Neuronal networks are the physical substrate of the information flow inside the brain. In LNMC we are interested in neuronal micro- and mesoscale connectivity, since this connectitvity defines the paths of information flow within and acros brain structures. In particular, we wish to classify, quantify and reconstruct the neuronal micro- and meso scale connectivity of the rodent brain with standardized neuroanatomical methods. To map the micro scale connectivity we use neurolucida to digitally reconstruct individual neurons in 3D. We presently have almost 1000 neuron reconstructions, which can be used to identify the physical constraints and most likely targets of local connectivity [1]. In combination with paired electrophysiological recordings this data is used to map local connectivity of cortical microcircuits. We are also currently developing new techniques for whole mount imaging, with the aim to map meso scale afferent and efferent projections of the primary somatosensory cortex.


Single cell Reconstruction

We routinely stain and reconstruct biocytin filled, electrophysiologically characterized cells in acute slice preparations. Continued effort in this direction has so far generated a database of approximately 1000 reconstructed unique cell morphologies. This resulting dataset forms the basis of all generative algorithms used by the Blue Brain Project to create unique virtual cells used in their cortical simulations. Together with gene expression data and electrophysiological characterization we hope to fully characterize neocortical cell populations


Immunohistochemical characterization of neuron subtypes

Different neuron subtypes express different combinations of genes and proteins. The expression of these protein markers can be visualized and used to identify different neuronal populations in brain slices. We routinely use immunohistochemistry (IHC), 3D confocal microscopy and stereological methods to calculate cell densities of different neuron populations in different regions of the brain. Combining IHC data with the single-cell gene expression data will allow us to map the anatomical distribution of neuronal populationes defined by their gene expression profiles.

Selected References

Modeling and simulation of rat non-barrel somatosensory cortex. Part I: Modeling anatomy

M. Reimann; S. Bolaños Puchet; J-D. Courcol; D. Egas Santander; A. Arnaudon et al. 

bioRxiv. 2022. DOI : 10.1101/2022.08.11.503144.

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

S. Ramaswamy; J-D. Courcol; M. Abdellah; S. R. Adaszewski; N. Antille et al. 

Frontiers In Neural Circuits. 2015. Vol. 9, p. 44. DOI : 10.3389/fncir.2015.00044.

An algorithm to predict the connectome of neural microcircuits

M. W. Reimann; J. G. King; E. B. Muller; S. Ramaswamy; H. Markram 

Frontiers In Computational Neuroscience. 2015. Vol. 9, p. 120. DOI : 10.3389/fncom.2015.00120.

Reconstruction and Simulation of Neocortical Microcircuitry

H. Markram; E. Muller; S. Ramaswamy; M. W. Reimann; M. Abdellah et al. 

Cell. 2015. Vol. 163, num. 2, p. 456-492. DOI : 10.1016/j.cell.2015.09.029.