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The microcircuits of striatum in silico

Authors: Johannes Hjorth2,*, Alexander Kozlov1,2,*, Ilaria Carannante2,**, Johanna Frost Nylén1,**, Robert Lindroos1,2,**, Yvonne Johansson1,***, Anna Tokarska1,***, Matthijs C. Dorst1,***, Shreyas M Suryanarayana1, Gilad Silberberg1, Jeanette Hellgren Kotaleski2,****, Sten Grillner1,****

Author information: 1Department of Neuroscience, Karolinska Institutet, SE 17165 Stockholm and 2Science for Life Laboratory, School of Computer Science and Communication, KTH Royal Institute of Technology, SE-10044, Stockholm, Sweden.

*JH and AK, overall design of the striatal simulation (equal contribution); **IC, JFN and RL contributed equally in simulating different subtypes of neurons and reconstructing their morphology and the dopaminergic input; ***YJ, AT and MD recorded experimentally subtypes of neurons and their connectivity that were modelled by the other team (equal contribution); SMS contributed with overall implementation; GS supervised the experimental part; ****JHK and SG supervised all aspects of the project (equal contribution).

Corresponding author: Sten Grillner (

Journal: Proc. Natl. Acad. Sci. USA

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Citation: Hjorth J, Kozlov A, Carannante I, Frost Nylén J, Lindroos R, Johansson Y, Tokarska A, Dorst MC, Suryanarayana SM, Silberberg G, Hellgren Kotaleski J, Grillner S (2020) The microcircuits of striatum in silico. Proc Natl Acad Sci USA 2020.


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The basal ganglia play an important role in decision-making and selection of action primarily based on input from cortex, thalamus and the dopamine system. Their main input structure, striatum, is central to this process. It consists of two types of projection neurons, together representing 95% of the neurons, and 5% of interneurons, among which are the cholinergic, fastspiking and low threshold spiking subtypes. The membrane-properties, soma-dendritic shape and intrastriatal- and extrastriatal synaptic interactions of these neurons are quite well described in the mouse, and therefore they can be simulated in sufficient detail to capture their intrinsic properties, as well as the connectivity. We focus on simulation at the striatal cellular/microcircuit level, in which the molecular/subcellular and systems levels meet. We present for the first time a nearly full-scale model of the mouse striatum using available data on synaptic connectivity, cellular morphology and electrophysiological properties to create a microcircuit mimicking the real network. A striatal volume is populated with reconstructed neuronal morphologies with appropriate cell densities, and then we connect neurons together based on appositions between neurites as possible synapses and constrain them further with available connectivity data. Moreover, we simulate a subset of the striatum involving 10 000 neurons, with input from cortex, thalamus and the dopamine system, as a proof of principle. Simulation at this biological scale should serve as an invaluable tool to understand the mode of operation of this complex structure. This platform will be updated with new data and expanded to simulate the entire striatum.

Data and models used in the paper are available at the links reported below.