Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.
voxelization
Ultraliser
in silico
mesh reconstruction
molecular simulations
optical imaging simulations
reaction–diffusion simulations
ultrastructure
watertight
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
19 01 2023
19 01 2023
Historique:
received:
02
08
2022
revised:
27
09
2022
accepted:
14
10
2022
pubmed:
27
11
2022
medline:
24
1
2023
entrez:
26
11
2022
Statut:
ppublish
Résumé
Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser). There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.
Identifiants
pubmed: 36434788
pii: 6847753
doi: 10.1093/bib/bbac491
pmc: PMC9851302
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : King Abdullah University of Science and Technology
ID : OSR-2017-CRG6-3438
Organisme : Swiss Federal Institute of Technology Lausanne
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
Références
Int J Mol Sci. 2015 Sep 07;16(9):21215-36
pubmed: 26370960
IEEE Trans Image Process. 2002;11(7):790-801
pubmed: 18244675
Front Neural Circuits. 2015 Oct 08;9:44
pubmed: 26500503
Front Neuroinform. 2017 Feb 10;11:13
pubmed: 28239346
BMC Syst Biol. 2012 May 10;6:36
pubmed: 22574658
Methods Mol Biol. 2012;804:519-42
pubmed: 22144170
Front Neuroinform. 2015 Jun 30;9:18
pubmed: 26175684
Biophys J. 2020 Mar 10;118(5):1003-1008
pubmed: 32032503
Sci Rep. 2018 Aug 22;8(1):12573
pubmed: 30135559
PLoS Comput Biol. 2021 Oct 8;17(10):e1009451
pubmed: 34624013
Neuroinformatics. 2017 Jul;15(3):247-269
pubmed: 28447297
J Biomech. 2020 May 7;104:109707
pubmed: 32220425
Neuroinformatics. 2014 Apr;12(2):277-89
pubmed: 24100964
J Mol Graph Model. 2008 Jun;26(8):1370-80
pubmed: 18337134
Biomech Model Mechanobiol. 2021 Apr;20(2):403-431
pubmed: 33037509
Brain Res Rev. 2011 Jun 24;67(1-2):94-102
pubmed: 21118703
Bioinformatics. 2021 Jul 12;37(Suppl_1):i426-i433
pubmed: 34252950
Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13711-6
pubmed: 26483464
Elife. 2020 Sep 07;9:
pubmed: 32880371
Cell. 2015 Jul 30;162(3):648-61
pubmed: 26232230
Microsc Microanal. 2003 Aug;9(4):296-310
pubmed: 12901764
Front Neurosci. 2018 Sep 25;12:664
pubmed: 30319342
Nature. 2007 Jan 4;445(7123):E1-2; discussion E2-3
pubmed: 17203021
Cereb Cortex. 2021 Oct 22;31(12):5686-5703
pubmed: 34387659
Front Neuroinform. 2017 Jun 22;11:38
pubmed: 28690511
Nat Neurosci. 2013 Jul;16(7):889-97
pubmed: 23749145
Bioinformatics. 2015 Jul 15;31(14):2406-8
pubmed: 25788627
Nat Commun. 2020 Feb 27;11(1):1104
pubmed: 32107377
BMC Bioinformatics. 2013 Oct 04;14:296
pubmed: 24090312
Sci Rep. 2017 Mar 23;7:44810
pubmed: 28333125
PLoS Comput Biol. 2010 Aug 05;6(8):
pubmed: 20700495
Front Neuroinform. 2014 Jul 29;8:68
pubmed: 25120463
Science. 2012 Oct 5;338(6103):60-5
pubmed: 23042882
Nat Methods. 2017 Apr;14(4):435-442
pubmed: 28250467
J Neurosci. 2007 Aug 29;27(35):9247-51
pubmed: 17728438
Cell. 2018 Jul 26;174(3):730-743.e22
pubmed: 30033368
Pharm Res. 2009 Nov;26(11):2369-400
pubmed: 19756975
Nat Methods. 2018 Aug;15(8):605-610
pubmed: 30013046
Cell Rep. 2022 Apr 5;39(1):110586
pubmed: 35385736
Cell. 2015 Oct 08;163(2):456-92
pubmed: 26451489
J Biomed Opt. 2014;19(7):75001
pubmed: 24996660
Int J Mol Sci. 2018 May 06;19(5):
pubmed: 29734794
Elife. 2022 Nov 16;11:
pubmed: 36382887
PLoS Comput Biol. 2020 Apr 6;16(4):e1007756
pubmed: 32251448
Neuroimage. 2019 Aug 15;197:792-805
pubmed: 28669910
Sci Am. 2012 Jun;306(6):50-5
pubmed: 22649994
IEEE Trans Vis Comput Graph. 2012 Feb;18(2):214-27
pubmed: 21383404
Nature. 2006 Oct 5;443(7111):527-33
pubmed: 17024084
Microscopy (Oxf). 2019 Aug 6;68(4):338-341
pubmed: 31220299
Front Neuroinform. 2022 Jun 27;16:884046
pubmed: 35832575
Science. 2005 Jul 15;309(5733):446-51
pubmed: 16020730
Nat Rev Neurosci. 2006 Feb;7(2):153-60
pubmed: 16429124
Front Neuroinform. 2009 Jun 29;3:15
pubmed: 19623245
IEEE Trans Med Imaging. 2010 Mar;29(3):583-97
pubmed: 20199906
Nat Methods. 2017 Jan 31;14(2):112-116
pubmed: 28139675
Front Cell Neurosci. 2015 Jun 26;9:233
pubmed: 26167146
Bioinformatics. 2020 Jul 1;36(Suppl_1):i534-i541
pubmed: 32657395
J Neurosci Methods. 2013 Nov 15;220(2):167-78
pubmed: 24091136
J Physiol. 2019 Jul;597(13):3473-3502
pubmed: 31099020
Neuroimage. 2013 Nov 15;82:170-81
pubmed: 23727319
J Chem Neuroanat. 2018 Dec;94:119-124
pubmed: 30385398
Bioinformatics. 2018 Jul 1;34(13):i574-i582
pubmed: 29949998
Neural Comput. 1997 Aug 15;9(6):1179-209
pubmed: 9248061
Front Neuroinform. 2019 Sep 19;13:63
pubmed: 31616273
Prog Neurobiol. 2019 Dec;183:101696
pubmed: 31550514
Nat Methods. 2013 Jun;10(6):508-13
pubmed: 23722210
PLoS Comput Biol. 2010 Mar 12;6(3):e1000705
pubmed: 20300644
J Cereb Blood Flow Metab. 2009 Aug;29(8):1429-43
pubmed: 19436317
BMC Bioinformatics. 2015;16 Suppl 11:S8
pubmed: 26329404
IEEE J Biomed Health Inform. 2019 Nov;23(6):2551-2562
pubmed: 30507542
Front Neuroanat. 2013 Jun 03;7:15
pubmed: 23761740
Nat Methods. 2022 Jan;19(1):119-128
pubmed: 34949809