Projects

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All Australasia Bay area Boston Nordic Donostia Geneva Krakow Western Marburg Marseille Montreal NYC Physiopy Toronto Washington DC Western Zagreb Zurich Git level: 0 none Git level: 1 commit push Git level: 2 branches PRs Git level: 3 continuous integration behavioral DWI ECG ECOG EEG eye tracking fMRI fNIRS MEG MRI PET TDCS TMS C++ containerization documentation html css Java Javascript Julia Matlab none Python R shell scripting Unix command line Web Skills: comfortable Skills: expert Skills: familiar Skills: none coding methods data management documentation method development pipeline development tutorial recording visualisation AFNI ANTs BIDS Brainstorm CPAC Datalad DIPY FieldTrip fMRIPrep Freesurfer FSL Jupyter MNE MRtrix Nipype NWB SPM Bayesian approaches causality connectome data visualisation deep learning diffusion diversity inclusivity equality EEG EventRelatedResponseModelling EEG source modelling

16s Metagenomic analysis of Gut Microbiome

16S rRNA gene sequencing is commonly used for identification, classification and quantitation of microbes within complex …

 Project URL Marseille fra documentation Python Unix command line documentation shell scripting R Skills: familiar reproducible scientific methods

Automatic detection of spiking motifs in neurobiological data

The study of spatio-temporal correlated activity patterns is very active in several fields related to neuroscience, like machine …

 Project URL Marseille fra Git level: 1 commit push documentation Python documentation Jupyter deep learning method development machine learning neural decoding information theory neural networks physiology statistical modelling

Automatise your processing pipelines with nipype / pydra

Neuroimaging and electrophysiology processing requires many steps, calling different softwares, possibly in different languages …

 Project URL Marseille fra Git level: 2 branches PRs MRI fMRI Matlab EEG MEG AFNI documentation Nipype BIDS FSL Python documentation SPM pipeline development reproducible scientific methods physiology

Bayes on the Brain in Python

Human brain imaging data is massively multidimensional, yet current approaches to modeling functional brain responses apply …

 Project URL Australasia aus Git level: 0 none Git level: 3 continuous integration Git level: 2 branches PRs MRI fMRI Git level: 1 commit push AFNI documentation BIDS Python coding methods documentation fMRIPrep Jupyter R pipeline development method development MR methodologies reproducible scientific methods statistical modelling

BIDS, electrophysiological data, open dat

We are currently developing a standard for organizing electrophysiological data recorded in animal models. It consists in …

 Project URL Marseille fra Julia documentation BIDS documentation data management NWB physiology

Big Neuroimaging Dataset Phenotype BIDS Tools

Information about phenotypes (i.e., age, responses to cognitive/clinical questionnaires, blood tests) is hard to share and varies …

 Project URL Washingtondc usa Git level: 0 none Git level: 2 branches PRs Git level: 1 commit push documentation BIDS Python documentation data management Skills: familiar

Brainhack projects database

This is a remote project

 Project URL Marseille fra Git level: 0 none Git level: 3 continuous integration Git level: 1 commit push documentation Python documentation data visualisation visualisation

Brainharmonic - Generating music from brain signal data using deep learning

This project aims to develop a tool to generate music from brain signals using deep learning models. There has been a lot of work …

 Project URL Australasia aus MRI fMRI Git level: 1 commit push EEG Julia documentation Python coding methods documentation fMRIPrep Freesurfer Jupyter pipeline development deep learning method development

Cerebro: One tool to view them all

  • What are you doing, for whom, and why? Cerebro aims to provide a visualization solution to advance the currently available …

 Project URL Australasia aus Git level: 0 none MRI fMRI DWI documentation Python coding methods documentation Jupyter Skills: expert Brainstorm data visualisation Skills: familiar visualisation

containerize bidspm

Donostia esp Git level: 3 continuous integration Git level: 2 branches PRs MRI fMRI Matlab Git level: 1 commit push containerization documentation BIDS coding methods documentation fMRIPrep SPM reproducible scientific methods

Decoding Fiber photometry & Rat behavior

  • What are you doing, for whom, and why? I am collecting calcium signals from Infalimbic, Prelimbic, and Anterior cingulate …

 Project URL Marseille fra Git level: 0 none Matlab documentation Python coding methods documentation method development neural decoding

dMRI QC: implementation and automation

  • What are you doing, for whom, and why? I am a USYD NIF fellow from school of biomedical engineering. I work under Prof Fernando …

 Project URL Australasia aus Git level: 0 none MRI DWI documentation Python documentation pipeline development diffusion

DSST defacing pipeline

  • What are you doing, for whom, and why?
  • What makes your project special and exciting?
  • How to get started?
  • Where to find key …

 Project URL Washingtondc usa Git level: 0 none Git level: 3 continuous integration Git level: 1 commit push AFNI documentation FSL Python documentation Jupyter pipeline development connectome reproducible scientific methods

Flexibly convert fmriprep confounds to censor files

Fmriprep gives a smorgasbord of confounds to be used in later processing. While the program provides the option for generating …

 Project URL Washingtondc usa Git level: 0 none MRI fMRI Git level: 1 commit push documentation BIDS Python Unix command line documentation fMRIPrep data management pipeline development MR methodologies reproducible scientific methods

GUI frontend for creating MEG bids

  • Build a gui front end for creating MEG bids. Currently this is a cmdline driven process, which isn’t always an accessible …

 Project URL Washingtondc usa MRI Git level: 1 commit push MEG documentation BIDS Python MNE documentation data management

Guidelines for tractography in primates

Create guidelines i.e. summarize all the important things to know, step by step, to make a good tractogram edition for non-human …

 Project URL Marseille fra Git level: 0 none DWI documentation FSL Python documentation Freesurfer MRtrix Skills: expert diffusion tractography

Hacking brainhack

 Project URL Donostia esp Git level: 0 none Git level: 2 branches PRs Git level: 1 commit push EEG MEG documentation documentation html css data visualisation diversity inclusivity equality Skills: familiar visualisation

Inferring task-related higher-order interactions from brain network signals

A central hypothesis in neuroscience posits that cognitive functions emerge from complex interactions between multiple brain …

behavioral Marseille fra Git level: 0 none Git level: 1 commit push EEG MEG ECOG documentation Python documentation method development information theory

Introduction to MATLAB Bootcamp

This project is aimed at those at the beginner to intermediate level of programming / coding and MATLAB, and/or those interested …

Washingtondc usa Git level: 0 none Git level: 3 continuous integration Git level: 2 branches PRs Matlab Git level: 1 commit push documentation coding methods Skills: comfortable documentation tutorial recording reproducible scientific methods statistical modelling

Large Scale FPGA Neuromorphic Interface precursor work. A GPU implementation of Allen Brain V1 measured model using Julia and or PyGeNN

  • Providing a ground truth for an FPGA based large scale simulation.
  • Making Julia+GPU potentially a more Democratic programming …

 Project URL Australasia aus Git level: 0 none Git level: 3 continuous integration Git level: 2 branches PRs Git level: 1 commit push Julia documentation Python coding methods documentation data visualisation visualisation connectome method development PCA reproducible scientific methods physiology

LFP and single units decoding in rats performing a distance estimation task

Navigating in space requires to continuously updating the representation of its own position in the environment. In poorly cued …

behavioral Marseille fra Git level: 0 none Matlab EEG documentation documentation Skills: expert method development neural decoding physiology

Lightweight BIDS Layouts for all

PyBIDS' [BIDSLayout](https://bids-standard.github.io/pybids/generated/bids.layout.BIDSLayout.html

 Project URL Git level: 3 continuous integration Git level: 2 branches PRs Git level: 1 commit push containerization documentation BIDS Python coding methods DIPY documentation reproducible scientific methods Bay area usa

MRIQC & fMRIPrep - physiology and task visualization with carpetplot

Donostia esp MRI fMRI AFNI Nipype BIDS ANTs FSL Python fMRIPrep ICA PCA physiology

MRIQC - QC Dashboard

Donostia esp MRI fMRI Python

Neural encoding of acoustic features during speech and music perception: traduction of matlab code into python

Marseille fra Matlab EEG documentation Python MNE documentation pipeline development neural decoding

NeuroCausal

Donostia esp Geneva che MRI Python

NeuroDesk -A flexible, scalable, and browser-based data analysis environment for reproducible neuroimaging

  • What are you doing, for whom, and why? Neurodesk provides a containerised data analysis environment to facilitate reproducible …

 Project URL Australasia aus Git level: 3 continuous integration MRI containerization documentation Python coding methods documentation shell scripting pipeline development method development reproducible scientific methods

Normalisation and artefact correction toolkit for fibre photometry data

Studies using optic fibres to record real-time fluorescent biosensors in-vivo are now commonplace, yet despite a large degree of …

Australasia aus behavioral Git level: 0 none Git level: 2 branches PRs Git level: 1 commit push documentation BIDS Python documentation data management pipeline development visualisation method development systems neuroscience

OpenXstim

Transcutaneous electrical spinal cord stimulation, a non-invasive, reversible spinal cord neuromodulation method holds tremendous …

 Project URL Australasia aus C++ documentation documentation method development physiology systems neuroscience

PhysioPy - peak detection toolbox for physiological signals

peakdet aims to provide a set of tools that will work with a variety of input data to reproducibly generate analysis-ready …

 Project URL Git level: 0 none ECG Git level: 2 branches PRs MRI fMRI Matlab Git level: 1 commit push documentation Python documentation pipeline development physiology Physiopy gathertown

Physiopy-documentation

Physiopy is a community formed around developing tools to operate physiological files in neuroimaging setups. This project …

 Project URL Geneva che Git level: 0 none Git level: 2 branches PRs MRI fMRI Git level: 1 commit push documentation documentation MR methodologies physiology Physiopy gathertown

PsychophyGit - a fast and flexible tool for online experiments

Acquiring human behavioural data through the Internet is on the rise, especially since the COVID-19 events. Often most, …

 Project URL behavioral Marseille fra Git level: 1 commit push documentation Java Javascript Python documentation method development systems neuroscience

Removing pink noise (1/f) in LFP across different electrophysiological recording systems

  • What are you doing, for whom, and why?
  • What makes your project special and exciting?
  • How to get started?
  • Where to find key …

 Project URL Marseille fra Git level: 1 commit push EEG documentation Python coding methods MNE documentation Jupyter pipeline development neural encoding

RTP2

Donostia esp MRI fMRI Matlab DWI AFNI BIDS ANTs FSL Python fMRIPrep Freesurfer MRtrix diffusion

Scrubbing with clinical samples

 Project URL Toronto can MRI fMRI Git level: 1 commit push documentation BIDS Python documentation fMRIPrep shell scripting Jupyter R pipeline development

SLAM - A pure python package for Surface anaLysis And Modeling

Slam (https://brain-slam.github.io/slam/) is an open source python package dedicated to the representation of neuroanatomical …

 Project URL Marseille fra MRI Git level: 1 commit push documentation Python coding methods documentation Skills: expert Skills: familiar

Strategies for modelling sub-cortical processes with RNNs

This project is currently at the thought-bubble stage, but I am interested in different ways recurrent neural networks (RNNs) can …

 Project URL Australasia aus Git level: 1 commit push documentation Python documentation deep learning machine learning neural networks systems neuroscience

Sulcilab: A collaborative sulci labelling web app

Sulcilab is a web base application to mannually labelize sulcal graphs (outputs of BrainVISA). I propose this project with 2 …

 Project URL Marseille fra Git level: 0 none MRI documentation Python documentation data visualisation visualisation

Tedana

Donostia esp MRI fMRI documentation Python documentation Jupyter ICA PCA

Viewing the world in third-person - experimental considerations for a successful study

  • What are you doing, for whom, and why?

  • I am conceiving an experiment to study the implications of living with a third-person …

 Project URL behavioral Marseille fra Git level: 0 none documentation documentation method development

Why a centralised project submission?

As the Brainhack Global team, we aim to :

  • create a (de)centralized collaborative working platform,
  • facilitate & increase across-site collaborations and interactions,
  • give more visibility to the projects run under Brainhack Global,
  • encourage sharing ideas, experiences and knowledge across parties,
  • to remove barriers and allow contributions by researchers from all origins and disciplines.

Given that many events in this year Brainhack Global might be in part run virtually, a common platform for project submission and listing will allow you to submit your initial project call to gather interests from researchers from all Brainhack Global event locations.

Submitting a project

Please read our Guidelines for Leading and Attending to Brainhack Projects to get more ideas about:

  • how to design your project and what to expect from a Brainhack experience,
  • how to lead a project,
  • how to be an attendee of a project.

The ideal project should convey ideas with respect to the development of tools, methodologies, guidelines and begets to brainstorming new ideas that would facilitate the implementation of open science practices in neuroscience and create more opportunities for collaborative work and information exchange within the community.

How does it work?

In order to submit a project to the Brainhack Global 2022 Project Gallery, please follow these steps:

  1. Register with an event listed in the Brainhack Global 2022 Events .
  2. Create a GitHub account.
  3. Use our project submission form and fill in the necessary/required information as requested.

Project submission form

What happens next?

Once you have submitted your project, a reviewer will check the information in your issue. They may request some changes if deemed necessary.

Once the review completed the project will be marked as status:web_ready and will be listed on the Brainhack Global 2022 Projects page after a short delay. A subpage dedicated to your own project will be automatically created.

Matching projects with participants

The Brainhack Global team will try to match event attendees to projects across the globe based the expertise/skill sets that attendees want to acquire and those the projects are looking for. Once the attendee registrations are completed, our matching algorithm will be run based on the information provided by the attendees during registration. The attendees will then receive an email listing the best fitting projects for their expertise and interests.

Of course, the project attendees decide to join is ultimately their own. They could either go with the suggested options or they could choose among the other projects listed in the Brainhack Global 2022 Projects page.

Please be aware that, at the very early stage of the interactions, attendees might just want to contact you for more information to make sure that the project is a good fit to the aims they want to achieve from a Brainhack. Therefore, please make sure that you welcome all attentions and explain your project with care and guide them as necessary.