@ARTICLE{10.3389/fcvm.2020.00029,
\nAUTHOR={Weber, Griffin M. and Ju, Yingnan and Börner, Katy},
\nTITLE={Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body},
\nJOURNAL={Frontiers in Cardiovascular Medicine}, VOLUME={7}, YEAR={2020},
\nURL={https://www.frontiersin.org/articles/10.3389/fcvm.2020.00029},
\nDOI={10.3389/fcvm.2020.00029}, ISSN={2297-055X},
\"Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level.\"
\n\"Their goals are to understand cell specialization, interactions, spatial organization in their natural context, and ultimately the function of every cell within the body. Multiple centers around the world are collecting tissue specimens from diverse populations that vary in age, race, sex, and body size.\"
\n\"A challenge will be combining these heterogeneous tissue samples into a 3D reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or “addresses,” in a reference body, from whole organs down to functional tissue units and individual cells.\"
\n\"An organ, such as the kidney, has tens of thousands of vasculature pathways if every capillary is considered distinctly. However, in order to make the construction of a CCF (Common Coordinate Framework) feasible, the authors made an additional simplifying assumption that many of these pathways are indistinguishable from each other.\"
\nLIMITATIONS of a VASCULAR CCF
\n\"Some additional positional information is lost by collapsing vascular pathways. For example, a vascular coordinate system might initially treat all glomerulus capillaries in the kidney as the same structure, potentially masking differences in glomeruli at the superior and inferior renal poles. Though, as the authors learned more about the biomolecular profiles of these pathways, the authors could iteratively refine the vascular CCF over time by splitting pathways into any subtypes that are discovered.\"
\n\"Vascularization naturally adapts to individual variations in tissue, body size and shape. Instead of having to map the 3D coordinates of each glomerulus in one person to those in another person, the vascular CCF would position each cell within a representative glomerulus capillary from each person. \"
\n\"No single CCF is ideal for all use cases, a vascular CCF defines a natural coordinate system that would make it easy to combine biomolecular data from multiple people and ask biologically relevant research questions.\"
\nhttps://www.frontiersin.org/articles/10.3389/fcvm.2020.00029/full
\nBoppana, Avinash, Lee, Sujin, Malhotra, Rajeev, Halushka, Marc, Quardokus, Ellen M, Herr, Bruce W, Börner, Katy, & Weber, Griffin M. (2022). Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) (1.4.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7542316
\n\"The Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) is a computer-readable and comprehensive database of the adult human blood vasculature.\"
\nhttps://zenodo.org/record/7542316#.ZGz38n3MK3A
", "messages": [ { "id": 2271210, "postDate": "2023-05-23T17:33:43.323Z", "content": "@ARTICLE{10.3389/fcvm.2020.00029,
\nAUTHOR={Weber, Griffin M. and Ju, Yingnan and Börner, Katy},
\nTITLE={Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body},
\nJOURNAL={Frontiers in Cardiovascular Medicine}, VOLUME={7}, YEAR={2020},
\nURL={https://www.frontiersin.org/articles/10.3389/fcvm.2020.00029},
\nDOI={10.3389/fcvm.2020.00029}, ISSN={2297-055X},
\"Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level.\"
\n\"Their goals are to understand cell specialization, interactions, spatial organization in their natural context, and ultimately the function of every cell within the body. Multiple centers around the world are collecting tissue specimens from diverse populations that vary in age, race, sex, and body size.\"
\n\"A challenge will be combining these heterogeneous tissue samples into a 3D reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or “addresses,” in a reference body, from whole organs down to functional tissue units and individual cells.\"
\n\"An organ, such as the kidney, has tens of thousands of vasculature pathways if every capillary is considered distinctly. However, in order to make the construction of a CCF (Common Coordinate Framework) feasible, the authors made an additional simplifying assumption that many of these pathways are indistinguishable from each other.\"
\nLIMITATIONS of a VASCULAR CCF
\n\"Some additional positional information is lost by collapsing vascular pathways. For example, a vascular coordinate system might initially treat all glomerulus capillaries in the kidney as the same structure, potentially masking differences in glomeruli at the superior and inferior renal poles. Though, as the authors learned more about the biomolecular profiles of these pathways, the authors could iteratively refine the vascular CCF over time by splitting pathways into any subtypes that are discovered.\"
\n\"Vascularization naturally adapts to individual variations in tissue, body size and shape. Instead of having to map the 3D coordinates of each glomerulus in one person to those in another person, the vascular CCF would position each cell within a representative glomerulus capillary from each person. \"
\n\"No single CCF is ideal for all use cases, a vascular CCF defines a natural coordinate system that would make it easy to combine biomolecular data from multiple people and ask biologically relevant research questions.\"
\nhttps://www.frontiersin.org/articles/10.3389/fcvm.2020.00029/full
\nBoppana, Avinash, Lee, Sujin, Malhotra, Rajeev, Halushka, Marc, Quardokus, Ellen M, Herr, Bruce W, Börner, Katy, & Weber, Griffin M. (2022). Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) (1.4.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7542316
\n\"The Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) is a computer-readable and comprehensive database of the adult human blood vasculature.\"
\n", "rawMarkdown": "#Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body\n\n@ARTICLE{10.3389/fcvm.2020.00029, \nAUTHOR={Weber, Griffin M. and Ju, Yingnan and Börner, Katy}, \t \nTITLE={Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body}, \nJOURNAL={Frontiers in Cardiovascular Medicine}, VOLUME={7}, YEAR={2020}, \nURL={https://www.frontiersin.org/articles/10.3389/fcvm.2020.00029}, \t\nDOI={10.3389/fcvm.2020.00029}, ISSN={2297-055X}, \n \n\"Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level.\"\n\n\"Their goals are to understand cell specialization, interactions, spatial organization in their natural context, and ultimately the function of every cell within the body. Multiple centers around the world are collecting tissue specimens from diverse populations that vary in age, race, sex, and body size.\"\n\n\"A challenge will be combining these heterogeneous tissue samples into a 3D reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or “addresses,” in a reference body, from whole organs down to functional tissue units and individual cells.\"\n\n\"An organ, such as the kidney, has tens of thousands of vasculature pathways if every capillary is considered distinctly. However, in order to make the construction of a CCF (Common Coordinate Framework) feasible, the authors made an additional simplifying assumption that many of these pathways are indistinguishable from each other.\" \n\nLIMITATIONS of a VASCULAR CCF\n\n\"Some additional positional information is lost by collapsing vascular pathways. For example, a vascular coordinate system might initially treat all glomerulus capillaries in the kidney as the same structure, potentially masking differences in glomeruli at the superior and inferior renal poles. Though, as the authors learned more about the biomolecular profiles of these pathways, the authors could iteratively refine the vascular CCF over time by splitting pathways into any subtypes that are discovered.\"\n\n\"Vascularization naturally adapts to individual variations in tissue, body size and shape. Instead of having to map the 3D coordinates of each glomerulus in one person to those in another person, the vascular CCF would position each cell within a representative glomerulus capillary from each person. \" \n\n\"No single CCF is ideal for all use cases, a vascular CCF defines a natural coordinate system that would make it easy to combine biomolecular data from multiple people and ask biologically relevant research questions.\"\n\nhttps://www.frontiersin.org/articles/10.3389/fcvm.2020.00029/full\n\n#Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF)\n\nBoppana, Avinash, Lee, Sujin, Malhotra, Rajeev, Halushka, Marc, Quardokus, Ellen M, Herr, Bruce W, Börner, Katy, & Weber, Griffin M. (2022). Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) (1.4.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7542316\n\n\"The Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) is a computer-readable and comprehensive database of the adult human blood vasculature.\"\n\nhttps://zenodo.org/record/7542316#.ZGz38n3MK3A", "votes": 8 } ], "comments": [], "raw_markdown_by_id": { "2271210": "#Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body\n\n@ARTICLE{10.3389/fcvm.2020.00029, \nAUTHOR={Weber, Griffin M. and Ju, Yingnan and Börner, Katy}, \t \nTITLE={Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body}, \nJOURNAL={Frontiers in Cardiovascular Medicine}, VOLUME={7}, YEAR={2020}, \nURL={https://www.frontiersin.org/articles/10.3389/fcvm.2020.00029}, \t\nDOI={10.3389/fcvm.2020.00029}, ISSN={2297-055X}, \n \n\"Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level.\"\n\n\"Their goals are to understand cell specialization, interactions, spatial organization in their natural context, and ultimately the function of every cell within the body. Multiple centers around the world are collecting tissue specimens from diverse populations that vary in age, race, sex, and body size.\"\n\n\"A challenge will be combining these heterogeneous tissue samples into a 3D reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or “addresses,” in a reference body, from whole organs down to functional tissue units and individual cells.\"\n\n\"An organ, such as the kidney, has tens of thousands of vasculature pathways if every capillary is considered distinctly. However, in order to make the construction of a CCF (Common Coordinate Framework) feasible, the authors made an additional simplifying assumption that many of these pathways are indistinguishable from each other.\" \n\nLIMITATIONS of a VASCULAR CCF\n\n\"Some additional positional information is lost by collapsing vascular pathways. For example, a vascular coordinate system might initially treat all glomerulus capillaries in the kidney as the same structure, potentially masking differences in glomeruli at the superior and inferior renal poles. Though, as the authors learned more about the biomolecular profiles of these pathways, the authors could iteratively refine the vascular CCF over time by splitting pathways into any subtypes that are discovered.\"\n\n\"Vascularization naturally adapts to individual variations in tissue, body size and shape. Instead of having to map the 3D coordinates of each glomerulus in one person to those in another person, the vascular CCF would position each cell within a representative glomerulus capillary from each person. \" \n\n\"No single CCF is ideal for all use cases, a vascular CCF defines a natural coordinate system that would make it easy to combine biomolecular data from multiple people and ask biologically relevant research questions.\"\n\nhttps://www.frontiersin.org/articles/10.3389/fcvm.2020.00029/full\n\n#Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF)\n\nBoppana, Avinash, Lee, Sujin, Malhotra, Rajeev, Halushka, Marc, Quardokus, Ellen M, Herr, Bruce W, Börner, Katy, & Weber, Griffin M. (2022). Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) (1.4.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7542316\n\n\"The Human Reference Atlas-Vasculature Common Coordinate Framework (HRA-VCCF) is a computer-readable and comprehensive database of the adult human blood vasculature.\"\n\nhttps://zenodo.org/record/7542316#.ZGz38n3MK3A" } }