CCF 3D Reference Object Library

Overview

The CCF 3D Reference Object Library provides anatomically correct reference organs. The organs are developed by a specialist in 3D medical illustration and approved by organ experts, see SOP.

Initially, reference objects were created using data from the Visible Human male and female datasets provided by the National Library of Medicine. The male dataset comprises 1,871 cross-sections at 1mm intervals for both CT and anatomical images at a resolution of 4,096 pixels by 2,700 pixels. The female data set has the same characteristics as the Visible Human Male but axial anatomical images were obtained at 0.33 mm intervals resulting in 5,189 cross-section anatomical images. The male was white, 180.3 cm (71 inch) tall, 199-pound and was 38 years old. The female was white, 171.2 cm (67.4 inch) tall, obese, and 59 years old.

For the 1st HuBMAP Portal Release, kidney and spleen reference organs are freely available in GLB format. They can be viewed and explored using free web browsers such as Babylon.js. Screenshots and major properties of the nested reference organ objects are given in table below.

For selected organs, 3D extraction site objects are provided. Some extraction sites resemble geometric objects (e.g., cuboids for heart) while others take the shape of one or more whole or partial anatomical structures (e.g., in spleen). The 3D extraction sites do not restrict registration to specific regions, instead they provide “expert defined landmarks” to help guide tissue registration. The extraction site objects are also used for automatic semantic annotation of tissue samples via collision detection during registration.

Terms of Use

HuBMAP data are supplied with no warranties, express or implied, including without limitation, any warranty of merchantability or fitness for a particular purpose or non-infringement. No warranty with respect to the HuBMAP infrastructure is provided, including without limitation, any uptime warranty. The Parties make no representations that the use of the data will not infringe any patent or proprietary rights of third parties.

License

The CCF 3D reference object data is released under Attribution 4.0 International (CC BY 4.0).

Citation

If you use the data files, please cite this effort as follows:

Browne K, Cross LE, Herr II, BW, Record EG, Quardokus EM, Bueckle A, Börner K. 2020. HuBMAP CCF 3D Reference Object Library. Accessed on June 20, 2020.

Reference Organs

Male: Colon
3D Model: Kidney, Male, Left
# Anatomical Structures 10
Appendix 1
Ascending Colon 1
Cecum 1
Descending Colon 1
Hepatic Flexure 1
Ileocecal Valve 1
Rectum 1
Sigmoid Colon 1
Splenic Flexure 1
Transverse Colon 1
Female: Colon
3D Model: Kidney, Male, Left
# Anatomical Structures 10
Appendix 1
Ascending Colon 1
Cecum 1
Descending Colon 1
Hepatic Flexure 1
Ileocecal Valve 1
Retum 1
Sigmoid Colon 1
Splenic Flexure 1
Transverse Colon 1
Male: Heart
3D Model: Heart, Male
# Anatomical Structures 39
Anterior Cardiac Vein 3
Anterior Papillary Muscle 1
Aortic Arch 1
Aortic Valve 1
Ascending Aorta 1
Brachiocephalic Vein, Left 1
Brachiocephalic Vein, Right 1
Coronary Sinus 1
Descending Aorta 1
Great Cardiac Vein 1
Inferior Vena Cava 1
Interventricular Septum 1
Left Atrium 1
Left Common Carotid Artery 1
Left Inferior Pulmonary Vein 1
Left Pulmonary Artery 1
Left Subclavian Artery 1
Left Superior Pulmonary Vein 1
Left Ventricle 1
Medial Papillary Muscle 1
Middle Cardiac Vein 1
Mitral Valve 1
Oblique Vein of Left Atrium 1
Posterior Cardiac Vein 1
Posterior Papillary Muscle 1
Posteromedial Papillary Muscle 1
Pulmonary Trunk 1
Pulmonary Valve 1
Right Atrium 1
Right Common Carotid Artery 1
Right Inferior Pulmonary Vein 1
Right Pulmonary Artery 1
Right Superior Pulmonoary Vein 1
Right Ventricle 1
Small Cardiac Vein 1
Superior Vena Cava 1
Tricuspid Valve 1
Female: Heart
3D Model: Heart, Male
# Anatomical Structures 46
Anterior Cardiac Veins 1
Anterior Papillary Muscle 1
Anterolateral Papillary Muscle 1
Aortic Arch 1
Aortic Valve 1
Ascending Aorta 1
Brachiocephalic Vein 1
Coronary Sinus 1
Descending Aorta 1
Great Cardiac Vein 1
Inferior Vena Cava 1
Interventricular Septum 1
Left Anterior Descending Artery 1
Left Atrium 1
Left Circumflex Artery 1
Left Common Carotid Artery 1
Left Diagonal Branch 1
Left Inferior Pulmonary Vein 1
Left Main Coronary Artery 1
Left Marginal Branch 1
Left Marginal Vein 1
Left Pulmonary Artery 1
Left Subclavian Artery 1
Left Superior Pulmonary Vein 1
Left Ventricle 1
Medial Papillary Muscle 1
Middle Cardiac Vein 1
Mitral Valve 1
Oblique Vein of Left Atrium 1
Posterior Descending Artery 1
Posterior Left Ventricular Branch 1
Posterior Papillary Muscle 1
Posterior Vein of Left Ventricle 1
Posteromedial Papillary Muscle 1
Pulmonary Trunk 1
Pulmonary Valve 1
Right Atrium 1
Right Coronary Artery 1
Right Inferior Pulmonary Vein 1
Right Marginal Artery 1
Right Pulmonary Artery 1
Right Superior Pulmonoary Vein 1
Right Ventricle 1
Small Cardiac Vein 1
Superior Vena Cava 1
Tricuspid Valve 1
Male: Kidney, L
3D Model: Kidney, Male, Left
# Anatomical Structures 38
Calyces (minor/major) 9/3
Capsule 1
Hilum 1
Medulla (renal columns) 1
Outer Cortex 1
Papilla 9
Pelvis 1
Pyramids 9
Ureter 1
Artery 1
Veins 1
Male: Kidney, R
3D Model: Kidney, Male, Right
# Anatomical Structures 39
Calyces (minor/major) 9/2
Capsule 1
Hilum 1
Medulla (renal columns) 1
Outer Cortex 1
Papilla 10
Pelvis 1
Pyramids 10
Ureter 1
Artery 1
Veins 1
Female: Kidney, L
3D Model: Kidney, Male, Right
# Anatomical Structures 44
Calyces (minor/major) 10/4
Capsule 1
Hilum 1
Medulla (renal columns) 1
Outer Cortex 1
Papilla 11
Pelvis 1
Pyramids 11
Ureter 1
Artery 1
Veins 1
Female: Kidney, R
3D Model: Kidney, Male, Right
# Anatomical Structures 41
Calyces (minor/major) 10/3
Capsule 1
Hilum 1
Medulla (renal columns) 1
Outer Cortex 1
Papilla 10
Pelvis 1
Pyramids 10
Ureter 1
Artery 1
Veins 1
Male: Spleen
3D Model: Kidney, Male, Left
# Anatomical Structures 8
Hilum 1
Spleen 1
Spleen Gastric Surface 1
Spleen Colic Surface 1
Spleen Renal Surface 1
Spleen Diaphramatic Surface 1
Artery 1
Veins 1
Female: Spleen
3D Model: Kidney, Male, Left
# Anatomical Structures 8
Hilum 1
Spleen 1
Spleen Gastric Surface 1
Spleen Colic Surface 1
Spleen Renal Surface 1
Spleen Diaphramatic Surface 1
Artery 1
Veins 1

Acknowledgements

The 3D Models were created by Kristen Browne for the 3D Printing and Biovisualization program operated by OCICB, NIAID. This research has been funded in part by the NIH Common Fund through the Office of Strategic Coordination/Office of the NIH Director under award OT2OD026671, by the NIDDK Kidney Precision Medicine Project grant U2CDK114886, and NIAID under BCBB Support Services Contract HHSN316201300006W/HHSN27200002to MSC, Inc; U.S.

References

  • Visible Human Project Data. U.S. National Library of Medicine. Accessed on June 20, 2020.
  • Börner K, Quardokus EM, Herr II, BW, Cross LE, Record EG, Ju Y, Bueckle A, Sluka JP, Silverstein J, Browne K, Jain S, Wasserfall CH, Jorgensen ML, Spraggins JM, Patterson NH, Weber GM. 2020. Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies. https://arxiv.org/abs/2007.14474.

June 20, 2020