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L.Guglielmi - F.Pinciroli

V ISIBLE H UMAN D ATASET - M ILANO M IRROR S ITE ®. L.Guglielmi - F.Pinciroli. Visible Human Project the idea.

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L.Guglielmi - F.Pinciroli

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  1. VISIBLE HUMAN DATASET - MILANO MIRROR SITE® L.Guglielmi - F.Pinciroli vhd-mms/tutorial/base/intro-copertina

  2. Visible Human Projectthe idea... • 1987 - The National Library of Medicine long time working draft contains the following item:(NLM should)..”thoroughly and systematically investigate the technical requirements and feasibility of instituting a biomedical images library” vhd-mms/tutorial/base/intro-1.1-1/2

  3. Visible Human Projectthe idea... • 1988 - During a meeting about 3D anatomical images, held at the NLM Lister Hill National Center for Biomedical Communications, the present people recommend NLM to phisically contribute to the progress of the applicative fileld, directly supporting the development of a image data base of an entire male and female body.The Visible Human Project Idea vhd-mms/tutorial/base/intro-1.1-2/2

  4. Visible Human Projectthe 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 a report that textually said:(The)”NLM should undertake a first project, building a digital image library of volumetric data representing a complete normal adult human male and female” vhd-mms/tutorial/base/intro-1.2

  5. Visible Human Projectthe announcement... • 1991 - NLM agreed with some medicals of the Colorado University with the aim to search for a good cadaver, and for acquiring the images needed by the project. • 1994, November 28 - NLM give the announcement of complete availability of a data set containing digital images of male anatomy. vhd-mms/tutorial/base/intro-1.3

  6. Visible Human DataSet CT and MR images acquisition • Because pilot studies prove that CT and MR images could have a degradation because the body freezing operations, the images, where applicable, are been taken before this frozen procedure • MR images acquisition at Colorado University Hospital (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 vhd-mms/tutorial/base/intro-2.1-1/3

  7. Visible Human DataSet CT and MR images acquisition • CT images acquisition need to immobilize the cadaver with a shape-retaining plastic material • 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 vhd-mms/tutorial/base/intro-2.1-2/3

  8. Visible Human DataSet CT and MR images acquisition Male • Freezing of the cadaver • operations start: 26 hours after death • put into a special freezing chamber until October, 15 1993 • moving to another maintaining freezing cell with constant 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 vhd-mms/tutorial/base/intro-2.1-3/3

  9. 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 been acquired in TIFF format 2048x2048x14-bit (“raw images”) vhd-mms/tutorial/base/intro-2.2

  10. Visible Human ProjectMale 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 medical research 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 reviewed all the medical records of each candidate • cadaver final choice vhd-mms/tutorial/base/intro-2.3-1/5

  11. 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 in Huntsville) • 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 orchiectomy at 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 vhd-mms/tutorial/base/intro-2.3-2/5

  12. Visible Human DataSet Final Male choice • September, 2 1993 NLM’s Visible Human Project Selection Panel, made up of anatomists and radiologists discuss about CT and MR images of two anonymous cadaver. The panel decided unanimously to proceed with SAB number 6022 as the Visible Human Male. So it gave start to all the technical procedures need for sectioning the cadaver and acquiring relative further images. vhd-mms/tutorial/base/intro-2.3-3/5

  13. Visible Human DataSet Female choiceCharacteristics • Death: September, 1993 • Motivazione: Arresto cardio-polmonare • Housewife • Etnia caucasica • 58 years old vhd-mms/tutorial/base/intro-2.3-4/5

  14. Visible Human DataSet Female choice General conditions • No fracture or subluxation • Standard bony mineralization • Bilateral degenerative variations at L4-5 and L5-S1 level • Minimum degenerative variations present at cervical level • Feet show a contraction, but they don’t seem abnorms • Ventricles have normal dimensions vhd-mms/tutorial/base/intro-2.3-5/5

  15. Visible Human DataSet Sectioning of the cadaver Male • The cutting system was developed at the University of Colorado Medical School in the former Department of Anatomy • The machine consisted of a milling device whose controls had 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 vhd-mms/tutorial/base/intro-2.4-1/5

  16. Visible Human DataSet Sectioning of the cadaver Male • OnJanuary, 20 1994, the cadaver was transfered from the walk-in freezer (-7°C) to the freezing chamber (-70°C). After 2 days, the cadaver was removed from the freezing chamber. • On January, 24, 1994, the frozen cadaver, immobilized in its Alpha 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 vhd-mms/tutorial/base/intro-2.4-2/5

  17. Visible Human DataSet Sectioning of the cadaver Male • Each block was embedded in a suitable medium, which when frozen would provide 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 partially disassembled. Mold was finally reassembled, with another layer of gelatine siphoned into it. When the final layer was solid, the mold was again transferred to the Ultra Freezer for complete freezing and storage. • Cutting operations • start: February, 17 1994 • end: May, 19 1994 vhd-mms/tutorial/base/intro-2.4-3/5

  18. Visible Human DataSet Sectioning of the cadaver Female • The Female dataset, instead of the Male one, has a different sectioning step along the Z direction. • Female sectioning step = 0,33-mm • Male sectioning step = 1-mm vvhd-mms/tutorial/base/intro-2.4-4/5

  19. Visible Human DataSet Sectioning of the cadaver 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 vhd-mms/tutorial/base/intro-2.4-5/5

  20. Visible Human DataSet Alignment of CT/MR/Fullcolor’s images • Individual fullcolor, CT and MR images have been analyzed 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 the correspondence, starting at 1,001 and proceeding to 2,878. The MR images were renumbered to reflect some anatomic correspondence to the CT and anatomic slices. vhd-mms/tutorial/base/intro-2.5

  21. Visible Human DataSet Digital image processing Male • All digital images were reduced from 42-bit (14 bits of red, green and blue) to 24-bits images by independently and logarithmically compressing the 14bits 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. vhd-mms/tutorial/base/intro-2.6.1

  22. Visible Human DataSet Data format Male • Fullcolor: 24-bit “raw” file format • CT: General Electric Genesis format • Fresh • Frozen • MR: General Electric Genesis format vhd-mms/tutorial/base/intro-2.6.2

  23. Visible Human DataSet Dataset content Male • 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 vhd-mms/tutorial/base/intro-2.6.3-1/5

  24. Visible Human DataSet Dataset content Male • 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) vhd-mms/tutorial/base/intro-2.6.3-2/5

  25. Visible Human DataSet Dataset content Fullcolor images Female • 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) vhd-mms/tutorial/base/intro-2.6.3-3/5

  26. Visible Human DataSet Dataset content Characteristics Female • 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 vhd-mms/tutorial/base/intro-2.6.3-4/5

  27. Visible Human DataSet Dataset content X-Ray, CT and MRI images Female • MRI Format: General Electric Genesis format 256x256x16 bits • CT Format: General Electric Genesis format spacing of 1mm • X-Ray Format: TIFF vhd-mms/tutorial/base/intro-2.6.3-5/5

  28. Visible Human DataSet Dataset dimensions • Man: about 15 GigaBytes • Woman: about 40 GigaBytes vhd-mms/tutorial/base/intro-2.6.4

  29. Visible Human DataSetFullcolor example Male vhd-mms/tutorial/base/intro-2.7.1

  30. Visible Human DataSetCT fresh cadaver example Male vhd-mms/tutorial/base/intro-2.7.2

  31. Visible Human DataSetCT frozen cadaver example Male vhd-mms/tutorial/base/intro-2.7.3

  32. Visible Human DataSetMRI example Male vhd-mms/tutorial/base/intro-2.7.4

  33. Visible Human DataSetexample of a visualization application vhd-mms/tutorial/base/intro-2.7.5

  34. Visible Human DataSet Data set access Directly form the National Library of Medicine(http://www.nlm.nih.gov/visible/visible_human.html) • Via Internet with FTP • Acquired on cassettes (both 4mm or 8mm) vhd-mms/tutorial/base/intro-3.1

  35. Visible Human DataSet Dataset amministrative access Directly from the National Library of Medicine(http://www.nlm.nih.gov/visible/visible_human.html) • Signature of a License Agreement directly with the Nationa Library of Medicine • assignment of a couple of userid/password to grant the access to the dataset via FTP on the NLM server (free access)(Free contract download) • delivery of the dataset on cassettes (by explicit request) (only charge mail expense and hardware support) vhd-mms/tutorial/base/intro-3.2

  36. Visible Human Dataset - Milano Mirror Site®Motivations • To solve all the problems European continental users had to download the data directly from NLM, due to network constrictions • To offer a repository service for all the applications built using Visible Human Project data set • To offer to the dataset users a simple, powerful and quick interface to find the data they neeed • To establish an European reference point for the NLM Visible Human Project • To found a reference and development point for applications based upon VHD vhd-mms/tutorial/base/intro-4.1

  37. Visible Human Dataset - Milano Mirror Site®Goals • A official continental Europe copy of the entire datasets present on NLM servers • Male dataset : about 15 GigaBytes • Female dataset : about 40 GigaBytes • Storing the entire datasets on RAID disks (about 60 GigaBytes!) for on-line download • WEB interface to the data, downloadable via FTP • European reference and help desk point for who need informations about VHD download and use vhd-mms/tutorial/base/intro-4.2

  38. Visible Human Dataset - Milano Mirror Site®Promoters • Agreeement between Politecnico of Milano (Department of BioEngineering) and CILEA (Consortium of the Italian NorthWest Universities) for the setup and the maintenance of the Continental Europe VHD mirror site vhd-mms/tutorial/base/intro-4.3-1/2

  39. Visible Human Dataset - Milano Mirror Site®Sponsors • Sponsorships to maintain the VHD-MMS services at very high level of quality vhd-mms/tutorial/base/intro-4.3-2/2

  40. Visible Human Dataset - Milano Mirror Site®Technical criteria • Availability on-line 365 day/year of all the datasets, storing them on SCSI disk with RAID technology (ca 60Gb) • WEB interface also for FTP download process • Excellent network access for European and Italian users • on a GARR node (Italian academic network) • near a gateway between GARR and commercial ISPs • near the main commercial ISPs italian gateway point vhd-mms/tutorial/base/intro-4.4.1

  41. Visible Human Dataset - Milano Mirror Site®Hardware/Software • HP Netserver LX PRO • Bi-processor Pentium 200 • 9 disks RAID, each one of 9Gb • SCO UNIX Open Server • Netscape Web Fasttrack Server vhd-mms/tutorial/base/intro-4.4.2

  42. Visible Human Dataset - Milano Mirror Site®Internet connection >8Mb/s Internet MIX NSP #n NSP #n NSP #n > 34Mb/s 2Mb/s NAP #n NAPCILEA 512Kb/s GARR VHD-MMS 2Mb/s vhd-mms/tutorial/base/intro-4.4.3

  43. Visible Human Dataset - Milano Mirror Site®Web site vhd-mms/tutorial/base/intro-4.4.4

  44. Coordinator Prof. Francesco Pinciroli Tel. (39) (2) 2399.3335 e-mail: pinciroli@biomed.polimi.it Technical Manager Dott. Luciano Guglielmi Tel. (39) (2) 26995.267 e-mail: guglielmi@cilea.it Services of theVisible Human Dataset - Milano Mirror Site®Qualified and continuos help desk http://vhd-mms.cilea.it/ Informations:VHDmilano@cilea.it vhd-mms/tutorial/base/intro-4.5.1

  45. Services of theVisible Human Dataset - Milano Mirror Site®Continuos access to the data via FTP, also using a WEB interface http://vhd-mms.cilea.it/ ftp://userid@vhd-mms.cilea.it vhd-mms/tutorial/base/intro-4.5.2

  46. Services of theVisible Human Dataset - Milano Mirror Site® To scrape together products based on the “Visible Human Dataset” based products Built of a collection of VHD based product at the Library of the Department of BioEngineering of the Politecnico di Milano, made available both from single editors or found on the market Web access to this repository for queries about availability and borrow purpose, will be ready as soon as possible. vhd-mms/tutorial/base/intro-4.5.3.1

  47. Services of theVisible Human Dataset - Milano Mirror Site® Web Site VHD-MMS in all the European language Availability of the Visible Human Dataset - Milano Mirror Site® Web site in all the European languages vhd-mms/tutorial/base/intro-4.5.3.2

  48. Services offered byVisible Human Dataset - Milano Mirror Site® Disk space availability for storing, and delivering via internet, any kind of applications built using the Visible Human Dataset (with special attention to those made up by individuals or groups coming from continental Europe) • availability confirmed • waiting for requests... vhd-mms/tutorial/base/intro-4.5.3.3

  49. Services of theVisible Human Dataset - Milano Mirror Site® Money and logistic contribution Contribution assignment, both money and logistic ones, with the goal to promote scientific PhD and university degree works, based on the use of the VHD and the optimization of the services offered by the Visible Human Dataset - Milano Mirror Site® vhd-mms/tutorial/base/intro-4.5.3.4

  50. Services of theVisible Human Dataset - Milano Mirror Site® ”Help us to serve you better…” Setup of a direct web line with the users, to collect: Advices Remarks Criticisms Suggestions Appreciations vhd-mms/tutorial/base/intro-4.5.3.5

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