Legends: | Link to a Model | Reference cited by multiple papers |
 • | The neocortical microcircuit collaboration portal (Markram et al. 2015) |
References and models cited by this paper | References and models that cite this paper | |||||||
Abdellah M (2017) Physically-plausible Reconstruction of Neocortical Somata. Blue Brain Project. 2017. https://www.youtube.com/watch?v= XJ8uVBL8CA8&feature=youtu.be Abdellah M, Bilgili A, Eilemann S, Markram H, Schürmann F (2015) Physically-based in silico light sheet microscopy for visualizing fluorescent brain models. BMC Bioinformatics 16 Suppl 11:S8 [Journal] [PubMed] Abdellah M, Bilgili A, Eilemann S, Shillcock J, Markram H, Schürmann F (2017) Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation. BMC Bioinformatics 18:62 [Journal] [PubMed] Abdellah M,Bilgili A,Eilemann S,Markram H,Schürmann F (2015) A computational model of light-sheet fluorescence microscopy using physically-based rendering Eurographics 2015 :2 [Journal] Azimipour M, Baumgartner R, Liu Y, Jacques SL, Eliceiri K, Pashaie R (2014) Extraction of optical properties and prediction of light distribution in rat brain tissue. J Biomed Opt 19:75001 [Journal] [PubMed] Berndt A, Schoenenberger P, Mattis J, Tye KM, Deisseroth K, Hegemann P, Oertner TG (2011) High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proc Natl Acad Sci U S A 108:7595-600 [Journal] [PubMed] Blender Institute Amsterdam (2016) Blender - 3D Modelling and Rendering Package http://www.blender.org/ Blender Online Community (2016) Mesh Primitives, Blender Reference Manual, Version 2.77 http://www.blender.org Brito JP, Mata S, Bayona S, Pastor L, Defelipe J, Benavides-Piccione R (2013) Neuronize: a tool for building realistic neuronal cell morphologies. Front Neuroanat 7:15 [Journal] [PubMed] Burtsev S,Kuzmin YP (1993) An efficient flood-filling algorithm Comput Graph 17(5):549-61 [Journal] Cai D,Cohen KB,Luo T,Lichtman JW,Sanes JR (2013) Improved tools for thebrainbowtoolbox NatMethods 10(6):540-7 [Journal] Chemla S, Chavane F (2010) Voltage-sensitive dye imaging: Technique review and models. J Physiol Paris 104:40-50 [Journal] [PubMed] Cignoni P,Corsini M,Ranzuglia G (2008) Meshlab: an Open-Source 3D mesh processing system Ercim News 73(45-46):6 Cohen-Or D,Kaufman A (1997) 3D line voxelization and connectivity control IEEE Comput Graph Appl. 17(6):80-7 [Journal] Dagum L, Menon R (1998) Openmp: An industry-standard api for shared-memory programming Ieee Computational Science Engineering 5:46-55 Di Ventura B, Lemerle C, Michalodimitrakis K, Serrano L (2006) From in vivo to in silico biology and back. Nature 443:527-33 [Journal] [PubMed] Dong Z,Chen W,Bao H,Zhang H,Peng Q (2004) Real-time voxelization for complex polygonal models Computer Graphics and Applications, 2004. PG 2004. Proceedings. 12th Pacific Conference On. IEEE :43-50 [Journal] Donohue DE, Scorcioni R, Ascoli GA (2002) Generation and description of neuronal morphology using L-Neuron: A case study Computational Neuroanatomy: Principles and Methods, Ascoli G, ed. pp.49 Eisemann E,Décoret X (2006) Fast scene voxelization and applications Proceedings of the 2006 Symposium on Interactive 3D Graphics and Games. ACM :71-8 [Journal] Eisemann E,Décoret X. (2008) Single-pass GPU solid voxelization for real-time applications Single-pass GPU solid voxelization for real-time applications :73-80 Fang S,Chen H (2000) Hardware accelerated voxelization Hardware accelerated voxelization 24(3):433-42 [Journal] Geschwind DH, Konopka G (2009) Neuroscience in the era of functional genomics and systems biology. Nature 461:908-15 [Journal] [PubMed] Glaser JR, Glaser EM (1990) Neuron imaging with Neurolucida--a PC-based system for image combining microscopy. Comput Med Imaging Graph 14:307-17 [PubMed] Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35 [Journal] [PubMed] Halavi M, Polavaram S, Donohue DE, Hamilton G, Hoyt J, Smith KP, Ascoli GA (2008) NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics 6:241-52 [Journal] [PubMed] He W, Hamilton TA, Cohen AR, Holmes TJ, Pace C, Szarowski DH, Turner JN, Roysam B (2003) Automated three-dimensional tracing of neurons in confocal and brightfield images. Microsc Microanal 9:296-310 [Journal] [PubMed] Hernando J,Schurmann F,Pastor L (2012) Towards real-time visualization of detailed neural tissue models: View frustum culling for parallel rendering BioVis :25-32 Kazhdan M,Hoppe H (2013) Screened poisson surface reconstruction ACM Trans Graph 32(3):29 [Journal] Koch C, Segev I (1998) Methods In Neuronal Modeling Koene RA, Tijms B, van Hees P, Postma F, de Ridder A, Ramakers GJ, van Pelt J, van Ooyen A (2009) NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 7:195-210 [Journal] [PubMed]
Kozloski J, Sfyrakis K, Hill S, Schurmann F, Peck C, Markram H (2008) Identifying, tabulating, and analyzing contacts between branched neuron morphologies Ibm J Res Dev 52:43-55 Lasserre S, Hernando J, Hill S, Schümann F, Anasagasti Pde M, Jaoudé GA, Markram H (2012) A neuron membrane mesh representation for visualization of electrophysiological simulations. IEEE Trans Vis Comput Graph 18:214-27 [Journal] [PubMed] Lippert T,Orth B (2014) Supercomputing infrastructure for simulations of the human brain Brain-Inspired Computing, Grandinetti L:Lippert T:Petkov N, ed. [Journal] Llamas I (2007) Real-time voxelization of triangle meshes on the GPU SIGGRAPH Sketches. San Diego: The 34th international conference and exhibition on computer graphics and interactive techniques :18 [Journal] Markram H, Muller E, Ramaswamy S, Reimann MW, Abdellah M, Sanchez CA, Ailamaki A, Alonso-Nanclares L, Antille N, Arsever S, Kahou GA, Berger TK, Bilgili A, Buncic N, Chalimourda A, Chindemi G, Courcol JD, Delalondre F, Delattre V, Druckmann S, Dumusc R, Dynes J, Eilemann S, Gal E, Gevaert ME, Ghobril JP, Gidon A, Graham JW, Gupta A, Haenel V, Hay E, Heinis T, Hernando JB, Hines M, Kanari L, Keller D, Kenyon J, Khazen G, Kim Y, King JG, Kisvarday Z, Kumbhar P, Lasserre S, Le Bé JV, Magalhães BR, Merchán-Pérez A, Meystre J, Morrice BR, Muller J, Muñoz-Céspedes A, Muralidhar S, Muthurasa K, Nachbaur D, Newton TH, Nolte M, Ovcharenko A, Palacios J, Pastor L, Perin R, Ranjan R, Riachi I, Rodríguez JR, Riquelme JL, Rössert C, Sfyrakis K, Shi Y, Shillcock JC, Silberberg G, Silva R, Tauheed F, Telefont M, Toledo-Rodriguez M, Tränkler T, Van Geit W, Díaz JV, Walker R, Wang Y, Zaninetta SM (2015) Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163:456-92 [Journal] [PubMed]
Markram H,Meier K,Lippert T,Grillner S,Frackowiak R,Dehaene S,Knoll A,Sompolinsky H,Verstreken K,DeFelipe J,et al. (2011) Introducing the human brain project Procedia Comput Sci. 7:39-42 [Journal] Mills MJL, Sale KL, Simmons BA, Popelier PLA (2017) Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. J Comput Chem 38:2538-2552 [Journal] [PubMed] Moser MB,Moser EI,Marcus G,Freeman J (2014) The Future of the Brain: Essays by the World's Leading Neuroscientists Nealen A,Müller M,Keiser R,Boxerman E,Carlson M (2006) Physically based deformable models in computer graphics Computer Graphics Forum :809-36 [Journal] Nikolic K,Jarvis S,Grossman N,Schultz S (2013) Computational models of optogenetic tools for controlling neural circuits with light 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) :5934-937 [Journal] Oberlaender M, Bruno RM, Sakmann B, Broser PJ (2007) Transmitted light brightfield mosaic microscopy for three-dimensional tracing of single neuron morphology. J Biomed Opt 12:064029 [Journal] [PubMed] Pawelzik H, Hughes DI, Thomson AM (2002) Physiological and morphological diversity of immunocytochemically defined parvalbumin- and cholecystokinin-positive interneurones in CA1 of the adult rat hippocampus. J Comp Neurol 443:346-67 [PubMed] Peng H, Meijering E, Ascoli GA (2015) From DIADEM to BigNeuron. Neuroinformatics 13:259-60 [Journal] [PubMed] Pharr M,Humphreys G (2010) Physically Based Rendering, Second Edition: From Theory To Implementation [Journal] Pharr M,Humphreys G (2012) Physically-based Rendering. From Theory to Implementation. 2012. http://www.pbrt.org/ Ramaswamy S, Courcol JD, Abdellah M, Adaszewski SR, Antille N, Arsever S, Atenekeng G, Bilgili A, Brukau Y, Chalimourda A, Chindemi G, Delalondre F, Dumusc R, Eilemann S, Gevaert ME, Gleeson P, Graham JW, Hernando JB, Kanari L, Katkov Y, Keller D, King JG, Ranjan R, Reimann MW, Rössert C, Shi Y, Shillcock JC, Telefont M, Van Geit W, Diaz JV, Walker R, Wang Y, Zaninetta SM, DeFelipe J, Hill SL, Muller J, Segev I, Schürmann F, Muller EB, Markram H (2015) The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Front Neural Circuits 9:44 [Journal] [PubMed]
Sanbonmatsu KY, Tung CS (2007) High performance computing in biology: multimillion atom simulations of nanoscale systems. J Struct Biol 157:470-80 [Journal] [PubMed] Schwarz M,Seidel HP (2010) Fast parallel surface and solid voxelization on gpus ACM Transactions on Graphics (TOG) :179 [Journal] Stosiek C, Garaschuk O, Holthoff K, Konnerth A (2003) In vivo two-photon calcium imaging of neuronal networks. Proc Natl Acad Sci U S A 100:7319-24 [Journal] [PubMed] Terzopoulos D,Platt J,Barr A,Fleischer K (1987) Elastically deformable models ACM Siggraph Computer Graphics. ACM :205-14 [Journal] Tomer R, Ye L, Hsueh B, Deisseroth K (2014) Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat Protoc 9:1682-97 [Journal] [PubMed] Torben-nielsen B, Tuyls K, Postma E (2008) EvOL-NEURON: Neuronal morphology generation Neurocomputing 71:963-972 Wilson MA, Bhalla US, Uhley JD, Bower JM (1989) GENESIS: a system for simulating neural networks Advances In Neural Information Processing Systems, Touretzky D, ed. pp.485 Zhu X,Guo X,Jin X (2013) Efficient polygonization of tree trunks modeled by convolution surfaces Sci China Inf Sci. 56(3):1-12 [Journal] |