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Jun 28, 2010

PhysiomeSpace: complete female 3D human skeleton model

By Martina Contin

Super Computing Solutions –SCS- and the Computational Bioengineering Lab –BIC- by the Istituto Ortopedico Rizzoli are happy to announce the release of the first dataset that composes the Living Human Digital Library –LHDL- multiscale musculoskeletal data collection.

The data represent the three-dimensional skeletal anatomy of the cadaver of a 78 years old woman with normal morphology (height: 171 cm, weight: 64 kg, from now on referred to as “LHDL_Donor1”).

From today the consortium will start releasing various datasets with a cadence of two weeks. By the end of the 2010 the entire LHDL multiscale collection on LHDL_Donor1 will be made available.

The bone surfaces of LHDL_Donor1 were obtained from the segmentation of whole body Computer Tomography (CT) images, in three stages:

a qualified technician performed gross segmentation;
a senior anatomist performed a refinement of the segmentation on all bones. Joint surfaces were segmented in order to respect joint morphology;
3D polygonal surface models were generated for the external surface of each bone.
The bone surfaces can be downloaded from the PhysiomeSpace service and freely used for no profit research purposes under the LHDL license agreement. The service currently provides free accounts with up to 1 Gb of on-line storage space. A license for commercial use of the LHDL data collection is also available. If you wish to have more information on this matter please contact:

How to access the PhysiomeSpace resources:
To be able to access the LHDL multiscale collection, you firstly need to:

register to the BiomedTown portal

subscribe to the PhysiomeSpace user group

install the PSLoader© client application

For detailed instructions, please read the “How to get access to the service” section.
You are now ready to download the data repository. Go to the PhysiomeSpace home page:

Search within the available data resources and then add those you wish to download to your basket, clicking on the shopping cart icon next to it.

Open PSLoader© and authenticate, inserting BT username and password.

To finalise the download into PSLoader©, follow this path: Operations>Manage>Download from basket. Proceed saving the data. A window called “Download from basket” will open, listing the resources currently in your basket.

At the end of the download process, the downloaded data resources will appear in the PSLoader© data tree, and you can start working on them.

About the LHDL multiscale musculoskeletal data collection:

The first large data collection that will be hosted by the PhysiomeSpace service is the LHDL multiscale musculoskeletal data collection, that when fully published will constitute one of the most extensive data collection publicly available of this kind.

The collection, generated by researchers at ULB and IOR, is based on two female cadavers obtained from the ULB donation program, and on a group of body-matched volunteers recruited at IOR.

The data collection includes:

Body level: in vitro whole-body CT and MRI scans were performed. From those imaging data 3D models of bones and muscles were obtained through segmentation. In parallel, in-vivo motion analyses (stereophotogrammetry, force plate measurements, and electromyography) were performed on volunteers, including two volunteers that anthropometrically matched the two cadavers.

Organ level: passive joint kinematics was obtained using conventional stereophotogrammetry with skeletal-attahced frames. Full deep dissection of the cadavers made it possible the digitization of various muscle parameters (pennation angles, origin & insertion location, etc.) and the measurement of muscle mass and volume. Long bones were then dissected and bone biomechanical properties measured (whole bone stiffness, strain distribution, bone strength).

Tissue level: bone properties were further processed at tissue level by performing microCT of cancellous bone biopsies taken from various regions of the skeleton and by testing the mechanical properties of both cortical and cancellous bone specimens.

Cell level: Muscle sarcomere length was obtained using a laser diffraction technique for various muscle biopsies.

Constituent level: to quantify bone structure at sub-tissue level, ash density, collagen orientation, micro-hardness, chemical composition were measured.

What makes this collection unique is that all data come from the same body, and are registered in space one to each other into a multiscale hierarchy defined in a unique global reference framework.