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VISIBLE HUMAN Project

Anatomy Atlas

http://www.nlm.nih.gov/exhibition/historicalanatomies/browse.html



Visible Human Project

the idea...

1987 - The National Library of Medicine long

time working draft contains the following item:

(NLM should)..”thoroughly and systematicallyinvestigate the technical requirements andfeasibility of instituting a biomedical imageslibrary”


the idea...

1988 - During a meeting about 3D anatomical

images, held at the NLM Lister Hill NationalCenter for Biomedical Communications, thepresent people recommend NLM to phisically

contribute to the progress of the applicativefileld, directly supporting the development of aimage data base of an entire male and female

body.

The Visible Human Project Idea




the evolution...

1989 - NLM Board of Regents starts a study to

evaluate the role of NLM inside the field,instantly variable, of Electronic Imaging.

1990, April - NLM Board of Regents approve areport that textually said:(The)”NLM should undertake a first project,building a digital image library of volumetricdata representing a complete normal adulthuman male and female”


the announcement...

1991 - NLM agreed with some medicalsof the Colorado University with the aim tosearch for a good cadaver, and foracquiring the images needed by theproject.

1994, November 28 - NLM give theannouncement of complete availability ofa data set containing digital images ofmale anatomy.



Visible Human DataSet

CT and MR images acquisition

Because pilot studies prove that CT and MR

images could have a degradation because the bodyfreezing operations, the images, where applicable,are been taken before this frozen procedure

MR images acquisition at Colorado UniversityHospital (male)

format: General Electric Genesis 256x256x16-bit matrix

operations start: 18 hours after dead

operations end : 21.75 hours after dead

storing: via ethernet to the Medicin School of the Colorado

University, and then directly on 4-mm DAT cartridges



CT images acquisition need to immobilizethe cadaver with a shape-retaining plasticmaterial

CT images acquisition at Colorado University

Hospital (male)

step dimension: 1/3/5-mm

operations start : 22.5 hours after dead

operations end : 25.5 hours after dead





Freezing of the cadaveroperations start: 26 hours after death

put into a special freezing chamber until October, 151993

moving to another maintaining freezing cell withconstant temperature of -7°C

Frozen CT images acquisition spacing of 1-mm

first step: (head to midcalf) August, 29 1993

second step: (midcalf to toes) October, 14 1993

Male


Tecnica di fotografia

All the slices photographed in red, green and

blue (RGB)

All the photos in the 3 tonality (together

forming the fullcolor version) has beenacquired in TIFF format 2048x2048x14-bit(“raw images”)




Male choice

Search for the cadavers

setup of a consortium of SABs (State Anatomical

Board) of Colorado, Texas and Maryland.Human bodies that become available for medicalresearch and teaching are btained in mosta states

through gifts by their citizens to the SAB.

inventory of a lot of possible cadaver, divided by

sex, and setup of a screening process reviewedall the medical records of each candidate

cadaver final choice


Male choice

Cadaver setup

dead at 12:31 AM on August, 5 1993(by court-ordered lethal injection at the Texas Department of Corrections inHuntsville)

body reaches the SAB of Texas about 1.5 hours later

final tests and cadaver setup (previous exams had showed the

“normality” of the candidate; only an appendectomy at age 21 and a left orchiectomyat age 15; number 14 teooth had been extracted at age 38)

body reaches the SAB of Colorado about 8 hours after

death

at 12.5 hours after death were obtained and later

digitized 15 radiographs




Final Male choice

September, 2 1993

NLM’s Visible Human Project Selection Panel,

made up of anatomists and radiologists discussabout CT and MR images of two anonymouscadaver. The panel decided unanimously to

proceed with SAB number 6022 as the VisibleHuman Male. So it gave start to all the technicalprocedures need for sectioning the cadaver and

acquiring relative further images.


Female choice

Characteristics

Death: September, 1993

Motivazione: Arresto cardio-polmonare

Housewife

Etnia caucasica

58 years old




Female choice

General conditions

No fracture or subluxation

Standard bony mineralization

Bilateral degenerative variations atL4-5 and L5-S1 level

Minimum degenerative variations present atcervical level

Feet show a contraction, but they don’t seemabnorms

Ventricles have normal dimensions


Sectioning of the cadaver

The cutting system was developed at the University of

Colorado Medical School in the former Department ofAnatomy

The machine consisted of a milling device whose controlshad been automated and drives upgrated to retain accuracy

when subjected to the intense cold

Cutting blade:

disk of 14 inches in dieameter

20 specially hardened teeth mounted around its edge

speed rotation: 300 rpm

it succesfully shaved blocks containing tissues to 0.1-mm intervals

Male





On January, 20 1994, the cadaver was transfered from the

walk-in freezer (-7°C) to the freezing chamber (-70°C). After 2days, the cadaver was removed from the freezing chamber.

On January, 24, 1994, the frozen cadaver, immobilized in itsAlpha Cradle mold, was positioned and clamped to the bed of

the backsaw.

The initial 4 blocks obtained consisted of:

legs, ankles and feet

thighs and knees

abdomen and pelvis

head, neck and thorax

The kerf loss between them was approximately 1.5 mm

Male



Each block was embedded in a suitable medium, which when frozen wouldprovide stability for the cutting process

Once the gelatine was solid, the mold was transferred to the Ultra Freezer(-85°C) for at least 12 hours. The mold was then removed and partiallydisassembled. Mold was finally reassembled, with another layer of gelatinesiphoned into it. When the final layer was solid, the mold was againtransferred to the Ultra Freezer for complete freezing and storage.

Cutting operations

start: February, 17 1994

end: May, 19 1994

Male





The Female dataset, instead of the Maleone, has a different sectioning step alongthe Z direction.

Female sectioning step = 0,33-mm

Male sectioning step = 1-mm

Female



The initial 4 blocks obtained consisted of:

1st head, neck and thorax

2nd abdomen and pelvis

3rd thighs and knees

4th legs, ankles and feet

Female




Alignment of

CT/MR/Fullcolor’s images

Individual fullcolor, CT and MR images have beenanalyzed to establish the correspondence between

them, to provide anatomic alignment.(The number of the images are not the same for all the three

types, and something has been lost in kerf)

Anatomic and CT slices wer renumbered to reflect thecorrespondence, starting at 1,001 and proceeding to 2,878.The MR images were renumbered to reflect some

anatomic correspondence to the CT and anatomicslices.


Digital image processing

All digital images were reduced from 42-bit (14 bits of

red, green and blue) to 24-bits images byindependently and logarithmically compressing the14bits of each channel to 8 bits.

The images were cropped in the anteroposterior (AP)dimension of the anatomy from 2,048 to 1,216 pixels.

Male




Data format

Fullcolor: 24-bit “raw” file format

CT: General Electric Genesis format

Fresh

Frozen

MR: General Electric Genesis format

Male


Dataset content

MRI images:

axial of head and neck spacing of 4-mm

coronal of the body spacing of 4-mm

256x256 pixels (12 bits of gray per pixel)

General Electric format

CT images:

axial spacing of 1-mm

512x512 pixel (12 bits of gray per pixel)

General Electric format

Male




Dataset content

FULLCOLOR images:

axials (aligned with the CT ones)

spacing of 1-mm for man

spacing of 0.33-mm for woman(more than 5,000 images only for the anatomic dataset)

2048x1216 pixel (24 bits of color per pixel)

raw format, UNIX compressed (e.g. xxx.raw.Z)

Male


Fullcolor images

Resolution : voxel 0.33mm(same spacing on all the 3 dimensions)

Photographic format: TIFF(with 14 significative bits per RGB channel)

Images format: raw format 24-bit(8bits per RGB channel)

Female




Characteristics

Fullcolor images:

block 1 (head, neck, thorax)

2048x2048x14 bit x RGB TIFF Format

blocks 2,3,4 (the other ones)

2048x1280x14 bit RGB TIFF Format

except: first 34 images of the block 2 (abdomen and pelvis)

1760x1280x14bit RGB TIFF Format

Female


X-Ray, CT and MRI images

MRI Format: General Electric Genesis format256x256x16 bits

CT Format: General Electric Genesis formatspacing of 1mm

X-Ray Format: TIFF

Female




Dataset dimensions

Man: about 15 GigaBytes

Woman: about 40 GigaBytes

Visible Human DataSetFullcolor example

Male



Visible Human DataSetCT fresh cadaver example

Male

Visible Human DataSetCT frozen cadaver example

Male



Visible Human DataSetMRI example

Male

Visible Human DataSetexample of a visualization application



Visible Human DataSetexample of a visualization application

http://www.dhpc.adelaide.edu.au/projects/vishuman2/VisibleHuman.html

http://www.cs.uoregon.edu/~tomc/jquest/SushiPlugin.html


Data set access

Via Internet with FTP

Directly form the National Library of Medicine

(http://www.nlm.nih.gov/visible/visible_human.html)




Dataset amministrative access

Signature of a License Agreement directly withthe National Library of Medicine

assignment of a couple of userid/password to grantthe access to the dataset via FTP on the NLM server

(free access)(Free contract download)

Directly from the National Library of Medicine

(http://www.nlm.nih.gov/visible/visible_human.html)

visible human project - genomics & bioinformatics graz, graz

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