Medical Imaging for Solving The Mummy’s Mystery

And More…Professor Aly A. Farag

Computer Vision and Image Processing LaboratoryUniversity of Louisville

Louisville, Kentucky, USAE-mail: aly.farag@louisville.edu

www.cvip.uofl.edu

The Computer Vision and Image Processing Laboratory (CVIP Lab)

The CVIP Lab. was established in 1994 at the University of LouisThe CVIP Lab. was established in 1994 at the University of Louisville.ville.

Has two broad focus areas: Has two broad focus areas: computer visioncomputer vision and and medical imagingmedical imaging. .

Hosts unique and modern hardware for imaging, computing and Hosts unique and modern hardware for imaging, computing and visualization. visualization.

CVIP Facilities

2 Supercomputers ImmersaDesk 3D Scanner

Robotic Arm

Card-Eye Panoramic Displays2 Robotic Platforms

CVIP People…

Egyptology 101

• Pyramids

• Heliographic

• Conquerors of Egypt

• Mummification

• Great VISIOTRS of Egypt (e.g., Prophets)

• Etc…

Mummification Story

• The process of mummification has two stages. • First, the

embalming of the body.

• Then, the wrapping and burial of the body.

Embalming the body

First, his body is taken to the tent known as 'ibu' or the 'place of purification'. There the embalmers wash his body with good- smelling palm wine and rinse it with water from the Nile.

One of the embalmer's men makes a cut in the left side of the body and removes many of the internal organs. It is important to remove these because they are the first part of the body to decompose.

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www.ancientegypt.co.uk/mummiesThe British Museum

Embalming the body

www.ancientegypt.co.uk/mummiesThe British Museum

The liver, lungs, stomach and intestines are washed and packed in natron which will dry them out. The heart is not taken out of the body because it is the centre of intelligence and feeling and the man will need it in the afterlife.

A long hook is used to smash the brain and pull it out through the nose.

The body is now covered and stuffed with natron which will dry it out. All of the fluids,and rags from the embalming process will be

saved and buried along with the body.

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Embalming the bodyAfter forty days the body is washed again with water from the Nile. Then it is covered with oils to help the skin stay elastic.

The dehydrated internal organs are wrapped in linen and returned to the body. The body is stuffed with dry materials such as sawdust, leaves and linen so that it looks lifelike.

Finally the body is covered again with good-smelling oils. It is now ready to be wrapped in linen.

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8www.ancientegypt.co.uk/mummiesThe British Museum

Wrapping the mummy

www.ancientegypt.co.uk/mummiesThe British Museum

First the head and neck are wrapped with strips of fine linen. Then the fingers and the toes are individually wrapped.

The arms and legs are wrapped separately. Between the layers of wrapping, the embalmers place amulets to protect the body in its journey through the underworld.

This is the 'Isis knot' amulet which will protect the body.

This is the 'Plummet' amulet which will keep the person balanced in the next life.

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Wrapping the mummy

www.ancientegypt.co.uk/mummiesThe British Museum

A priest reads spells out loud while the mummy is being wrapped. These spells will help ward off evil spirits and help the deceased make the journey to the afterlife

The arms and legs are tied together. A papyrus scroll with spells from the Book of the Dead is placed between the wrapped hands.

More linen strips are wrapped around the body. At every layer, the bandages are painted with liquid resin that helps to glue the bandages together.

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Wrapping the mummy

www.ancientegypt.co.uk/mummiesThe British Museum

A cloth is wrapped around the body and a picture of the god Osiris is painted on its surface.

Finally, a large cloth is wrapped around the entire mummy. It is attached with strips of linen that run from the top to the bottom of

the mummy, and around its middle. A board of painted wood

is placed on top of the mummy before the mummy is lowered into

its coffin. The first coffin is then put inside a second coffin

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TchaenhotepTchaenhotep•• Ta= 'the', and Ta= 'the', and hotephotep= 'content or calm'. = 'content or calm'.

•• The overall name may be translated as 'the one who is The overall name may be translated as 'the one who is content'.content'.

Tchaenhotep’s History•• The tombs were first discovered The tombs were first discovered

in 1903, over one hundred in 1903, over one hundred years ago.years ago.

•• The mummy and the sarcophagus The mummy and the sarcophagus came to the came to the United StatesUnited States to be to be displayed at the 1904 St. Louis displayed at the 1904 St. Louis World’s Fair in the “Streets of Cairo World’s Fair in the “Streets of Cairo Exhibit”.Exhibit”.

Tchaenhotep’s History•• LouisvillianLouisvillian SamualSamual ThrustonThruston

BallardBallard was later responsible was later responsible for bringing the mummy to for bringing the mummy to Louisville where the mummy Louisville where the mummy became a favorite attraction at became a favorite attraction at the museum in the the museum in the Louisville Louisville Free Public LibraryFree Public Library, at 4th & , at 4th & York.York.

Tchaenhotep’s History

•• During the During the Ohio River Ohio River FloodFlood of 1937, the of 1937, the mummy was nearly mummy was nearly destroyed. destroyed.

Tchaenhotep’s History•• Rising waters caused a Rising waters caused a pianopiano to to

fall on the mummy and, the head fall on the mummy and, the head became separated from the body. became separated from the body.

•• The mummy was later moved to The mummy was later moved to 5th and York Streets and, in 5th and York Streets and, in 1977, arrived at the present 1977, arrived at the present location of West Main Street. location of West Main Street.

The mummy and coffin were on The mummy and coffin were on continuous display there until early in continuous display there until early in this century when they came to rest in this century when they came to rest in the collections storage areas of the the collections storage areas of the Louisville Science Center. Louisville Science Center.

What Can we Salvage from The Mummy?

Medical Imaging Some Marvels…

X-Ray

Nov 8, 1895Wilhelm Konrad Röntgenreported discovery of new “rays” (Nobel Prize in physics in 1901).

Jan 13, 1896First clinical use of XFirst clinical use of X--rays by 2 rays by 2 British doctors to find a needle British doctors to find a needle in a hand.in a hand.

Image FormationA beam of X-rays is directed through a patient onto a film.The film provides a measure of the ray attenuation in tissue.

+ Excellent for imaging bones.+ Excellent for imaging bones.--

No depth information, bad for soft tissue, excessive radiationNo depth information, bad for soft tissue, excessive radiation

Sample X-Ray Slices

Computed Tomography (CT)

1965G. Hounsfield

(computer expert)

and A.M Cormack

(physicist)

(Nobel Prize in Medicine in 1979).

Image FormationThe object is viewed from a number of different angles and then a cross-

sectional image of it can be computed (reconstructed).

+ Provide 3D anatomical information+ Provide 3D anatomical information

+ Preserves topology (bones)+ Preserves topology (bones)

--

Excessive radiationExcessive radiation

--

Not good for all soft tissuesNot good for all soft tissues

Computed Tomography (CT)

• The object is viewed from a number of different angles and then a cross- sectional image of it can be computed (reconstructed).

Sample CT Slices

CT Acquisition Techniques

slice-by-slice scanning

Spiral (volume) scanning(Very Fast) 3D Reconstruction

Magnetic Resonance Imaging (MRI)

1952F. Bloch and

E. Purcel, extended by R. Ernst)(Bloch & Purcel: Nobel Prize in Physics in 1952)(Ernst: Nobel Prize in Chemistry in 1991)

Paul Luterberg: Nobel Prize in Physcis

in 2004For Basic MRI Research

Image Formation- Hydrogen nuclei (protons) under a strong magnetic field spin in phase with one another and align with the field.

-

Relaxed protons induce a measurable radio signal.

+ Main modality for image guided surgery.+ Superb ability to discriminate between

subtle differences in tissue characteristics.+ Very safe.-

Less accurate for bone scanning.

Sample MRI Slices

Ultrasound (US)

1979: Samuel H. Maslak

Image FormationAn ultrasonic energy is propagated into the patient from a transducer placed on the skin and back-scattered echo signal is recorded by the same transducer.

+ Noninvasive+ Clean & safe+ In-expensive- Noisy-

Gas filled and bony structures cannot be imagedbecause they absorb ultrasound waves.

Positron Emission Tomography (PET)

1998-2001: Dr. David Townsend and Dr. Ron Nutt.

Image Formation-

Detection of radiation from the emission of positrons.

+ Valuable technique for some diseases and disorders.

+ Amount of radiation is small-

Invasive (inject radioactive material)

3D Model Building3D Model Building

MRI

CT

MRA

SegmentationSegmentation

SegmentationSegmentation

SegmentationSegmentation

Multimodal Multimodal RegistrationRegistration FusionFusion

3D Brain Models from MRI Scans

vascular treevascular treeAn MRI ScanAn MRI Scan

Fusion of Multiple scansFusion of Multiple scans Structural Brain ModelStructural Brain Model

Back to The Mummy….

X-ray

Capture the Data Base

••The team at Baptist East Hospital performed The team at Baptist East Hospital performed a CT scan on the Tchaenhotep mummy’s a CT scan on the Tchaenhotep mummy’s and a data base of images of the heard was and a data base of images of the heard was supplied on CDs.supplied on CDs.

•• Each image consisted of 512x512 pixels Each image consisted of 512x512 pixels (picture elements).(picture elements).

••Each pixel in the image slice was Each pixel in the image slice was represented by a 16 bit grayscale value represented by a 16 bit grayscale value giving a gray level range from 0 (completely giving a gray level range from 0 (completely black) to 65535 (completely white). black) to 65535 (completely white). CT IMAGES

Capture the Data Base

••The team at Baptist East Hospital performed The team at Baptist East Hospital performed a CT scan on the Tchaenhotep mummy’s a CT scan on the Tchaenhotep mummy’s and a data base of images of the heard was and a data base of images of the heard was supplied on CDs.supplied on CDs.

•• Each image consisted of 512x512 pixels Each image consisted of 512x512 pixels (picture elements).(picture elements).

••Each pixel in the image slice was Each pixel in the image slice was represented by a 16 bit grayscale value represented by a 16 bit grayscale value giving a gray level range from 0 (completely giving a gray level range from 0 (completely black) to 65535 (completely white). black) to 65535 (completely white). CT IMAGES

• Difference between the mummy’s CT slice and a living person’s CT Slice.

<< Mummy << Mummy

Normal >>Normal >>

CT SCAN Slice

Registration of slices and 3D stack

• By reading the images into a computer and stacking them, a 3D volume of the CT scans can be made, creating a virtually 3D skull inside the computer’s memory.

• The process required aligning various features from slice to slice =

Segmentation

CT Image were all gray levels are mapped to white.

CT Image with gray level values above 255

CT Image• The next stage is the process of segmentation where we assign labels to each data that declares if the voxel is bone tissue or air or other tissue.

• In this Segmentation we used a simple thresholding method.

• In the CT image air is black (or has a zero value) and the bone tissue is white. We set a range where any pixel above a value of 255 is labeled bone.

• Difference between the mummy’s CT slice and a living person’s CT Slice.

<< Mummy << Mummy

Normal >>Normal >>

CT SCAN Slice

Reducing the Triangle Count•• The number of X,Y,Z coordinates The number of X,Y,Z coordinates creating the ISOcreating the ISO--surface is quite large.surface is quite large.

•• Our volume consists of 512x512x198 or Our volume consists of 512x512x198 or 51,904,512 voxels and each voxel has an 51,904,512 voxels and each voxel has an X,Y,Z coordinate. X,Y,Z coordinate.

•• If half of the volume is labeled bone, If half of the volume is labeled bone, then there are more than 25 million X,Y,Z then there are more than 25 million X,Y,Z coordinates. coordinates.

•• We reduce this by using a process We reduce this by using a process called DECIMATION. called DECIMATION.

•• Decimation reduces the number of Decimation reduces the number of triangles which make up the ISOtriangles which make up the ISO--Surface Surface by removing duplicate or unneeded by removing duplicate or unneeded triangles.triangles.

Polydata Mapping

•Once the we have the triangles reduced, two more actions are performed.

•First we create a surface for the computer to display by filling the triangles in a process we call polydata mapping.

•Second, we create a stereo lithography (STL) file for use by the rapid prototype machine which creates the 3D plastic model.

3D Reconstuction and STL Wire Mesh

• We save only the bone voxels for our final virtual model’s data base. ( voxels are 3d pixels )

• Next we create a stereo lithography (STL) file for use by the rapid prototype machine which creates the 3D plastic model.

Generate STL file, 3D Reconstuction and STL Wire

• We are then ready for the SLA process in the rapid prototyping machine.

Summary Movie

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