requires a machine-specific license issued by the author Anders Kaestner

on request, so it cannot be copied freely.

MuhRec can do the whole reconstruction chain from projection to reconstructed slices.

At the time of writing, a new version was coming out.





B.Schillinger 28

screenshot of MuhRec:




B.Schillinger 29

A budget tomography controller and camera system

A typical neutron imaging detector uses a neutron scintillation screen, a mirror and a cooled

CCD camera.

For computed tomography, a rotation table for the sample is required, and images must be

recorded of multiple angular positions of the sample.

Cheap, but good quality cameras (< € 500 to € 1200 ) are available at

https://astronomy-imaging-camera.com/

and whole simple systems at

http://www.neutronoptics.com/cameras.html

but…

http://www.isnr.de/

http://www.isnr.de/

http://www.isnr.de/

http://www.isnr.de/

http://www.isnr.de/

http://www.isnr.de/

http://www.isnr.de/

http://www.isnr.de/

http://www.isnr.de/




B.Schillinger 30

…but all these budget cameras do not have a hardware interface (trigger input) to

synchronize the rotation table and the camera.

Some offer a programming kit, but this is a very tedious path.

So you must either control your motor and camera by hand, triggering each for hundreds of

images alternately,

Image:comfo.ca




B.Schillinger 31

…or you can ask your cat to do it for you…

Image: Dozens of

web pages, no

clear origin




B.Schillinger 32

…or you can ask a Raspberry Pi with a Gertbot motor controller to do it for you!




B.Schillinger 33

To let the Raspberry Pi click your mouse for the camera program, simply solder two wires to

the left mouse button, and connect these to the Raspberry Pi.

Place the mouse pointer on the trigger button of your camera software on your windows PC,

and the Raspberry Pi will control your rotation table, then start an image after each rotation.




B.Schillinger 34

All components needed for the Raspberry Pi tomography controller




B.Schillinger 35

The motor was built into a rudimentary rotation table with a 1:5 reduction, giving 1000 steps

per rotation instead of only 500.




B.Schillinger 36

Then, an old desktop radiation monitor from the trash bin was converted into a cheap camera box.




B.Schillinger 37

Holes were cut, two pocket mirrors were simply glued onto an Aluminium wedge.




B.Schillinger 38

An optical test pattern was installed.

Later, a piece of ZnS(AU,Cu) +LiF scintillation screen was quickly taped onto a paper, and

installed for a quick neutron test.




B.Schillinger 39

The first test with visible light was promising. The gap between the mirrors is visible.




B.Schillinger 40

The first neutron image was quickly taken between other beam times, just before the conference.




B.Schillinger 41

The first neutron image was quickly taken between other beam times, just before the conference.

The picture is not normalized, white spots are cause by gammas hitting the CCD directly.




B.Schillinger 42

The simple setup has a lot of faults as:

• Adjustment of camera and mirror

• Two mirrors instead of one – the gap is clearly visible

• Light reflections on tape etc. inside the box

• Crude mechanical work

• Bad fixation of the scintillation screen

• Mirror holder in the beam

So you can do much better than that!

Go ahead, and build your own!




B.Schillinger 43

ALL web links for hardware (Raspberry Pi, Gertbot, ZWO camera)

and software (H-PITRE, N-Recon, DatViewer, CTVox, Slicer)

PLUS text files with detailed instructions

as well as the software for the Raspberry controller

will be available for download on

www.isnr.de/index.php/tools

Good luck !

http://www.isnr.de/index.php/tools

Documents

Forschungsneutronenquelle A freeware path to - isnr.de Technische ... A freeware path to neutron computed tomography Burkhard Schillinger Heinz Maier ... budget to build a tomography