The objective of SP1 is to generate neuroscientific concepts, knowledge, experimental datasets and tools, which will be used to build models for the simulation of the brain.

An important role for SP1 is to provide data and knowledge to support activities undertaken by other SPs. The mouse remains the model of choice to investigate human brain function because it is possible to directly study genetic, molecular and cellular biological processes, including neuronal and glial physiology and cognitive processes, in living animals, as well as in valid genetic models of human disease. From the outset of the HBP, we recognized that it was not feasible to study all aspects of mouse biology at the same time. We therefore proposed a phased strategy with long-term milestones and objectives, and the Project was designed to evolve accordingly.

During the Ramp-Up Phase, we established valid methods to be used for mapping the mouse brain, including: an optimized clarity method for clearing of brain samples; 3D automated electron microscopy techniques; intracellular injections, cell physiology and 3D reconstructions; and, visualization tools and mathematical models for micro-anatomical data. We also delivered a first draft of strategic mouse brain datasets across the key domains of transcriptome, proteome, neuroanatomy, channel function and behavior, as well as data aggregation, integration and dissemination of data. These initial studies established a strong foundation for the development of the HBP platforms, particularly the Neuroinformatics Platform (SP5) and Brain Simulation Platform (SP6), and the data generated was uploaded to the HBP Mouse Brain Atlas.

SP1 is currently focused on four major brain circuits: neocortex (including the thalamocortical system), hippocampus, basal ganglia and cerebellum, and to examine the molecular, genetic and anatomical patterns separately in particular regions.

In line with the long-term strategy and objectives of the HBP, our immediate future plan is to continue acquiring strategic data focusing on the following considerations:

  1. use of the developed techniques to obtain high quality integrative maps of the mouse brain at the molecular and anatomical level, including maps of vasculature and different cellular types;
  2. inter-domain and microcircuitry analyses, including proteins and receptor distributions and fibre architecture;
  3. spatial organization principles and whole-brain activation maps related to selected behaviours;
  4. reconstructed morphologies of neuron types, including maps of cellular distributions, axonal projections and synaptic proteins;
  5. generation of realistic computational models by establishing new methodologies to study the brain and by promoting interdisciplinary collaboration.


SP Leader: Javier DEFELIPE

Deputy SP Leaders: Egidio D'ANGELOSten GRILLNER

Work Package Leaders:


Publication highlights:

Bielza, C., Benavides-Piccione, R., López-Cruz, P., Larranaga, P., & DeFelipe, J. (2014). Branching angles of pyramidal cell dendrites follow common geometrical design principles in different cortical areasScientific Reports4: 5909.

Chiovini, B., Turi, G.F., Katona, G., Kaszás, A., Pálfi, D., Maák, P., Gergely Szalay, G., Szabó, M.F., Szabó, G., Szadai Z., Káli, S. & Rózsa, B. (2014). Dendritic spikes induce ripples in parvalbumin interneurons during hippocampal sharp wavesNeuron82: 908-924.

Costantini, I., Ghobril, J.P., Di Giovanna, A.P., Mascaro, A.L.A., Silvestri, L., Müllenbroich, M.C., Onofri, L., Conti, V., Vanzi, F., Sacconi, L., Guerrini, R., Markram, H., Iannello, G. & Pavone, F.S. (2015). A versatile clearing agent for multi-modal brain imaging. Scientific Reports, 5: 9808.