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Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex

Lida Kanari, Idan Segev, Guy Antoine Atenekeng Kahou, Guy Eyal, Yair Deitcher

There have been few quantitative characterizations of the morphological, biophysical, and cable properties of neurons in the human neocortex. We employed feature-based statistical methods on a rare data set of 60 3D reconstructed pyramidal neurons from L2 and L3 in the human temporal cortex (HL2/L3 PCs) removed after brain surgery. Of these cells, 25 neurons were also characterized physiologically. Thirty-two morphological features were analyzed (e.g., dendritic surface area, 36 333 +/- 18 157 mu m(2); number of basal trees, 5.55 +/- 1.47; dendritic diameter, 0.76 +/- 0.28 mu m). Eighteen features showed a significant gradual increase with depth from the pia (e.g., dendritic length and soma radius). The other features showed weak or no correlation with depth (e.g., dendritic diameter). The basal dendritic terminals in HL2/L3 PCs are particularly elongated, enabling multiple nonlinear processing units in these dendrites. Unlike the morphological features, the active biophysical features (e.g., spike shapes and rates) and passive/cable features (e.g., somatic input resistance, 47.68 +/- 15.26 M Omega, membrane time constant, 12.03 +/- 1.79 ms, average dendritic cable length, 0.99 +/- 0.24) were depth-independent. A novel descriptor for apical dendritic topology yielded 2 distinct classes, termed hereby as "slim-tufted" and "profusetufted" HL2/L3 PCs; the latter class tends to fire at higher rates. Thus, our morpho-electrotonic analysis shows 2 distinct classes of HL2/L3 PCs.

Oxford University Press2017

Framework for efficient synthesis of spatially embedded morphologies

Lida Kanari, Julian Charles Shillcock, Liesbeth Maria L Vanherpe, Guy Antoine Atenekeng Kahou, Juan Pablo Palacios

Many problems in science and engineering require the ability to grow tubular or polymeric structures up to large volume fractions within a bounded region of three-dimensional space. Examples range from the construction of fibrous materials and biological cells such as neurons, to the creation of initial configurations for molecular simulations. A common feature of these problems is the need for the growing structures to wind throughout space without intersecting. At any time, the growth of a morphology depends on the current state of all the others, as well as the environment it is growing in, which makes the problem computationally intensive. Neuron synthesis has the additional constraint that the morphologies should reliably resemble biological cells, which possess nonlocal structural correlations, exhibit high packing fractions, and whose growth responds to anatomical boundaries in the synthesis volume. We present a spatial framework for simultaneous growth of an arbitrary number of nonintersecting morphologies that presents the growing structures with information on anisotropic and inhomogeneous properties of the space. The framework is computationally efficient because intersection detection is linear in the mass of growing elements up to high volume fractions and versatile because it provides functionality for environmental growth cues to be accessed by the growing morphologies. We demonstrate the framework by growing morphologies of various complexity.

Amer Physical Soc2016

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex

Henry Markram, Sean Lewis Hill, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, Daniel Keller, Werner Alfons Hilda Van Geit, James Gonzalo King, Marwan Muhammad Ahmed Abdellah, Lida Kanari, Julian Charles Shillcock, Ying Shi, Jean-Denis Georges Emile Courcol, Rajnish Ranjan, John Richard Walker, Michael Emiel Gevaert, Idan Segev, Yun Wang, Giuseppe Chindemi, Juan Bautista Hernando Vieites, Stefan Eilemann, Martin Telefont, Ahmet Bilgili, Guy Antoine Atenekeng Kahou, Nicolas Antille, Raphael Dumusc, Jeffrey Christopher Muller, Jafet Villafranca Diaz, Selim Arsever, Joseph William Graham, Athanassia Chalimourda, Stefano Zaninetta, Yury Brukau, Stanislaw Ryszard Adaszewski

We have established a multi-constraint, data-driven process to digitally reconstruct, and simulate prototypical neocortical microcircuitry, using sparse experimental data. We applied this process to reconstruct the microcircuitry of the somatosensory cortex in juvenile rat at the cellular and synaptic levels. The resulting reconstruction is broadly consistent with current knowledge about the neocortical microcircuit and provides an array of predictions on its structure and function. To engage the community in exploring, challenging, and refining the reconstruction, we have developed a collaborative, internet-accessible facility-the Neocortical Microcircuit Collaboration portal (NMC portal; https://bbp.epfl.ch/nmc-portal). The NMC portal allows users to access the experimental data used in the reconstruction process, download cellular and synaptic models, and analyze the predicted properties of the microcircuit: six layers, similar to 31,000 neurons, 55 morphological types, 11 electrical types, 207 morpho-electrical types, 1941 unique synaptic connection types between neurons of specific morphological types, predicted properties for the anatomy and physiology of similar to 40 million intrinsic synapses. It also provides data supporting comparison of the anatomy and physiology of the reconstructed microcircuit against results in the literature. The portal aims to catalyzee consensus on the cellular and synaptic organization of neocortical microcircuitry (ion channel, neuron and synapse types and distributions, connectivity, etc.). Community feedback will contribute to refined versions of the reconstruction to be released periodically. We consider that the reconstructions and the simulations they enable represent a major step in the development of in silica neuroscience.

Frontiers Research Foundation2015