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Basic Terminologies

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1 Pixel 2 Voxel 3 2D Imaging 4 3D Imaging 5 4D Imaging 6 CT/CAT 7 MRI 8 Segmentation 9 Surface

Generation 10 VolumetricRendering

11 Isosurface

Pixel

A square display unit. All 2D pictures are composed of pixels. A 3 pixel by 3 pixel pictures contains 9 pixels. Pixel is flat with unit length of 1 and width of 1.

Voxel

A cube display unit.All 3D data sets are made from voxels. A 3 voxel by 3 voxel by 3 voxel matrix contains 27 voxels. voxel is 3D and has length of 1 and width of 1 and height of1.

2D Imaging

eg. Histology Data measurment including length and width.

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NOTE: histology is always considered 2D but it does includeheight. Hence if you are given many histological slices, you canreconstitute them into a 3D data set as well.

3D Imaging

eg. Modeling, plastic, virtual,etc Data measurement including height, length and

width.

Note: Model is considered 3D most of the time. However,once you start dynamically swapping 3D data sets (eg. a heartbeating through time). Hence, a series of 3D data sets of relevantstructures are considered 4D.

4D Imaging

Data measurement including height, length, width and time. Time is the key here.

This is the hardest dataset to work with. Make sure you recycle labels should it be

necessary.

CT/CAT

Known as Computed Tomography (CT)or Computed AxialTomography (CAT) The basic idea behind CT is the idea of density.

o In CT, the denser the object, the more bright it appearsin the final result.o Hence a tissue of heterogeneous density creates agray scale spectrum. Each voxels will have its own gray scalevalue (each voxel can only have one value only just like howpixel cannot be two colors.)

CT is in many sense very similar to advanced array of X raymachines.

o Traditional X ray is only exposed ONCE (eg. you standin front of the X ray machine and get shoot via X rays foronce and develop the filem.) However, CT has moreexposures and at lower dosages during each exposure.Simplest way I can explain it would be try to imagine a

Circular track with an X ray emitter mounted on the track andthe patient inside the circular ring while the receiver at theopposite end of the circular track. As the scan proceeds, theemitter starts at 12 o clock position with the receiver at 6 oclock position, the density reading from 12 to 6 position isready... and then the emitter/detector moves along the trackand keeps take reading... The ending result is a 2D reading ofthe plane being scanned(This is EXTREMELY simplifiedexplanation). Here is a BRIEF intro to CT/CAT principles.

http://health.howstuffworks.com/cat-scan.htm%7Chttp://health.howstuffworks.com/cat-scan.htm%7C

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MRI

Nuclear Magnetic Resonance Imaging They take out "Nuclear" because they don't

want to scare the public. It is must less intuitive to grasp the understanding of MRI. I

do not believe I am qualified to really explain it well so I will share my view with

you. basicly, a HUGE magnet is used to generate a radiofrequency pulse that excitesparticles (1H or 13C) inside the issue and once the magnetic field is reduced, the

energy absorbed by the excited particle is re-emitted back to the surroundings and

picked up by the MRI.

The signal strength is not significantly influenced by the density of the object but

more by the concentration of the excitable particles and the way radio pulse was

generated (echo time and repetition time). I highly recommend at least skim through

the Wikipedia articles on MRI. I think the most important information you will need

is to be able to differentiate T1, T2 weighting and what they each excel at visualizing.

So far, we have not dealt with any fMRI imaging data but I imagine with 4D data

processing, fMRI should not be too huge a concern.

Segmentation

The process of partitioning a digital image into multiple regions (sets of pixels).

Surface Generation

Volumetric Rendering

Isosurface

a three-dimensional analog of an isocontour. It is a surface that represents points of a

constant valueFile:Example.jpg

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A voxel is a volume element (volumetric pixel) representing a

value in the three dimensional space (expressed in units of mm3),

corresponding to a pixel for a given slice thickness. Voxels are

frequently used in the visualization and analysis of medical data.

The CT pixel intensity is proportional to the signal intensity of the

appropriate voxel. Voxels are associated with CT numbers.

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Uses and Advances of Computed Tomography for

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By Julien Noel

Wednesday, July 21, 2010

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Computed tomography (CT) has come a long way

since its public inception in 1972. The rapid

improvement of computer technology and the

increasing capabilities of CT scans have gone hand

in hand. CT scans that used to take hours are nowbeing completed in seconds. This increase in

capabilities has led to CT scans being used more

often and in more ways than ever before. The use

of CT in the medical nondestructive testing (NDT)

field is one example that has grown tremendously

in the past few years, and it is also the focus of the

following article.

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Industrial Computed Tomography Process

Industrial CT uses a series of 2-dimensional images taken at specific intervals around

the entire sample. Almost all types of industrial CT systems use three principal

components: an X-ray Tube, an X-ray Detector, and a rotational stage. Everything is

enclosed in a radiation shielding steel/lead/steel cabinet that usually ranges between 4and 10 feet cubed. This allows use of the system in a public environment without any

additional safety concerns.

Micro computed tomography (MicroCT) is primarily the same as standard CT except

it uses a microfocus tube instead of a traditional tube. A MicroCT scan yields

resolutions in microns due to the fact that the focal spot of a microfocus tube is only a

few microns in size. For comparison, MicroCT resolution is about 100 times better

than the best CAT scan in the medical field.

High quality industrial X-ray detectors used for CT, are typically a new generation

Amorphous Silicon Flat Panel Area Detector, offering very high sensitivity,

resolution, and bit depth. The resulting 2D X-ray images are very clear and the

contrast is unparalleled.

Acquisition

A modern high-end CT scan consists of taking several 2D X-ray images around the

object, preferably covering 360 degrees (complete rotation). CT systems typically

acquire between 360 images (1 image every degree) and 3600 images (1 image every0.1 degree), depending on the final desired resolution. Each image is between 3 to 10

Megapixels and is also averaged and filtered to reduce noise. The 2D digital images

taken during this step are saved directly into a single folder which will be used in the

next step of the CT process.

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General principle of a modern industrial CT scan.

Reconstruction and Visualization

Once the acquisition process of the CT scan is completed, CT calibration and CT

reconstruction algorithms are used to reconstruct the 3D CT volume. These 3D

images are made of Voxels (three dimensional Pixels), and with the use of

visualization software, the 3D volume can be manipulated in real time. Because of

this, it is possible to slice through anywhere inside the object, inspect and look for

defects, take accurate measurements, reconstruct a surface model, etc.

Industrial CT technology is improving very quickly. While a few single CT slices

could take hours to generate years ago, it is now possible to reconstruct complete 3D

models with billions of Voxels in just seconds. This opens the door for numerous new

applications like 3D inline automatic defect recognition, 3D reverse engineering,

rapid prototyping, 3D metrology, etc. In that regard, industrial CT has become a very

competitive technology for 3D scanning.

The principal benefit of using 3D CT for scanning or digitization is that a complete

model with both external and internal surfaces of an object is obtained without

destroying it. Moreover, CT works with any surface, shape, color, or material (up to a

certain density and/or thickness penetrable with X-rays). Generally, a modern start-to-finish CT scan can finish in as fast as two seconds or take longer than an hour,

depending on the resolution requirements and size and/or density of the object.

Overall, the resolution is excellent both internally and externally, which in turn can

fulfill virtually any designers needs.

Computed Tomography in Use

Computed Tomography has proven to be an outstanding tool for many industries.

Industries such as medical device, pharmaceutical, aerospace, electronics, and many

more have made CT a part of everyday life. The demand for CT continues to be

tremendous, largely due its versatility and capabilities to do what other technologies

cannot. CT scans nondestructively provide excellent resolution internally and

externally, which then allows for measurement on surfaces both inside and outside an

object. Also, due to the penetration of X-rays, CT scans are unaffected by certain

object characteristics such as dark, reflective or transparent surfaces and/or shaded

zones on the item that can cause difficulty with other 3D scanning methods.

Furthermore, 3D CT reconstruction models can be directly compared to CAD models

and/or other CT models in order to display differences or commonalities in

measurements, densities, voids, etc.

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Sliced 3D CT volume

and its femur

showing measurement functionality.

The 3D CT reconstruction, which is made of several million or billion Voxels, can

also be transformed to a surface model. The resolution of the 3D model depends on

the number of Voxels generated from CT reconstruction. A threshold value of

radiodensity is chosen by the operator and set using edge detection image processing

algorithms. From this, a 3-dimensional model can be constructed and displayed on

screen. Multiple models can be constructed from various different radiodensity

thresholds, therefore allowing different colors to represent each component of anassembly. Typically, models are composed of polygons numbering from the

thousands to 50 million.

The pictures below show a surface reconstruction (polygon mesh) of an extracted

wisdom tooth and an inhaler device. All the internal structural features are

reconstructed as well since the CT reconstruction provides volumetric information.

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3D CT surface

reconstruction of a

tooth and an inhaler.

With the generated polygon mesh surface model, many different applications become

available to the user. The output format (points cloud, STL, WRL) is compatible withmost CAD software for Reverse Engineering applications, rapid prototyping machines

for modeling, Finite Element Analysis software for simulations, etc.

In most cases, the polygon mesh generated by the CT system can be used in the above

applications without modification and typically, the resolution is higher than needed.

However, in order to modify or take measurements of the CT surface model with a

CAD software, the CT model needs to be processed to make it editable. New

generation modeling software (e.g. Geomagic, Rapidform, Polyworks) propose semi-

automatic tools to transform the polygon mesh to Nurbs Surfaces and parametric

CAD models. Manual operation is still necessary to transform the scanning surface to

real solid CAD.

Comparing 3D CT Image to CAD Model

Dimensional analysis is one key application available for model comparison. Since

CT and especially microCT provides very accurate dimensions on surfaces, the

technology is often used for metrology studies. Measurements can be done either

directly on the surface using any CAD or Metrology software, or it can automatically

compare the CT model with the CAD model, or even the CT model with another CTmodel.

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Geomagic Qualify is a very efficient software for this type of application. It has the

capability to perform a 3D and/or 2D dimensional comparison in very few steps, as

well as export metrology reports containing tons of information. Once again, the data

includes both internal and external surface information.

Comparison of a 3D CT

model reconstructed by

NSI with a CAD model.

Due to the proprietary nature of medical devices, a CAD to CT comparison is not

available for display. As a replacement, examples above show a dimensional

comparison between the Solidworks CAD model of a casting provided by Twin Cities

Die Casting, and the CT surface reconstruction created by NSI.

In order to do this comparison, the two models needed to be aligned. Different

alignment tools are available, ranging from very fast and automatic Best Fit, to

manual alignment. Once the two models are aligned, a simple 3D comparison option

automatically creates a colored view showing all the dimensional differences between

the two models. In the example above, all the dimensional differences between the

Solidworks model and the actual CT surface (polygon mesh) are represented by

colors. Tolerances between -0.3mm and 0.3mm are shown in green. Yellow denotesthe areas where the CT scan measurements are larger than the original CAD model

and blue indicates smaller measurements. It is possible to change tolerance values and

the color code to cater to a specific project or preferences. Numerical values are an

available option as well.

All in all, 3D CT is now accessible for most industries as a viable tool; user-friendly

interfaces, increased scan speeds, and decreasing prices have all attributed to the rapid

growth of this technology in the marketplace. Having very accurate internal

dimensions without destroying the item, along with the ability to compare to a

reference model is entirely unique to CT. There are no shaded zones, it works with all

kinds of shapes and surfaces, there is no post-processing work needed and theresolution is excellent. Above all, the greatest benefit is the ability to nondestructively

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obtain the internal structure of the object, and CT is the only technology capable of

achieving such performance.

Julien Noel is the Computed Tomography Product Manager for North Star Imaging,Inc. based in Minneapolis, Minnesota.

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