Citations for Generating neuron geometries for detailed 3D simulations using AnaMorph (Morschel et al 2017)

Legends: Link to a Model Reference cited by multiple papers

Mörschel K, Breit M, Queisser G (2017) Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph. Neuroinformatics 15:247-269 [PubMed]

References and models cited by this paper

References and models that cite this paper

Ascoli GA (2006) Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat Rev Neurosci 7:318-24 [Journal] [PubMed]
Barnhill R,Farin G,Jordan M,Piper B (1987) Surface/surface intersection Computer Aided Geometric Design 4(1):3-16 [Journal]
Barton M,Jüttler B (2007) Computing roots of polynomials by quadratic clipping Computer Aided Geometric Design 24(3):125-141 [Journal]
Barton M,Jüttler B (2007) Computing roots of systems of polynomials by linear clipping Technical Report 2007-18 SFB F013
Biermann H,Kristjansson D,Zorin D (2001) Approximate boolean operations on free-form solids Proceedings of the 28th annual conference on computer graphics and interactive techniques, ACM, New York, NY, USA, SIGGRAPH ’01 :185-194 [Journal]
Borg-Graham LJ (1999) chap Interpretations of data and mechanisms for hippocampal pyramidal cell models Models of cortical circuits :19-138 [Journal]
Breit M, Stepniewski M, Grein S, Gottmann P, Reinhardt L, Queisser G (2016) Anatomically Detailed and Large-Scale Simulations Studying Synapse Loss and Synchrony Using NeuroBox. Front Neuroanat 10:8 [Journal] [PubMed]
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]
CGAL THE (2016) The CGAL Project CGAL User and reference manual.
Cignoni P,Corsini M,Ranzuglia G (2008) Meshlab: an Open-Source 3D mesh processing system Ercim News 73(45-46):6
Coombs J, van der List D, Wang GY, Chalupa LM (2006) Morphological properties of mouse retinal ganglion cells. Neuroscience 140:123-36 [Journal] [PubMed]
do_Carmo M (1976) Differential geometry of curves and surfaces
Elsheikh AH,Elsheikh M (2014) A reliable triangular mesh intersection algorithm and its application in geological modelling Engineering with Computers 30(1):143-157 [Journal]
Farouki RT,Rajan VT (1988) Algorithms for polynomials in Bernstein form Computer Aided Geometric Design 5(1):1-26 [Journal]
Farouki RT (2012) The Bernstein polynomial basis: a centennial retrospective Computer Aided Geometric Design 29(6):379-419 [Journal]
Farouki RT,Goodman TNT (1996) On the optimal stability of the Bernstein basis Mathematics of Computation 65:1553-1566
Floater MS,Surazhsky T (2006) Parameterization for curve interpolation Studies in Computational Mathematics 12:39-54
Garland M,Heckbert PS (1997) Surface simplification using quadric error metrics Proceedings of the 24th annual conference on computer graphics and interactive techniques :209-216 [Journal]
Grein S, Stepniewski M, Reiter S, Knodel MM, Queisser G (2014) 1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time. Front Neuroinform 8:68 [Journal] [PubMed]
Greiner H (1991) A survey on univariate data interpolation and approximation by splines of given shape Mathematical and Computer Modelling 15(10):97-106 [Journal]
Groh A, Meyer HS, Schmidt EF, Heintz N, Sakmann B, Krieger P (2010) Cell-type specific properties of pyramidal neurons in neocortex underlying a layout that is modifiable depending on the cortical area. Cereb Cortex 20:826-36 [Journal] [PubMed]
Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]
Ishizuka N, Cowan WM, Amaral DG (1995) A quantitative analysis of the dendritic organization of pyramidal cells in the rat hippocampus. J Comp Neurol 362:17-45 [Journal] [PubMed]
Jüttler B (1998) The dual basis functions for the Bernstein polynomials Advances in Computational Mathematics 8(1998):S345-S352
Jüttler B,Moore B (2011) A quadratic clipping step with superquadratic convergence for bivariate polynomial systems Mathematics in Computer Science 5(2):223-235 [Journal]
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]
Levien R,Séquin CH (2009) Interpolating splines: which is the fairest of them all? Computer-Aided Design and Applications 6(1):91-102
Liu L,Zhang L,Lin B,Wang G (2009) Fast approach for computing roots of polynomials using cubic clipping Computer Aided Geometric Design 26(5):547-559 [Journal]
Lo SH (1995) Automatic mesh generation over intersecting surfaces International Journal for Numerical Methods in Engineering 38(6):943-954 [Journal]
Lorensen HE (1987) Marching cubes: a high resolution 3D surface construction algorithm ACM Siggraph Computer Graphics 21:163-169
Maekawa T,Patrikalakis NM,Sakkalis T,Yu G (1998) Analysis and applications of pipe surfaces Computer Aided Geometric Design 15(5):437-458
McDonald CG, Eppolito AK, Brielmaier JM, Smith LN, Bergstrom HC, Lawhead MR, Smith RF (2007) Evidence for elevated nicotine-induced structural plasticity in nucleus accumbens of adolescent rats. Brain Res 1151:211-8 [Journal] [PubMed]
McDougal RA, Hines ML, Lytton WW (2013) Water-tight membranes from neuronal morphology files. J Neurosci Methods 220:167-78 [Journal] [PubMed]
   Constructed Tessellated Neuronal Geometries (CTNG) (McDougal et al. 2013) [Model]
Moerschel K (2013) AnaMorph: a framework for geometric modelling consistency analysis and surface mesh generation of anatomically reconstructed neuron morphologies Diploma thesis, Goethe-Universität Frankfurt am Main
Nielson GM (2004) Dual marching cubes Proceedings of the conference on visualization ’04, IEEE Computer Society, Washington, DC, USA, VIS ’04 :489-496 [Journal]
Patrikalakis NM,Maekawa T (2002) Shape interrogation for computer aided design and manufacturing
Queisser G, Wiegert S, Bading H (2011) Structural dynamics of the cell nucleus: basis for morphology modulation of nuclear calcium signaling and gene transcription. Nucleus 2:98-104 [Journal] [PubMed]
Reiter S (2012) ProMesh – meshing of unstructured grids in 1, 2, and 3 dimensions.
Reiter S (2014) Effiziente Algorithmen und Datenstrukturen für die Realisierung von adaptiven hierarchischen Gittern auf massiv parallelen Systemen. PhD thesis, Universität Frankfurt am Main
Rossignac JR (1985) Blending and offsetting solid models (cad/cam, computational geometry, representations, curves, surfaces, approximation). Phd Thesis, The University of Rochester, aAI8528560
Schroeder W,Martin KM,Lorensen WE (2006) The visualization toolkit (4th ed.). Kitware
Schulz C (2009) Bézier clipping is quadratically convergent Computer Aided Geometric Design 26(1):61-74 [Journal]
Sederberg T,Nishita T (1990) Curve intersection using Bézier clipping Computer-Aided Design 22(9):538-549 [Journal]
Shemer I, Brinne B, Tegnér J, Grillner S (2008) Electrotonic signals along intracellular membranes may interconnect dendritic spines and nucleus. PLoS Comput Biol 4:e1000036 [Journal] [PubMed]
Si H (2015) TetGen, a Delaunay-based quality tetrahedral mesh generator ACM Transactions on Mathematical Software 41(2):11:1-11:36 [Journal]
Vogel A,Reiter S,Rupp M,Nägel A,Wittum G (2013) UG 4: a novel flexible software system for simulating PDE based models on high performance computers Computing and Visualization in Science 16(4):165-179 [Journal]
Vollmer J,Mencl R,Müller H (1999) Improved laplacian smoothing of noisy surface meshes Computer graphics forum :131-138
Vuksic M, Del Turco D, Bas Orth C, Burbach GJ, Feng G, Müller CM, Schwarzacher SW, Deller T (2008) 3D-reconstruction and functional properties of GFP-positive and GFP-negative granule cells in the fascia dentata of the Thy1-GFP mouse. Hippocampus 18:364-75 [Journal] [PubMed]
Wittmann M, Queisser G, Eder A, Wiegert JS, Bengtson CP, Hellwig A, Wittum G, Bading H (2009) Synaptic activity induces dramatic changes in the geometry of the cell nucleus: interplay between nuclear structure, histone H3 phosphorylation, and nuclear calcium signaling. J Neurosci 29:14687-700 [Journal] [PubMed]
(49 refs)