The biological function of cortical neurons can often be understood only in the context of large, highly interconnected networks of neurons. These networks typically form two-dimensional topographic maps, such as the retinotopic maps in the visual system. As part of the Human Brain Project, we are developing a general-purpose simulator called Topographica to allow neuroscientists and computational scientists to understand brain function at this level. At the same time, we are using Topographica in our own research into how the visual cortex develops.
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Topographica complements the many good low-level neuron simulators that are available, such as Genesis, Neuron, NeoSIM, and Catacomb. Those simulators focus on modeling the detailed internal behavior of neurons and small networks of them. Topographica instead focuses on the large-scale structure and function that is visible when many thousands of such neurons are connected into maps containing millions of connections. Important phenomena that cannot be studied without such large networks include the two-dimensional organization of visual orientation and motion direction maps, as well as object segmentation and recognition.
To make such models practical, in Topographica the fundamental unit is a map rather than a neuron or a part of a neuron. For most simulations, the maps can be implemented at a high level, consisting of abstract firing-rate or integrate-and-fire neurons. When required for validation or for specific phenomena, Topographica will also interface to maps developed using more detailed neuron models running in other simulators. Less-detailed maps can also be used temporarily, e.g. when interacting with the model in real time. Throughout, Topographica makes it simple to use an appropriate level of detail and complexity, as determined by the available computing power, phenomena of interest, and amount of biological data available for validation.
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Topographica is still under development, but prototype versions have proven useful for simulating large networks that would not otherwise be practical to study. For example, the figure below shows an example Topographica model of the early stages in the visual system, modeling how retinal input is transformed by the thalamus, primary visual cortex, and higher cortical areas.
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