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VISIBLE HUMAN Project
Anatomy Atlas
http://www.nlm.nih.gov/exhibition/historicalanatomies/browse.html
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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”
Visible Human Project
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
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Visible Human Project
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”
Visible Human Project
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.
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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
Visible Human DataSet
CT and MR images acquisition
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
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Visible Human DataSet
CT and MR images acquisition
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
Visible Human DataSet
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”)
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Visible Human Project
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
Visible Human Project
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
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Visible Human DataSet
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.
Visible Human DataSet
Female choice
Characteristics
Death: September, 1993
Motivazione: Arresto cardio-polmonare
Housewife
Etnia caucasica
58 years old
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Visible Human DataSet
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
Visible Human DataSet
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
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Visible Human DataSet
Sectioning of the cadaver
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
Visible Human DataSet
Sectioning of the cadaver
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
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Visible Human DataSet
Sectioning of the cadaver
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
Visible Human DataSet
Sectioning of the cadaver
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
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Visible Human DataSet
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.
Visible Human DataSet
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
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Visible Human DataSet
Data format
Fullcolor: 24-bit “raw” file format
CT: General Electric Genesis format
Fresh
Frozen
MR: General Electric Genesis format
Male
Visible Human DataSet
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
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Visible Human DataSet
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
Visible Human DataSet
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
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Visible Human DataSet
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
Visible Human DataSet
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
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Visible Human DataSet
Dataset dimensions
Man: about 15 GigaBytes
Woman: about 40 GigaBytes
Visible Human DataSetFullcolor example
Male
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Visible Human DataSetCT fresh cadaver example
Male
Visible Human DataSetCT frozen cadaver example
Male
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Visible Human DataSetMRI example
Male
Visible Human DataSetexample of a visualization application
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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
Visible Human DataSet
Data set access
Via Internet with FTP
Directly form the National Library of Medicine
(http://www.nlm.nih.gov/visible/visible_human.html)
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Visible Human DataSet
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)