Papers using or about Topographica

Journal Articles

• Ryan T. Philipps and V. Srinivasa Chakravarthy. The mapping of eccentricity and meridional angle onto orthogonal axes in the primary visual cortex: An activity-dependent developmental model. Frontiers in Computational Neuroscience, 2015. In press.
• Jean-Luc R. Stevens and James A. Bednar. An automated and reproducible workflow for running and analyzing neural simulations using Lancet and IPython Notebook. Frontiers in Neuroinformatics, 7:44, 2013.
• Jan Antolik and Andrew Davison. Integrated workflows for spiking neuronal network simulations. Frontiers in Neuroinformatics, 2013, 7:34. (Uses Param and ImaGen.)
• Jean-Luc R. Stevens, Judith S. Law, Jan Antolik, and James A. Bednar. Mechanisms for stable, robust, and adaptive development of orientation maps in the primary visual cortex. Journal of Neuroscience, 33:15747-15766, 2013.
• James A. Bednar. Building a mechanistic model of the development and function of the primary visual cortex. Journal of Physiology (Paris), 106:194-211, 2012.
• Alessio Plebe. A model of the response of visual area V2 to combinations of orientations. Network, 23(3):105-122, 2012.
• Jan Antolik and James A. Bednar. Development of maps of simple and complex cells in the primary visual cortex. Frontiers in Computational Neuroscience, 5:17, 2011.
• Stuart P. Wilson, Judith S. Law, Ben Mitchinson, Tony J. Prescott, and James A. Bednar. Modeling the emergence of whisker direction maps in rat barrel cortex. PLoS One, 5(1):e8778, 2010.
• James A. Bednar. Topographica: Building and analyzing map-level simulations from Python, C/C++, MATLAB, NEST, or NEURON components. Frontiers in Neuroinformatics, 3:8, 2009.
• James A. Bednar. Understanding neural maps with Topographica. Brains, Minds, and Media, 3:bmm1402, 2008.
• James A. Bednar, Yoonsuck Choe, Judah De Paula, Risto Miikkulainen, Jefferson Provost, and Tal Tversky. Modeling cortical maps with Topographica. Neurocomputing, pages 1129-1135, 2004.
• James A. Bednar, Amol Kelkar, and Risto Miikkulainen. Scaling self-organizing maps to model large cortical networks. Neuroinformatics, 2:275-302, 2004.

Book Chapters

• James A. Bednar and Christopher E. Ball. Topographica. In Eugene M. Izhikevich, editor, The Encyclopedia of Computational Neuroscience. Scholarpedia, 2014. In preparation.
• James A. Bednar. Topographica. In Dieter Jaeger and Ranu Jung, editors, The Encyclopedia of Computational Neuroscience. Springer, 2014.
• James A. Bednar. Constructing complex systems via activity-driven unsupervised Hebbian self-organization. In Growing Adaptive Machines: Combining Development and Learning in Artificial Neural Networks, Studies in Computational Intelligence. Springer, Berlin, 2014.

Conference Papers

• Jaewook Yoo, Jinho Choi, and Yoonsuck Choe. Development of target reaching gesture map in the cortex and its relation to the motor map: A simulation study. In Advances in Self-Organizing Maps: Proceedings of the 10th International Workshop, pages 187-197. Springer, 2014.
• James A. Bednar. Visual cortex as a general-purpose information-processing device. In A. Fusiello et al., editors, ECCV 2012 Workshops, Part I, Lecture Notes in Computer Science 7583, pages 480-485, Berlin, 2012. Springer.
• Choonseog Park, Yoon H. Bai, and Yoonsuck Choe. Tactile or visual?: Stimulus characteristics determine receptive field type in a self-organizing map model of cortical development. In Proceedings of the 2009 IEEE Symposium on Computational Intelligence for Multimedia Signal and Vision Processing, pages 6-13, 2009. Best Student Paper Award.
• Choonseog Park, Heeyoul Choi, and Yoonsuck Choe. Tactile receptive fields: Exploring their textural origin and their representational properties. In Advances in Self-Organizing Maps: Proceedings of the 7th International Workshop, pages 228-236. Springer, 2009.
• Alessio Plebe, Vivian De la Cruz, and Marco Mazzone. Artificial learners of objects and names. In Development and Learning, 2007. ICDL 2007. IEEE 6th International Conference on, pages 300-305, 2007.

PhD Theses

• Stuart P. Wilson. Figuring Time by Space: Representing Sensory Motion in Cortical Maps. PhD thesis, Department of Psychology, The University of Sheffield, Sheffield, UK, 2011. Co-supervised with Tony J. Prescott.
• Chen Zhao. Neural Mechanisms for Face and Orientation Aftereffects. PhD thesis, School of Informatics, The University of Edinburgh, Edinburgh, UK, 2011.
• Jan Antolik. Unified Developmental Model of Maps, Complex Cells and Surround Modulation in the Primary Visual Cortex. PhD thesis, School of Informatics, The University of Edinburgh, Edinburgh, UK, 2010.
• Judith S. Law. Modeling the Development of Organization for Orientation Preference in Primary Visual Cortex. PhD thesis, School of Informatics, The University of Edinburgh, Edinburgh, UK, 2009.
• Christopher M. Palmer. Topographic and Laminar Models for the Development and Organisation of Spatial Frequency and Orientation in V1. PhD thesis, School of Informatics, The University of Edinburgh, Edinburgh, UK, 2009.

MSc Theses

• Tobias Fischer. Model of all known spatial maps in primary visual cortex. Master’s thesis, The University of Edinburgh, Scotland, UK, 2014.
• Giacomo Spigler. Neural modelling of the McCollough Effect in Colour Vision. Master’s thesis, The University of Edinburgh, Scotland, UK, 2014.
• Annabelle Gee. Neural Modelling of Congenitally Abnormal Visual Pathways. Master’s thesis, The University of Edinburgh, Scotland, UK, 2014.
• Bharath Chandra Talluri. Characterising the Properties of Natural and Laboratory Animal-Rearing Environments and Their Impact on Models of Visual Cortex Development. Master’s thesis, The University of Edinburgh, Scotland, UK, 2013.
• Yvonne Kneisel. Feasibility of random wiring in primate colour vision. Master’s thesis, The University of Edinburgh, Scotland, UK, 2013.
• Gautham Ganapathy. Reconciling models of visual cortex development with anatomical patterns of lateral connectivity. Master’s thesis, The University of Edinburgh, Scotland, UK, 2011.
• Bilal Khan. Modelling the pathway to auditory cortex. Master’s thesis, The University of Edinburgh, Scotland, UK, 2011.
• Konstantin Kudryavtsev. High performance cortical simulator. Master’s thesis, The University of Edinburgh, Scotland, UK, 2011.
• Ravikiran Mattaparthi. User interface with real-world units. Master’s thesis, The University of Edinburgh, Scotland, UK, 2011.
• Jean-Luc Stevens. A temporal model of neural activity and VSD response in the primary visual cortex. Master’s thesis, The University of Edinburgh, Scotland, UK, 2011.
• John Jacob. Enhancing the performance of a cortical simulator by running it on a graphics processing unit. Master’s thesis, The University of Edinburgh, Scotland, UK, 2009.
• Kateryna Gerasymova. Computational model of all known feature maps in the primary visual cortex. Master’s thesis, Humboldt-Universitaet zu Berlin, Germany, 2008.
• Stuart P. Wilson. Self-organisation can explain the mapping of angular whisker deflections in the barrel cortex. Master’s thesis, The University of Edinburgh, Scotland, UK, 2007.
• Veldri Kurniawan. Self-organizing visual cortex model using a homeostatic plasticity mechanism. Master’s thesis, The University of Edinburgh, Scotland, UK, 2006.
• Chok Ming Ng. Topographica model of somatosensory cortex. Master’s thesis, The University of Edinburgh, Scotland, UK, 2006.
• Tikesh Ramtohul. A self-organizing model of disparity maps in the primary visual cortex. Master’s thesis, The University of Edinburgh, Scotland, UK, 2006.

Please send citations for any Topographica papers not listed above to Jim Bednar so that they can be included here.