A Model of Rodent Neocortical Micro- and Mesocircuitry
Creators
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Isbister, James B.1
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Ecker, András1
- Pokorny, Christoph1
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Bolaños-Puchet, Sirio1
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Egas Santander, Daniela1
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Arnaudon, Alexis1
- Awile, Omar1
- Barros-Zulaica, Natali1
- Blanco Alonso, Jorge1
- Chindemi, Giuseppe1
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Courcol, Jean-Denis1
- Damart, Tanguy1
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Delemontex, Thomas1
- Dietz, Alexander1
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Ficarelli, Gianluca1
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Gevaert, Michael1
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Herttuainen, Joni1
- Ivaska, Genrich1
- Ji, Weina1
- Keller, Daniel1
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King, James1
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Kumbhar, Pramod1
- Lapere, Samuel1
- Litvak, Polina1
- Mandge, Darshan1
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Muller, Eilif B.1
- Pereira, Fernando1
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Planas, Judit1
- Ranjan, Rajnish1
- Reva, Maria1
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Romani, Armando1
- Rössert, Christian1
- Schürmann, Felix1
- Sood, Vishal1
- Teska, Aleksandra1
- Tuncel, Anil1
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Van Geit, Werner1
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Wolf, Matthias1
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Markram, Henry1
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Ramaswamy, Srikanth1
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Reimann, Michael W.1
- 1. Blue Brain Project, EPFL, Switzerland
Description
We present a data-driven computational model of the anatomy and physiology of non-barrel primary somatosensory cortex of juvenile rat. The modeling process is based on a previously established workflow for a single cortical column, but is extended here to build a much larger circuit in an atlas-based geometry. Neurons in the model belong to 60 different morphological types and are connected by synapses placed by two established algorithms, one modeling local connectivity determined by axo-dendritic overlap, and one for long-range connectivity between sub-regions. Long-range connectivity is defined with topographic mapping and laminar connectivity profiles, providing intrinsic feed-forward and feedback pathways. Additionally, we incorporate core- and matrix-type thalamocortical projection systems, associated with VPM and POm thalamic nuclei respectively, that enable extrinsic input.
The full model contains over 4 million modeled neurons. Due to the immense size of that data, it is hard to publish it in its entirety. Here we release a 1.5 mm diameter subset of the full volume comprising 211712 neurons in the front limb and jaw subregions and the dysgranular zone of the Paxinos & Watson rat brain atlas.
To get access to the full model (or other parts of the model) contact one of the lead authors of the accompanying publication.
The model is formatted in the open SONATA standard and contains neuron locations and their properties (such as morphological types, cortical layer, etc.), their detailed morphologies, and synaptic connectivity associated with all systems described above. Modeled synapses are associated with their exact location in the dendritic tree, and additional anatomical parameters, such as spine length (where biologically plausible). Extrinsic synaptic connections from neurons in the remainder of non-barrel somatosensory cortex and thalamic inputs are also contained.
This model can be simulated. We will provide exemplary simulations and instruction how to run them in a separate dataset.
The model can be analyzed in terms of its anatomy, physiology and connectivity using the packages NeuroM and BlueBrain SNAP. Exemplary jupyter notebooks of instructive analyses are included.
Creation of this model was supported by funding to the Blue Brain Project, a research center of the Ecole polytechnique federale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.
Notes
Files
Analyze connectivity reach.ipynb
Additional details
Related works
- Continues
- Dataset: 10.5281/zenodo.6906784 (DOI)