title: A novel toolbox to investigate tissue spatial organization applied to the study of the islets of Langerhans.
abstract: Thanks to the development of new 3D Imaging techniques, volumetric data of thick samples, especially tissues, are commonly available. Several algorithms were proposed to analyze cells or nuclei in tissues, however these tools are limited to two dimensions. Within any given tissue, cells are not likely to be organized randomly and as such have specific patterns of cell-cell interaction forming complex communication networks. In this paper, we propose a new set of tools as an approach to segment and analyze tissues in 3D with single cell resolution. This new tool box can identify and compute the geographical location of single cells and analyze the potential physical interactions between different cell types and in 3D. As a proof-of-principle, we applied our methodology to investigation of the cyto-architecture of the islets of Langerhans in mice and monkeys. The results obtained here are a significant improvement in current methodologies and provides new insight into the organization of alpha cells and their cellular interactions within the islet's cellular framework.
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, UJF, CNRS, IMT, NUS, Image and Pervasive Access Lab (IPAL), 138632, Singapore.|Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 138671, Singapore.
authors.forename: Hoa
authors.initials: H
authors.lastname: Tran Thi Nhu
authors.affiliation: Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Drive, Research Techno Plaza, Level 4, 637 553 Singapore.|Nanyang Institute of Structural Biology, Nanyang Technological University, Proteos, 61 Biopolis Drive, 138673, Singapore.
authors.forename: Rafael
authors.initials: R
authors.lastname: Arrojo E Drigo
authors.affiliation: Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Drive, Research Techno Plaza, Level 4, 637 553 Singapore.|Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Per-Olof
authors.initials: PO
authors.lastname: Berggren
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, UJF, CNRS, IMT, NUS, Image and Pervasive Access Lab (IPAL), 138632, Singapore.|Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 138671, Singapore.
authors.forename: Thomas
authors.initials: T
authors.lastname: Boudier
mesh_terms: D000465:Algorithms; D000818:Animals; D002450:Cell Communication; D002467:Cell Nucleus / Q000378:metabolism / Q000648:ultrastructure*; D015870:Gene Expression; D005934:Glucagon / Q000235:genetics / Q000378:metabolism; D000882:Haplorhini; D007091:Image Processing, Computer-Assisted / Q000379:methods* / Q000706:statistics & numerical data; D021621:Imaging, Three-Dimensional; D007328:Insulin / Q000235:genetics / Q000378:metabolism; D007515:Islets of Langerhans / Q000033:anatomy & histology / Q000166:cytology*; D051379:Mice; D008810:Mice, Inbred C57BL; D061848:Optical Imaging / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods*; D013004:Somatostatin / Q000235:genetics / Q000378:metabolism
chemical_list: D007328:Insulin; D013004:Somatostatin; D005934:Glucagon