Exploring Open Brain Platform: A Collaborative Platform for Computational Neuroscience, from single cells to circuits

Open Brain Institute

Brief Description
Computational neuroscience increasingly relies on open-access data, tools, and workflows to build,
simulate, and analyze brain models. The Open Brain Institute (OBI) offers a state-of-the-art platform
(https://www.openbraininstitute.org) that provides a collaborative environment to drive scientific
discovery, enabling researchers to work together seamlessly across disciplines. OBI streamlines
computational neuroscience research by enabling standardized experiments within a controlled and
consistent cloud-based infrastructure, fostering reproducibility and efficiency across the community.
This tutorial will provide participants with a hands-on introduction to the core functionalities of the
Open Brain Platform (OBP), including the exploration and analysis of single-cell morphological and
electrophysiological datasets, the construction of biophysically detailed neuron models, and the
simulation and analysis of small neural circuits. Attendees will gain practical experience navigating
OBP’s diverse features at both the single-cell and network levels, through powerful computational
tools to accelerate their research through standardized and reproducible workflows. Finally, we will
highlight the platform’s expanding capabilities, including region-to-region brain interactions, AI-driven
discovery for collaborative exploration, and the potential to accelerate breakthroughs in computational
neuroscience.

Detailed program

9:00–9:10 Exploration of the Open Brain Platform (Lida Kanari)
9:10–9:55 What makes human brains unique? Interactive topological analysis of neuronal morphologies (Lida Kanari)
9:55–10:10 Introduction and interactive demonstration to Single Cell Biophysical Modeling (Darshan Mandge)
Coffee break
10:40–11:10 The Age of Biophysics and Connectomics (Idan Segev)
11:10–11:40 From Spines to Synapses: Simulating the First Full EM Neuron in the Open Brain Platform (Sapir Shapira)
11:40–11:50 Inside Human Wiring Networks: Analyzing the Harvard EM Connectome (Lida Kanari)
11:50–12:20 Interactive Demonstration: Investigating Proximal vs. Distal Dendritic Inhibition using the Open Brain Platform (Darshan Mandge)
Lunch break
14:00–14:30 General Biophysically-detailed Brain Models: predictions in cortical plasticity, neural coding, and spike sorting in a single model (James Isbister)
14:30–15:00 Modeling Human Cortical Microcircuits in Depression and Aging (Alexandre Guet-McCreight)
15:00–15:40 Interactive demonstration: Analysis and simulation of atlas-based cortical and hippocampal circuits on the Open Brain Platform (James Isbister and Armando Romani)
Coffee break
16:00 Discussion

List of speakers

Alexandre Guet-McCreight, Postdoctoral Research Fellow, Krembil Centre for Neuroinformatics, CAMH
James Isbister, Scientist, Open Brain Institute, Lausanne, Switzerland
Lida Kanari, Early-Career Investigator, EPFL, Open Brain Institute, Lausanne, Switzerland
Darshan Mandge, Scientist, Open Brain Institute, Lausanne, Switzerland
Armando Romani, Early-Career Investigator, Open Brain Institute, Lausanne, Switzerland
Idan Segev, Professor, The Edmond and Lily Safra Center for Brain Sciences, the Hebrew University of Jerusalem, Israel.
Sapir Shapira, PhD Student, Hebrew University, Edmond J. Safra Campus, Jerusalem, Israel

Requirements to attend

Please bring your laptop! 

Related publications 

Kanari et al. 2024
Reimann et al. 2024
Isbister et al. 2023

Title: Population activity : the influence of cell-class identity, synaptic dynamics, plasticity and adaptation.

Organizers: 
Michele GIUGLIANO (co-organizer)
Università degli Studi di Modena e Reggio Emilia - Dipartimento di Scienze Biomediche, Metaboliche e Neuroscienze sede ex-Sc. Biomediche - Italy
michele.giugliano@unimore.it

Simona OLMI (co-organizer)
Institute for Complex Systems - National Research Council - Italy
simona.olmi@fi.isc.cnr.it

Alessandro TORCINI (co-organizer)
Laboratoire de Physique Théorique et Modélisation - CY Cergy Paris Université- Cergy-Pontoise, France
alessandro.torcini@cyu.fr

Abstract:
In recent years tremendous developments have been achieved in the comprehension of neural activity at the population level. This has been possible on one side thanks to the new investigation methods recently developed (e.g. the neuropixels probes and large-scale imaging) that allows for the contemporary registration of the activity of (tens/hundreds of) thousands of neurons in alive and behaving mice as well as established dynamic-clamp protocols.
On the other side by the elaboration of extremely refined mean field models able to describe the population activity of spiking neural networks encompassing realistic biological features, from different forms of synaptic dynamics to plastic and adaptive aspects present at the neural level.
The aim of this workshop is to gather neuroscientists, mathematicians, engineers, and physicists all working on the characterization of the population activity from different point of views, ranging from data analysis of experimental results to simulations of large ensembles of neurons, from next generation neural mass models to dynamical mean field theories. This workshop will favour the exchanges and the discussion on extremely recent developments in this extremely fluorishing field.

Key Words : Neuropixels probes; neural mass models; Fokker Planck formulation; dynamical mean field theory; short- term and long-term plasticity; excitatory and inhibitory balanced networks; spike frequency adaptation

Program:
July 8th -- Room 4
9:15-9:30 Opening
9:30-10:00 Anna Levina (University of Tübingen, Germany)
Talk title: "Balancing Excitation and Inhibition in connectivity and synaptic strength"
10:00-10:30 Giacomo Barzon (Padova Neuroscience Center, University of Padova, Italy)
Talk title: "Optimal control of neural activity in circuits with excitatory-inhibitory balance"

10:30-11:00 Coffee break

11:00-11:30 Eleonora Russo (Scuola Superiore Sant'Anna, The BioRobotics Institute, Italy)
Talk title “Integration of rate and phase codes by hippocampal cell-assemblies supports flexible encoding of spatiotemporal context”
11:30-12:00 Tobias Kühn (University of Bern, Switzerland)
Talk title: "Discrete and continuous neuron models united in field theory: statistics, dynamics and computation"
12:00-12:30 Gianluigi Mongillo (Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France)
Talk title: “Synaptic encoding of time in working memory”

July 9th -- Room Hall 1A
9:30 - 10:00 Magnus J.E. Richardson (Warwick Mathematics Institute, UK)
Talk title: "Spatiotemporal integration of stochastic synaptic drive within neurons and across networks"
10:00-10:30 Gianni Valerio Vinci (Istituto Superiore di Sanita’, Rome, Italy)
Talk title: "Noise induced phase transition in cortical neural field: the role of finite-size fluctuations"

10:30-11:00 Coffee break

11:00-11:30 Simona Olmi (Institute for Complex Systems - National Research Council - Italy)
Talk title: “Relaxation oscillations in next-generation neural masses with spike-frequency adaptation”
11:30-12:00 Ferdinand Tixidre (CY Cergy Paris University, France)
Talk title: "Is the cortical dynamics ergodic? A numerical study in partially-symmetric networks of spiking neurons"
12:00-12:30 Letizia Allegra Mascaro (Neuroscience Institute, National Research Council, Italy)
Talk title: "State-Dependent Large-Scale Cortical Dynamics in Neurotypical and Autistic Mice"

12:30-14:00 Lunch break

14:00-14:30 Alessandro Torcini (CY Cergy Paris Université- Cergy-Pontoise, France)
Talk title : “Discrete synaptic events induce global oscillations in balanced neural networks"
14:30-15:00 Rainer Engelken (Columbia University, NY, United States)
Talk title:"Sparse Chaos in Cortical Circuits: Linking Single-Neuron Biophysics to Population Dynamics"
15:00-15:30 Tilo Schwalger (Technische Universität Berlin, Institut für Mathematik, Germany)
Talk title: "A low-dimensional neural-mass model for population activities capturing fluctuations, refractoriness and adaptation"

15:30-16:00 Coffee break

16:00-16:30 Giancarlo La Camera (Stony Brook University, NY, United States)
Talk title: “Prefrontal population activity during strategic behavior in context-dependent tasks”
16:30-17:00 Gorka Zamora-López (Universitat Pompeu Fabra, Barcelona, Spain)
Talk title: "Emergence and maintenance of modular hierarchy in neural networks driven by external stimuli"
17:00-17:30 Sacha van Albada (Research Center Juelich and University of Cologne, Germany)
Talk title: "Determinants of population activity in full-density spiking models of cerebral cortex"

Abstracts of the Talks ----------------------------------------------------------------------

Anna Levina (University of Tübingen, Germany)
"Balancing Excitation and Inhibition in connectivity and synaptic strength"

Maintaining a balance between excitation and inhibition (E/I) is fundamental for stable neuronal dynamics and proper brain function. The efforts to maintain this balance are reflected in the conserved ratios of excitatory and inhibitory neurons across different brain regions and development. I will discuss how neuronal networks with artificially altered E/I cell-count ratios can adapt by modifying their connectivity to restore the equilibrium.

At the level of synaptic strength, theoretical studies suggest that a combination of plasticity rules can drive the emergence of E/I co-tuning (detailed balance) in neurons receiving independent, low-noise inputs. I will explore how recurrent network structures influence this process. Furthermore, at the level of single neurons with complex morphologies, I will demonstrate how the spatial distribution of excitatory and inhibitory inputs across the dendritic tree affects both the stability of learned orientation preference and the sharpness of tuning.                   

Giacomo Barzon (Padova Neuroscience Center, University of Padova, Italy)
"Optimal control of neural activity in circuits with excitatory-inhibitory balance"

 Excitatory-inhibitory balance governs how information is processed and transmitted through cortical circuits. In this talk, we show how the input-output properties of a balanced circuit can be naturally explained by control theory. We explain how excitatory-inhibitory interactions sculpt network controllability through the lens of balanced amplification. We capture the spatiotemporal features of cell-type specific control in spatially extended networks by introducing two new observables: controllability horizon and Gramian dimensionality. Extending these insights to networks trained on cognitive tasks, we highlight control theory as a unifying principle for understanding both information processing and causal circuit manipulations.

Eleonora Russo (Scuola Superiore Sant'Anna, The BioRobotics Institute, Ital
“Integration of rate and phase codes by hippocampal cell-assemblies supports flexible encoding of spatiotemporal context”

Spatial information is encoded by location-dependent hippocampal place cell firing rates and sub-second, rhythmic entrainment of spike times. These rate and temporal codes have primarily been characterized in low-dimensional environments under limited cognitive demands; but how is coding configured in complex environments when individual place cells signal several locations, individual locations contribute to multiple routes and functional demands vary? Quantifying CA1 population dynamics of male rats during a decision-making task,  we show that the phase of individual place cells\u2019 spikes relative to the local theta rhythm shifts to differentiate activity in different place fields. Theta phase coding also disambiguates repeated visits to the same location during different routes, particularly preceding spatial decisions. Using unsupervised detection of cell assemblies alongside theoretical simulations, we show that integrating rate and phase coding mechanisms dynamically recruits units to different assemblies, generating spiking sequences that disambiguate episodes of experience and multiplexing spatial information with cognitive context.

Tobias Kühn (University of Bern, Switzerland)
"Discrete and continuous neuron models united in field theory: statistics, dynamics and computation"

Depending on the question at hand, different neuron models are chosen to model the activity in neural networks - amongst the most basic descriptions for example, there are rate neurons and binary neurons. Because the mathematical frameworks for these descriptions are traditionally quite different, a direct comparison has been difficult so far. Here, we develop a generalized path-inte...

Full workshop program

Schedule
9:00-9:30 Fleur Zeldenrust
Heterogeneity, non-linearity and dimensionality: how neuron and network properties shape computation
9:30-10:00 Vassilis Cutsuridis
Synapse strengthening in bistratified cells leads to super memory retrieval in the hippocampus
10:00-10:30 Spyridon Chavlis
Dendrites as nature's blueprint for a more efficient AI
10:30-11:00 Coffee Break
11:00-11:30 Andreas Tolias
Foundation models and digital twins of the brain (online)
11:30-12:00 Robert Legenstein
Spatio-Temporal Processing with Dynamics-enhanced Spiking Neural Networks
12:00-12:30 Max Garagnani
Concept superposition and learning in standard and brain-constrained deep neural networks
12:30-14:00 Lunch
14:00-14:30 Martin Trefzer
Motifs, Modules, and Mutations: Building Brain-like Networks
14:30-15:00 Julian Göltz
From biology to silicon substrates: neural computation with physics
15:00-15:30 Maxim Bazhenov
Do Neural Networks Dream of Electric Sheep?
15:30-16:00  Coffee Break
16:00-16:30 Dhireesha Kudithipudi
Temporal Chunking Enhances Recognition of Implicit Sequential Patterns
16:30-17:00 Thomas Nowotny
Auto-adjoint method for gradient descent in spiking neural networks
17:00-18:00 Questions and Debate
18:00 End of Workshop

Full workshop program