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CCF Organ VR Gallery

A user in action in the CCF Organ VR Gallery, looking at the whole body, many organs, and the number of cells in a kidney, as well as exploding a heart.

Welcome to this repo! The CCF Organ VR Gallery lets the user explore 21 human organs, journeying from the Whole Body, to the Organ, to the Cell stage and back, presented in real-world size and 3D. The user discovers hidden regions by exploding and collapsing organs into their individual anatomical structures. We show cell type populations for a kidney using a data-driven dot density visualization. The organ models were developed to map trillions of cells for the Human BioMolecular Atlas Program (HuBMAP).

For more information about the Common Coordinate Framework (CCF), see the HuBMAP CCF Portal at https://hubmapconsortium.github.io/ccf/.

Video demo

We present the CCF Organ VR Gallery in this demo: https://www.youtube.com/watch?v=S9pBOlSfsnc

Changelog

See the Changelog for the latest developments.

Credits

This software is developed by Andreas Bueckle the Cyberinfrastructure for Network Science Center at Indiana University.

Become a test user

If you would like to become a test user, please email Andreas Bueckle at [email protected].

Data

K. Browne et al. "HuBMAP CCF 3D Reference Object Library." https://hubmapconsortium.github.io/ccf/pages/ccf-3d-reference-library.html (accessed Jan 7, 2022).

Anatomical data from the National Library of Medicine’s Visible Human Project. https://www.nlm.nih.gov/databases/download/vhp.html

V. Spitzer, M. J. Ackerman, A. L. Scherzinger, and D. Whitlock, "The visible human male: a technical report," (in eng), Journal of the American Medical Informatics Association, vol. 3, no. 2, pp. 118-130, Mar-Apr 1996, doi: 10.1136/jamia.1996.96236280.

VHMOOC

To access all Visible Human Massive Open Online (VHMOOC) materials, register for free at https://expand.iu.edu/browse/sice/cns/courses/hubmap-visible-human-mooc.

References

K. Börner et al. "Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas." https://www.biorxiv.org/content/10.1101/2021.12.30.474265 (accessed Jan 7, 2022).

K. Börner et al., "Anatomical structures, cell types and biomarkers of the Human Reference Atlas," Nature Cell Biology, vol. 23, no. 11, pp. 1117-1128, 2021/11/01 2021, doi: 10.1038/s41556-021-00788-6.

M. P. Snyder et al., "The human body at cellular resolution: the NIH Human Biomolecular Atlas Program," Nature, vol. 574, no. 7777, pp. 187-192, 2019/10/01 2019, doi: 10.1038/s41586-019-1629-x

Other software credits

Cyberinfrastructure for Network Science Center. "Registration User Interface." https://hubmapconsortium.github.io/ccf-ui/rui/ (accessed Jan 7, 2022).

Cyberinfrastructure for Network Science Center. "Exploration User Interface." https://portal.hubmapconsortium.org/ccf-eui (accessed Jan 7, 2022).