Shape analysis of 3D nanoscale reconstructions of brain cell nuclear envelopes by implicit and explicit parametric representations
Veloz Castillo, Maria Fernanda
Garnica Molina, Javier F.
Morales Tapia, Alex
Magistretti, Pierre J.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Visual Computing Center (VCC)
KAUST Grant NumberCRG grant no. 2313
Online Publication Date2019-06-06
Print Publication Date2019-06
Permanent link to this recordhttp://hdl.handle.net/10754/656323
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AbstractShape analysis of cell nuclei is becoming increasingly important in biology and medicine. Recent results have identified that large variability in shape and size of nuclei has an important impact on many biological processes. Current analysis techniques involve automatic methods for detection and segmentation of histology and microscopy images, but are mostly performed in 2D. Methods for 3D shape analysis, made possible by emerging acquisition methods capable to provide nanometric-scale 3D reconstructions, are still at an early stage, and often assume a simple spherical shape. We introduce here a framework for analyzing 3D nanoscale reconstructions of nuclei of brain cells (mostly neurons), obtained by semiautomatic segmentation of electron micrographs. Our method considers two parametric representations: the first one customizes the implicit hyperquadricsformulation and it is particularly suited for convex shapes, while the latter considers a spherical harmonics decomposition of the explicit radial representation. Point clouds of nuclear envelopes, extracted from image data, are fitted to the parameterized models which are then used for performing statistical analysis and shape comparisons. We report on the analysis of a collection of 121 nuclei of brain cells obtained from the somatosensory cortex of a juvenile rat.
CitationAgus, M., Veloz Castillo, M., Garnica Molina, J. F., Gobbetti, E., Lehväslaiho, H., Morales Tapia, A., … Calí, C. (2019). Shape analysis of 3D nanoscale reconstructions of brain cell nuclear envelopes by implicit and explicit parametric representations. Computers & Graphics: X, 1, 100004. doi:10.1016/j.cagx.2019.100004
SponsorsThis work was supported by the CRG grant no. 2313 from King Abdullah University of Science and Technology KAUST-EPFL Alliance for Integrative Modeling of Brain Energy Metabolism. We also acknowledge the contribution of Sardinian Regional Authorities under project VIGECLAB. We finally thank Helmut Pottmann (King Abdullah University of Science and Technology) for useful comments and suggestions.
JournalComputers & Graphics: X
Except where otherwise noted, this item's license is described as This is an open access article under the CC BY-NC-ND license. (http://creativecommons.org/licenses/by-nc-nd/4.0/)