Outcome

The event was a success with around 90 participants (project instigators included) and 9 projects prototypes. You can see below a slideshow of groups hard at work. The results of each project (when available) can be accessed simply by clicking on the associated GitHub icon in the projects section. Courtesy of all the participants supporting Open Science !
PROJECTS

Team

We are here to help. Don't hesitate to ask us any question.

Michael Dayan

Fondation Campus Biotech Geneva

Jelena Brankovic

CERN

Margaux Dubessy

Fondation Campus Biotech Geneva

Victor Ferat

Fondation Campus Biotech Geneva

Speakers

Participating to provide examples of cutting-edge neuroimaging research.



"Sleep as a key factor in the consolidation of memories in children and adults" by Virginie Sterpenich

Recent research has demonstrated that freshly encoded memory traces are replayed during sleep. This mechanism allows information to be integrated into an existing network of representations. During wakefulness, the brain is bombarded with large amounts of information. Thus, to better understand how replay during sleep contributes to memory processes, we need to determine what type of information is prioritized for subsequent replay during sleep. We hypothesized that information with an affective value, which might require long-term behavioral changes, would benefit from offline reprocessing during sleep. Thus, memories of emotionally relevant experiences may have a higher probability of being reprocessed during sleep.

Using simultaneous EEG-fMRI recordings, we measured brain activity while healthy participants played alternating blocks of two distinct games, one of which they would eventually win. We also measured brain activity during different sleeps stages.

Using a neural decoding approach we found that the pattern of brain activity associated with the rewarded game occurs spontaneously during deep sleep and more frequently than the non-rewarded game. These findings suggest a general mechanism whereby the brain selectively consolidates memories with a high value for survival. The replay of relevant memories occurs during a physiological state, i.e. sleep, that is highly favorable for neural plasticity.

"Tracking brain dynamics using human neuroimaging" by Dimitri Van De Ville

Abstract: State-of-the-art magnetic resonance imaging (MRI) provides unprecedented opportunities to study brain structure (anatomy) and function (physiology). Computational methods are key to extract information from this type of data and advance our understanding of brain function or develop markers of dysfunction. I will highlight a few exciting recent trends in neuroimaging research.

"Brain-Computer Interfaces for speech decoding" by Silvia Marchesotti

Aphasia is an impairment in the comprehension and formulation of language caused most commonly by stroke, traumatic brain-injuries, and other pathological conditions affecting the speech production and comprehension. Current neuro-rehabilitation techniques are effective only partially and in a fraction of patients, leaving the remaining in the impossibility to communicate with the external world. During this talk I will present latest advances from our and other research groups, aiming at developing the new generation of speech neuroprosthesis to decode inner speech in real-time from intracranial (ECoG) and surface (EEG/MEG) brain recording.

Projects

Projects can be filered by keywords / skills

  • All
  • Programming
  • Machine Learning
  • MRI
  • EEG
  • Virtual Reality
  • 3D Design
  • Neurosciences

Project 1. Screenless AR-guided Neuronavigation for non-invasive brain stimulation by Olivier Reynaud, Matilde Damiani and Margaux Dubessy

The essence of this project is to develop an augmented reality neuro-navigation device in order to optimize non-invasive brain stimulation (NIBS) techniques using magnetic and/or electronical stimuli (TMS/TDCS). Although NIBS is used to study electrophysiological fundaments of brain function, and is already applied to treat depression, stroke and several other brain pathologies, the technique could benefit from the latest developments in augmented reality to further enhance computer-assisted neuro-navigation. Using augmented reality, the physician / scientist could focus on the precise positioning of the stimulation while keeping the patient / subject in plain sight. Such a system would drastically improve patient AND physician comfort, while targeting specific brain areas with the utmost precision without effort.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 2. EEG microstates neurofeedback by Arnaud Desvachez and Gwenael Birot

Microstates are transient, quasi-stable patterns of eeg scalp topography. It has been shown that psychiatric disorders elicit abnormal quantity of one of these microstates. This project aims at developing a neuro-feedback to regulate this microstate.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 3. Hearing fMRI data by Thomas Bolton and Raphael Liegois

Functional magnetic resonance imaging (fMRI) enables to measure activity time courses at the whole-brain scale. In this project, we will be using standardly preprocessed data of size 360 (brain regions) x 1190 (time points) acquired during the resting-state (i.e., scanned volunteers let their mind wander without performing any external task). The large majority of fMRI analyses ultimately give rise to results figures, which are laid on paper and visually interpreted. Our goal will be to instead generate an audio recording that reflects functional brain processing as a melody. The project will require: 1) The definition of a pipeline to generate such audio data, which may be jointly informed by knowledge about fMRI data and music 2) The implementation of the pipeline, and generation of sound waveforms 3) The analysis of a series of outputs generated from a set of healthy subjects

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 4. Cooperative Neurofeedback - A multiplayer game controlled with your brain by Victor Ferat, Louis Albert and Antoine Provost

Tired of playing alone, annoyed to hold a controller? The goal of this project is to create a multiplayer game controlled by players brain. How ? Using real time electroencephalography (EEG) recordings, we want to get people connected and working together to progress through the game. Why ? Not only for fun , but also for its medical applications: playing with its brain can teach you self-regulation of brain function. This process called neurofeedback can be used as a complementary or alternative therapy in various brain dysfunctions. ( Tinnitus, ADHD, Depression...)

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 5. SINAPP (Modular BIDS App) for Motion-robust Super-Resolution MRI by Sebastien Tourbier

This project started at a previous brainhack (cf related github repository) and aims to develop a modular pipeline packaged as a SINAPP (Modular BIDS App) which uses the Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK), a set of C++ image processing tools, to perform motion-robust super-resolution of fetal brain MRI.

It integrates new advances in the neuroimaging field over the past three years including:
  • the Brain Imaging Data Structure (BIDS), a standard to organize and describe neuroimaging data
  • the BIDS App framework based on software containerization, which promotes reproducibility and portability
Please see this presentation which presents the achievements and perspectives of the project.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 6. Brain-computer interface for syllable decoding by Silvia Marchesotti, Michael Pereira and Arnaud Desvachez

The main goal of the proposed internship is to contribute to the development of a new generation of speech neuroprosthesis to restore communication in patients with aphasia. Aphasia is an impairment in the comprehension and formulation of language caused most commonly by stroke, traumatic brain-injuries, and other pathological conditions affecting speech production and comprehension.

Here we will use electroencephalography signals to decode in real-time the mental imagery of syllables - the “building blocks” of words. We will start by characterizing which neural signatures of syllables imagination provide the most discriminable signal to be classified. More specifically, we aim at identifying
  1. the best time window around the onset of the syllable-imagery
  2. the most relevant brain regions able to optimally discriminate between two different imagined syllables
Later, these spatio-temporal features will be integrated into a closed-loop brain-machine interface, that according to the classifier output, will provide an auditory feedback.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 7. ClearMap to register LightSheet data to Reference Atlas by Audrey Tissot, Laura Batti and Stephane Pages

The objective of the project is to test ClearMap registration pipeline (https://idisco.info/clearmap-2/) on data generated within the Advanced LightSheet Imaging Center (ALICE) of the Wyss Center at Campus Biotech.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 8. Interface for online analysis of dyslexic children tests by Kinkini Bhadra

Interventional approaches to treat dyslexia is yet to evolve from the traditional rehabilitation procedures like speech therapies. Based on evidences of the potential of transcranial alternating current stimulation (tACS) in accelerating the rehabilitation process in dyslexic adults (Marchesotti, 2019), we now want to replicate similar experimentation on the population of children to better understand the neuronal basis of dyslexia and the link between a phonological deficit and activity in the auditory cortex.

What do we measure during the experiment?
  1. Phonological awareness and reading skills through a battery of linguistic tests.
  2. Analyze the evolution of performance post tACS application.
Objective

As a part of the current study, we propose to build an interface that would automatize the behavioural test results by instantly quantifying and displaying reading time, reaction time, prosodic breaks and reading speed. We propose to build the interface using MATLAB. This would facilitate the experimenter to have online access of the response data and its preliminary interpretation, helping to understand the trend of the effect of pre and post tACS application almost instantly.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 9. Python interfaces for EEG (as connectome-mapper add-on) by Jonathan Wirsich and Sebastien Tourbier

Several frameworks exist to automatically extract brain connectivity information from experiments with different preprocessing pipelines. Flexible pipelines for both diffusion MRI and functional MRI have been implemented in different software such as the Connectomemapper but solutions for EEG and MEG are lacking.

This project intents to develop new EEG interfaces and implement them inside the Connectomemapper workflow. The new functionalities to be developped consist in:
  1. being able to import brain atlases optimized for M/EEG
  2. providing an interface to common EEG analysis software (e.g. MNE python)
  3. being able to import lead field matrices generated by common EEG analysis software in order to compute the inverse solutions
The project will include two parts: the first one to develop general functions, and the second one to integrate them specifically inside the Connetomemapper.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project 10. Through your eyes -- reconstruct visual stimuli from EEG data by Konstantinos Samaras-Tsakiris, Timokleia Kousi, Florian Laurent, Carolina Lindqvist and Nefeli Kousi

Humans are viscerally visual creatures. However communicating what you see or imagine is very hard, if you don't have an artistic talent or a way with words. Imagine a more direct way to interact with the world: keyboards and mice give way to EEG devices directly tapping into brain signals. This is the promise and threat of BCIs (brain computer interfaces). This project will attempt to reconstruct what a person sees from their brain signals: ideally EEG, or alternatively fMRI. Based on prior work, we propose to experiment with deep neural networks to reconstruct the images.

Project skills

At least one of these preferred, but contributing to general ideas / discussion always welcome!

Programming
Machine Learning
Terminal / git
Neurosciences
MRI
EEG
Virtual Reality
3D Design

Project instigators

Here is the list of project instigators who will help giving the "big picture" of each project.

Olivier Reynaud

Olivier's expertise: TMS; non invasive brain stimulation; brain imaging; MRI; physics

Matilde Damiani

Matilde's expertise: virtual reality, augmented reality, Unity, Matlab

Margaux Dubessy

Margaux's expertise: Mechanical engineer, virtual reality development

Arnaud Desvachez

Arnaud's expertise: bci, neuro-feedback, eeg

Gwenael Birot

Gwenael's expertise: EEG, signal processing

Thomas Bolton

Thomas's expertise: fMRI analysis, dynamic functional connectivity, hidden Markov models, graph signal processing

Raphael Liegois

Raphael's expertise: brain connectivity, dynamical systems theory, functional MRI, Helene Grimaud

Victor Ferat

Victor's expertise: EEG, Signal processing, Electronics

Louis Albert

Louis' expertise: virtual reality, C/C#/C++, Unity

Antoine Provost

Antoine' expertise: 3D Game Designer & Developper

Sebastien Tourbier

Seb' expertise: C++/Python, Docker, Reproducible processing Workflows, Super-Resolution

Silvia Marchesotti

Silvia's expertise: Brain-computer interfaces, neuromodulation, tACS, dyslexia

Michael Pereira

Michael's expertise: Cognitive neuroscience, consciousness, eeg, bci, fmri, human single neuron

Audrey Tissot

Audrey's expertise: Fluorescence imaging

Laura Batti

Laura's expertise: Bio-imaging and Neuroscience

Stephane Pages

Stephane's expertise: Neurosciences, Imaging, Image Analysis

Kinkini Bhadra

Kinkini's expertise: EEG, Matlab

Jonathan Wirsich

Jon's expertise: multimodal data integration, EEG-fMRI, functional connectivity

Konstantinos Samaras-Tsakiris

Konstantinos's expertise: Cloud software engineering, EEG analysis, AI, Julia

Timokleia Kousi

Tim's expertise: veterinary medicine

Florian Laurent

Florian's expertise: programming, machine learning, reinforcement learning

Carolina Lindqvist

Carolina's expertise: Software development, Python, DevOps

Nefeli Kousi

Nefeli's expertise: : UI/UX, Interaction Technology, Web Development

Program (event concluded)

The Brainhack took place over two and a half days, on November Friday 8th and Saturday 9th,
with project pitches and a social event the day before, on Thursday 7th.

8:30
Breakfast
Breakfast
9:00
Ignite talk
Open Hacking
09:30
Open Hacking
Open Hacking
12:00
Lunch
Lunch
13:00
Open Hacking
Ignite Talk
13:30
Ignite talk
Open Hacking
14:00
Open Hacking
Open Hacking
16:30
Collect Badges
Open Hacking
Open Hacking
17:00
Intro / Project pitches
Open Hacking
Debrief Projects
18:00
Social Drinks
Debrief Day 1
Wrap up
19:00
Social Drinks
Social Drinks / Dinner

Contact & Venue

Address

Chemin des Mines 9, 1202 Geneva, Switzerland

Phone Number

Email