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Science and medicine

INCF

An open & FAIR neuroscience standards organization

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Participation history

11 GSoC years

20262025202420232022202120202019201820172016

2026

23 projects

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SciCommons Fullstack Development and AI Features

SciCommons is an open source platform for researchers to interact, review, and discuss scientific papers. My project focuses on making the platform a...

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Explainable Spatio-Temporal Graph Evolution for Developmental Neuroscience

This project studies the development of a tiny worm called Caenorhabditis elegans, focusing on how its cells divide, grow, and interact during its...

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EBRAINS Modular Software Environments and Service Integration

The EBRAINS Software Distribution is a monolithic Spack environment that takes over 48 hours to build, making rapid deployment and testing difficult....

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Semi-automated iEEG analysis and viewing in a clinical and research environment

This project aims to further develop an open-source intracranial EEG (iEEG) analysis platform by integrating clinically relevant seizure detection...

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BreathState: A Cross Platform App for HRV Biofeedback and Resonance Breathing Protocols

Problem: Currently, resonance frequency-based HRV training is backed by robust scientific evidence, but it remains inaccessible to the masses due to...

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The Virtual Brian : New graphical widgets for JupyterLab

The Virtual Brain (TVB) provides an open-source simulation framework for whole-brain network modeling. Unlike the traditional approach of using...

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ActiveVision: continued development of a data and model portal for the study of goal-directed vision

This project builds an automated benchmarking ecosystem for goal-directed vision. It implements a high-priority leaderboard featuring automatic...

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Project #27: Integrating Personalized HRF in The Virtual Brain & EBRAINS

This project will have the aim to derive the empirical HRF for each brain region and each subject from BOLD recordings, and then to use this HRF in a...

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Integrating velocity modelling into PCNToolkit package

The project aims to improve longitudinal normative modelling in PCNtoolkit by validating, debugging, and extending velocity-based models to support...

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Towards a Generalized Mapping Framework For Gesture-Responsive Music and Speech Generation

This project proposes a modular, real-time gesture-to-sound mapping framework for the GestureCap system. It will enable users to translate hand...

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Expressive Gesture to Sound Mapping Framework for GestureCap

This project develops an expressive gesture-to-sound mapping layer for GestureCap, enabling low-latency gesture data to control playable instruments...

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Reusable DSOMM Security Pipeline for EBRAINS MIP Platform

The Medical Informatics Platform (MIP) currently lacks standardized automated governance for its federated infrastructure, leading to deployment...

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Strengthening Core Workflows and Notebook Integration in AnalySim

This project will improve AnalySim’s core reliability by addressing fragile user workflows, improving query and search behavior, and making the...

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Contribute to LORIS: Improving reliability and maintainability in the electrophysiology browser

This project aims to improve the reliability and maintainability of the LORIS electrophysiology browser through scoped enhancements to browser...

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#40: QC-Studio-integrated quality control toolkit for MRI datasets

MRI quality control (QC) is an essential but highly manual and repetitive process in neuroimaging research. Currently, reviewers must navigate...

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ImageJ Active Segmentation platform: Parallel Engine for ASP/IJ

This project accelerates the convolution core of the Active Segmentation Plugin (ASP) in ImageJ by offloading its most compute-intensive pixel...

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A Python Command Line Interface (CLI) for the CBRAIN Distributed Computing Platform

The project develops an improved Python-based CLI for the CBRAIN distributed computing platform, aiming on usability and modular design. It replaces...

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#17 Project Experanto

Implement an ast based behavioral filter enabling queries like `(treadmill>0 and eye is not nan) & screen == video`, and expand dataset support with...

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HarmonyHub Music Education Interface: Mobile App Hardening and Relative Intonation Learning

HarmonyHub is an open-source platform designed to improve music education through interactive and technology-driven learning experiences. While the...

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Project 39 NeuroSim As A Physics Constrained Model for Finite Horizon Network Control Theory

The application of Network Control Theory to medical neuroimaging consistently faces the approximation crisis. Current tools rely on infinite-horizon...

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Refactoring Synaptic Behavior in HNN-Core

This project focuses on improving the computational efficiency and biological realism of synaptic modeling in HNN-Core by refactoring how synapses...

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Fix outstanding issues in Brian2CUDA

Problem: Brian2CUDA offers significant GPU acceleration for neural simulations, but its current "beta" state contains friction points that hinder...

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Improving Statistical Efficiency, Methodological Coverage, and Contributor Onboarding in NiMARE

This project enhances NiMARE’s performance and developer accessibility through a dual-phase optimization strategy. The first phase modernizes the...

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2025

25 projects

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Conda packaging for GeNN

GeNN is a C++ library that generates code for efficiently simulating Spiking Neural Networks (SNNs) using GPUs. In order to compile this generated...

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Studying Peripheral Physiological Modulation of Brain Activity (INCF #27)

Traditionally, brain activity has been analyzed independently from peripheral physiological measurements like the electrocardiogram (ECG), but our...

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Python API for new cell types

This project will involve refactoring the Human Neocortical Neurosolver (HNN-core) codebase to enable flexible development of neural circuits with...

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GestureCap: Using markerless motion capture and gesture recognition for music generation

Last year, work on GestureCap focused on developing an Arduino-based latency measurement system and optimizing the pipeline for low-latency...

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Developing standardised biophysically detailed neuronal circuit models using NeuroML

This project will convert Macaque auditory thalamocortical circuits model based on NetPyNE implementation into NeuroML standard formats and testing...

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Developing an ISPC Backend for GeNN to Enable CPU-Based SNN Simulations

GeNN is a C++ library used for simulating Spiking Neural Networks through GPU-based code generation (CUDA/HIP). Currently, its accessibility is...

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DevoTG: Dynamic Graph Neural Networks for Modeling C. elegans Development

The nematode Caenorhabditis elegans serves as a pivotal model organism in developmental biology due to its well-defined cell lineage, compact genome,...

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3. HarmonyHub: Front-end interface refactoring and expansion for multi-instrument support

HarmonyHub is an open-source, modular web application designed to revolutionize music education by integrating modern technologies and pedagogical...

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MODELING NEURAL DEVELOPMENTAL PROGRAMS OF C. elegans USING GROWING HYPERGRAPH NEURAL NETWORKS

This proposal outlines a novel computational framework for modeling neural developmental programs using Growing Hypergraph Neural Networks (Growing...

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ActiveVision: a data and model portal for the study of goal-directed vision

This project develops an open portal for goal-directed vision research, integrating eye-tracking datasets and machine learning models with tools for...

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Develop Python API for Multi-Network Simulations in Human Neocortical Neurosolver (HNN)

​The Human Neocortical Neurosolver (HNN) is an open-source neural modeling tool designed to help researchers and clinicians interpret human brain...

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A Python Command Line Interface (CLI) for the CBRAIN Distributed Computing Platform

The project will develop a Python-based CLI for CBRAIN using its Python API Client Swagger API, allowing advanced users to manage research data and...

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BreathState: an open-source Android/iOS and PC app for breathing and heart-rate synchronization

The project will develop the first version of an app that uses Bluetooth to connect with heart-rate and respiration sensors, calculate metrics of...

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#23 SciCommons : A Social-Web Tool For Scientific Discussion, Interaction, Rating and Peer Review

SciCommons is an open-source platform aimed at improving the scientific peer review process through better user experience and web application...

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Transitioning from Simulation-Based Inference to Automatic MCMC for Virtual Brain Inference

This project aims to replace Simulation-Based Inference (SBI) methods with Markov Chain Monte Carlo (MCMC) techniques for inference problems...

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PROJECT #8: Brian Simulator :: Replace Brian’s just-in-time compilation mechanism

This project aims to replace Brian’s current just-in-time (JIT) compilation system, which relies on Cython. While functional, Cython introduces slow...

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Brian2Wasm: simulations in the browser

This project focuses on enhancing the overall workflow by improving the detection and configuration of the Emscripten toolchain. It aims to optimize...

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Harmony Hub: Using Generative AI for Adaptive Learning in Music

While music educators strive to provide personalized learning paths, existing educational tools often lack the flexibility to adapt to diverse...

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Automating BIDS Dataset Registration into the EBRAINS Knowledge Graph

This project aims to build an automated workflow to register BIDS-compliant neuroimaging datasets from external repositories (e.g. Public nEUro) into...

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Parallel Filter Implementation for ASP/IJ

The Active Segmentation Platform for ImageJ (ASP/IJ) aims to provide a general-purpose workbench that allows biologists and other domain experts to...

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[Project 20] Build an AI Agent for KnowledgeSpace using Retrieval-Augmented Generation (RAG)

This project builds an AI-powered agent for KnowledgeSpace using Retrieval-Augmented Generation (RAG) to deliver precise, context-aware, and...

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19. Contribute to LORIS

LORIS is a comprehensive data management platform that supports diverse datasets in neuroscience research, including imaging, behavioural, clinical,...

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Fullstack cloud deployment for NiiVue

NiiVue is a versatile tool for visualizing and handling neuroimaging data, but insufficient documentation creates friction in using it in deploying...

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Project 28 Analysim , Preparing for beta release by adding admin section, forking datasets etc.

Project Deliverables • Admin Section : Implement an admin dashboard to manage users, projects, and datasets. Add moderation tools for handling...

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Open Source Community Sustainability

SustainHub is an AI-driven simulation platform designed to study and enhance the sustainability of open-source communities. It models contributors,...

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2024

27 projects

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Implementation of SWC to NeuroML converter in PyNeuroML

I am proposing a project for Google Summer of Code to develop an interactive SWC to NeuroML converter in Python. The converter will simplify the...

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Developmental Graph Neural Networks (D-GNNs) and Visualizations

DevoGraph is an open-source GNN framework designed specifically for analyzing embryogenetic data. It utilizes Graph Neural Networks (GNNs) as a...

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Improving and Extending the User Interface of the Neuroptimus Parameter Optimization Software Tool

Neuroptimus, an open-source parameter optimization software tailored for neuroscience applications, has been instrumental in advancing the...

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Project 15.1 Analysim, INCF- implementing new features in project dashboard and notebook management.

Project Deliverables • Implement a Project edit button, file and project rename functionality, fix edit project popup , allow editing list of...

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Visualization and UI update for ASP/IJ

The Active Segmentation Platform for ImageJ (ASP/IJ) aims to provide a general-purpose workbench that allows biologists and other domain experts to...

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Implement batch simulation and optimization routines

The Human Neocortical Neurosolver (HNN) is a computational tool that enables scientists to study brain responses at the cellular and circuit levels....

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Using markerless motion capture to drive music generation

Gesture-based music generation has existed for some years now, thanks to software such as Wekinator. However, they use machine learning methods that...

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(Project Idea - 18.2)Improve-Brian's-markdown-exporter

This proposal aims to improve the capability of markdown exporter package inorder to cover multicompartment model, and also to support generation of...

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Package Brian's unit system

The project aims to refactor the Brain's unit system into a standalone package. Additionally, it aims to incorporate additional functionalities from...

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21.1 HarmonyHub: A Web-Based Platform for Learning Variable-Pitch Musical Instruments

This project aims to build HarmonyHub, a web platform for personalized and engaging learning experiences with variable-pitch instruments like wind...

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A natural language interface for querying federated research data

Neurobagel is a federated data ecosystem that allows researchers and other data users to find and consume research data that has to remain at their...

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A Social web tool to facilitate rating and commenting on research reports

SciCommons aims to revolutionize academic publishing by providing an open peer review platform. The current system faces challenges such as time...

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INCF GSoC 2024 Project 8.2 Proposal

We aim to further enhance model development with NetPyNE’s “batch” subpackage by refactoring the code base for ease of use and scalability, then use...

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14.1 INCF Impact Visualization Portal with ML and Data Analytics (175 h)

The proposal focuses on prospective ideas that can be employed for enhancement of the existing INCF Impact Visualization Portal. It goes into depth,...

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HyperDevoGraph: Modeling C. elegans Development with Hypergraph Convolution Techniques

This project studies the development of a tiny worm called Caenorhabditis elegans, focusing on how its cells grow and interact from its early stages....

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Open Source Community Sustainability

The ‘Open Source Community Sustainability’ project is about simulating open-source community interactions to encourage conditions leading to...

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1.1 - Enhancing tvb-widgets by developing new widgets

TheVirtualBrain (TVB) is the first integrative neuroinformatics platform for the modeling of full brain network dynamics. TVB simulator, written in...

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Scicommons: A social-web tool to facilitate rating and commenting on research reports

The proposal aims to address the issue of the expensive and inaccessible research publishing industry by leveraging modern internet-based social...

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LORIS Data Platform Web Modules and API Development

The project aims to enhance the LORIS web platform, a widely used tool in neuroimaging research with databases utilized by research teams in 22...

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Contribute to LORIS

The proposal involves contributing to the LORIS codebase, a pivotal resource for neuroscience research. LORIS plays a crucial role in facilitating...

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17.1 Semi-Automated Workflows for Physiological Signals

This project entails the upgrade of the existing physiopy packages, peakdet and phys2denoise, for optimized interoperability and the development of...

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Incorporate new features into an advanced, cross-platform 3D viewer for NeuroML cells and networks

The project is about incorporating new features into an existing 3D viewer which allows for visualisation of cells and networks using the NeuroML...

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8.1 Automated In-Silico Representation of Published Literature

Project synopsis / summary: This project is dedicated to developing a set of automated tools and processes for extracting useful neuronal...

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Efficient app-based measurement of visual functions in infants and young children

Ensuring healthy vision in infants requires early detection of potential problems. Current Infant Visual Function Measurement Systems built in...

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Integration of inference based models to Neuroptimus

With the advent of machine learning, statistical learning and modelling becoming more prevalent in today’s world, we can estimate values for an...

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Best of both worlds – let’s cherish the features of parametric AND explicit knowledge retrieval

The annotation of research data is essential to ensure its findability and reusability. High-quality data annotations require domain expertise, so...

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LLM-assisted tool to annotate research data with machine-understandable, semantic data dictionaries

To participate in the Neurobagel query federation, datasets must conform to Neurobagel’s data model, so annotating the datasets is necessary to...

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2023

22 projects

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Image feature and classification database

The Active Segmentation platform for ImageJ (ASP/IJ) was developed in the scope of GSOC 2016 - 2021. The plugin provides a general-purpose...

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1.1 Integrate Zenodo API with The Virtual Brain

The Virtual Brain (TVB) is a scientific simulation platform that provides all means to generate, manipulate and visualize connectivity and network...

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Idea 22.3 - Abhishek Tiwari - Code editor support for Brian model equations

This project involves creating a VS Code extension that provides enhanced support for the Brian2 neural simulator. The extension aims to improve the...

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Adding new workers and resource management to new dataflow engine written in Python: Pydra

My proposal aims to extend Pydra's worker classes to handle a wider range of systems by utilizing PSI/J, which offers a unified API for various...

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Technical Improvements to enhance the usability of The Turing Way chapters by different user groups

The Turing Way is an open source, open collaboration and community-led handbook on data science. The book is hosted online in a browsable format....

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Impact visualization portal for global neuro-informatics community

The International Neuroinformatics Coordinating Facility (INCF) is a non-profit organization dedicated to advancing the field of neuroscience and...

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GSoC 2023 Project Idea 2.2 Generalize parameter optimization routines

The Human Neocortical Neurosolver (HNN) is open-source, computational neural modeling software that allows us to examine the cellular- and...

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NWB File Compatibility Testing and Summary Generation via Docker

The "NWB File Compatibility Testing and Summary Generation via Docker" project aims to streamline the process of testing NWB (Neurodata Without...

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Optimization of the computations of HOIs and integration in the Frites python package

Activity patterns of neurons have so far been examined both singly and in pairs. Higher order interactions (HOIs), or non-pairwise interactions...

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Integration of Automated Model Testing and Parameter Fitting Tools for Neuroscience Applications.

Biologically detailed models are essential tools in neuroscience, and automated methods are frequently used to build and validate such models based...

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3.1 D-GNNs: developing DevoGraph for computational developmental biology - Himanshu

This project is about using Graph Neural Networks(GNNs) as a method to discover underlying connectivity to characterize a growing network that...

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Replicating Auditory Steady-State Response (ASSR) in an auditory cortex model. Project idea 9.1

ASSR refers to the cortical entrainment to frequency and phase of an auditory signal that is presented in a fixed “train of clicks”, in a gamma range...

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A Social web tool to facilitate rating and commenting on research reports

The currently available open-review portal helps in reviewing the research articles, By facilitating official reviewers to comment on the research...

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Project 7.1: Working on Implementing CSV Data Browser and Querying Component

We are trying to solve the difficulty of collaboration among multiple users working on large datasets, particularly in analyzing datasets with many...

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7.2 Working on improving graphical interface and user experience on AnalySim

To Remove Bootstrap from the application and substitute the design with pure SCSS.To finish implementing the CSS global variables and add component...

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Exploring Open Source Sustainability via Agent based Modelling and Reinforcement learning

The proposed project aims to address the sustainability challenges faced by open-source software projects by using an agent-based modelling and...

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Develop IO Routines for HNN-core outputs

The idea of the project is to develop IO routines adapted from HNN-core objects while maintaining backwards compatibility with HNN-GUI. The...

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Improving LORIS data platform

Deliverables - Improving existing LORIS Codebase and API features, Write test cases for code changes - handling and serving the data efficiently,...

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Efficient app-based measurement of visual functions in infants and young children

The measurement of visual function in infants and young children is crucial for early detection and treatment of eye conditions that can lead to...

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Improving Automatic Reviewer Assignment using Large Language Models For NBDT Journal

Matching papers to reviewers based on topics is a crucial task for the Neurons, Behavior, Data Analysis, and Theory (NBDT) journal. However, the...

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Advancements in 3D Cellular Microscopy Imaging Through Fine-Tuned CellSAM and DevoNet Models

This project centers on the enhancement and integration of the CellSAM and DevoNet models to elevate the analysis of 3D microscopy images stored in...

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4.2 Virtual Reality for Distributed Research (Orthogonal Research and Education Lab) (175 h)

Virtual Reality for Distributed Research (VRDR) encompasses a VR showroom, immersive anatomy exploration, model organism studies, and a VR Morris...

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2022

35 projects

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Converting existing scientific workflows to the new dataflow engine Pydra (Python)

Scientific workflows often require sophisticated analyses that encompass an extensive collection of algorithms. In neuroimaging, Nipype (Python) is a...

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Digital Microsphere

In some organisms like axolotl, the surface of the embryo is transparent and thus allowing us to see the embryogenetic events taking place before the...

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Upgrading the source code for the EEG-Notebook Experiment Library

Conducting Cognitive Neuroscience Experiments has always been limited to research-grade EEG devices that cost tens of thousands of dollars. Since the...

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23.1 An Open-Source Software Suite for EEG Artifact Annotation on Web Browsers

Artifacts are parts of a measured signal generated from sources other than those of interest. For electroencephalography (EEG) data, artifacts from a...

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NEUROsim - Cortical Simulator

Cerebral cortex is the outermost layer of the brain and is associated with highest mental capabilities like consciousness, emotion, reasoning,...

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INCF GSoC 2022 1.1. Implementation of White Matter Substrates in Disimpy

Diffusion MRI is a non-invasive imaging technique which provides information about the cellular structure of the brain tissue at microscopic scale....

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Conversion of a public neurophysiology dataset to Neurodata Without Borders (NWB) format

The ever-growing body of data in Neuroscience, which has been enabled by the advancement of state-of-the-art techniques, calls forth collaborative...

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Eye-tracker using deep learning with Python + TensorFlow/Pytorch

Eye tracking has varieties of applications ranging across usability and user experience research, gaming, driving, and gaze-based interaction for...

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Efficient app-based measurement of visual functions in infants and young children

Accurate visual function measurements (e.g., resolution acuity) are vital for assessing vision in clinical practice. It is especially crucial for...

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22.1 GNNs as Developmental Networks

I will seek to create GNNs that resemble actual biological networks found throughout development by analyzing time-series microscopy data. This...

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1.2 Improving GPU-accelerated Monte Carlo simulations in Disimpy

Several attempts have been made in recent years to develop, collect and analyze data in the field of neuroscience. This proposal aims at helping...

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DevoGraph: Modeling Cell Developmental Process of C. elegans using Graph Neural Network

DevoGraph is an open-source framework that models cell developmental process as graphs, extracts and converts latent information into high-level...

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21.1 A Collective Cognition Model for AI Ethics

A Collective Cognition Model to serve as automated guidelines to open source communities. The model will project the activities, interrelationships,...

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Eye-Tracker using Deep Learning with Python + TensorFlow/Pytorch

Eye tracking can be used for a range of purposes, from improving accessibility for people with disabilities to improving driver safety. However,...

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Developing a tool to easily store data and study details

The project aims to create a user-friendly GUI to select simulation results and convert them to a BIDS-compliant structure following the BEP034...

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A GPU-accelerated Model of the Mouse Primary Visual Cortex

PyGeNN is a Python package for simulating spiking neural networks using GPUs. For this project, I will construct and simulate a PyGeNN model of the...

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TVB Data Importer

The Virtual Brain (TVB) is a brain stimulation platform. It offers tools for computing, simulating and analyzing functional and structural data of...

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Improving Graphical Interface and User Experience for AnalySim

I am planning to improve how AnalySim looks by simplifying pages to assure that it is both practical and easy for users to navigate through it. I...

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Ethical Regulators: Could they prove valuable for AI ethics?

During Google Summer of Code 2022, I propose a project in which these feedback loops (recurrent relationships) and causal loops (reciprocal...

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Automatic reviewer matching using Natural Language Processing: Infrastructure for NBDT Journal

Building recommendation engine for suggesting reviewers using Natural Language Processing and Huggingface library. I will be using the editors’...

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17.1: Adding BIDS Prov to new dataflow engine written in Python: Pydra

This project aims to add brain imaging data structure (BIDS) provenance to a workflow engine written in Python called ‘Pydra’. The brain imaging data...

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Automatic Reviewer Matching Using Natural Language Processing: Infrastructure for NBDT Journal

The peer-review process is one of the most crucial processes in science, yet the process can be burdensome and is not free of bias. As the research...

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Simulating multiscale models of the mouse visual cortex in NeuroML

Computational models, based on detailed neuroanatomical and electrophysiological data, are heavily used as an aid for understanding the brain. An...

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Eye-tracker using deep learning with Python + TensorFlow/Pytorch

Eye tracking has varieties of applications, ranging across usability and user experience research, gaming, driving, and gaze-based interaction for...

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Contribute to LORIS: Development of modules and API

This is a proposal to focus on general web development of LORIS modules and API, mentioning key deliverables such as familiarization with the LORIS...

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AnalySim

Editing CSV/Displaying CSV files CSV file viewing and sorting for AnalySim datasets, that can be sorted and filtered. I will study how to create and...

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13.1 Integration of automated model testing and parameter fitting for neuroscience applications

Biologically detailed models are useful tools in neuroscience, and automated methods are now routinely applied to construct and validate such models...

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A Collective Cognition Model for AI Ethics

The proposed project is an approach to the problems of sustainability and collective cognition within small open-source organizations, proceeding in...

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Creating Benchmark Datasets for Object Recognition with Event-based Cameras

Event-based vision is a subfield of computer vision that deals with data from event-based cameras. Event cameras, also known as neuromorphic cameras,...

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9.1 Open source, cross simulator, large scale cortical models in NeuroML and PyNN

NeuroML and PyNN are open, simulation independent formats that are used to convert large scale network models. Network models incorporating realistic...

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Developing a Latex to XML pipeline and exploring a standalone platform for NBDT Journal

I am planning to develop a Latex to XML pipeline and adapt the final format to PMC requirements and integrate the pipeline with the current...

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A GUI for HNN-core with ipywidgets and the calculation and visualization of CSD signals

GUI: In this part, we aim to build a new GUI for HNN, using the HNN core functions and open source practices, in the form of an ipywidget. Mimicking...

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Modelling Axolotl Embryos (Proposal for Project Idea 22.2 Digital Microsphere)

The main objective of this project is to generate a 3D model based on a set of 2D axolotl embryo images to aid as a research tool. The problem can be...

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Developing a LaTeX to XML Pipeline and Exploring a Standalone Platform for NBDT Journal

The platinum open access overlay neuroscience journal - Neurons, Behavior, Data Analysis, and Theory – NBDT is ready for inclusion in PubMed Central...

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Automatic reviewer matching using Natural Language Processing: Infrastructure for NBDT Journal

It often becomes taxing for editors to assign reviewers to a paper in journals, simply because of the vast number of potential reviewers, or even if...

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2021

21 projects

Official year page

Adding more functionality to AnalySim: a data sharing and analysis platform

AnalySim is a data sharing platform similar to GitHub, but specialized for scientific projects. It seeks to simplify the analysis and visualization...

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SOVABIDS: A python package for the automatic conversion of MEG/EEG datasets that makes the most out of metadata

BIDS is a standard for neuroimaging datasets that helps with data sharing and reusability; as a result it has been widely adopted by the community....

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A Django Platform for comparing scientific methods for analyzing neural time series analysis methods

Time-series analysis is a broad, interdisciplinary field, and features for analyzing time-series datasets are ever-increasing. This has led to...

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Maxima Demo and Documentation Tool.

The purpose of this project is to create functions which convert a wxMaxima worksheet to Texinfo. The functions to convert a worksheet will be...

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Conversion of public neurophysiology datasets to NeuroData Without Borders format

Neuroscientists have begun to publicly share more and more datasets, however there are still barriers to making these datasets easily reusable by the...

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Measure the Quality of CerebUnit Validation Tests

This Project is about quantifying the quality of the Validation Tests (CerebTests), a part of CerebUnit Ecosystem for validation tests which needs to...

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Improving Test Coverage and Implementing CI/CD in BrainBox

The idea of the project is to extend the coverage of tests in the BrainBox project and also implement Continuous Integration and Continuous...

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Eye Tracking

Eye tracking has many applications from driver safety to improved accessibility for people with disabilities. There exist expensive and bulky...

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LORIS Codebase Maintenance and Automated Testing

LORIS is an open source data platform that stores data important for numerous ongoing neuroscience projects. These data include brain scans, genetic...

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Population-specific tractography bundle atlas creation

Understanding the inner wiring of the human brain is one of the most long-pursued goals of neuroscientists. In this journey, diffusion MRI (dMRI) and...

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Upgrading DevoLearn

DevoLearn is a python library that contains pre-trained Deep Learning models for the segmentation/analysis of microscopy images. It is specialized...

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Decentralized storage of versioned BIDS datasets with IPFS, datalad and Ceramic

The objective of this project is to build a pipeline for decentralized (IPFS) storage of BIDS-compliant neuroimaging data, with support for version...

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Re-creating the Leech Heartbeat Network Model Tutorial using the Neuron Simulator in Python and NeuroML

The Calabrese Lab 8-cell Leech Tutorial that is described by Hill et al 2001 has been a staple for teaching computational neuroscience at Emory...

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Input/Out Workflows for Active Segmentation Platform

ImageJ is extensively used in major areas of biological and material sciences. Previously developed active segmentation platform as a plugin for...

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Analyzing stimulus prediction capabilities of neurons: predictive information estimation methods

To guide behaviour, it has been proposed that neurons eventually learn to predict future states of sensory inputs. The project mentors have worked in...

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Times Series Classification of EEG Data with Sktime

Electroencephalograms (EEG) and magnetoencephalography (MEG) are techniques for measuring, directly or indirectly, actual or relative changes in...

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TVB for Jupyter and Collaboratory

Make TVB Visualization Tools compatible with Jupyter Notebooks and Google Colaboratory

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SciUnit: integration with NetPyNE and other simulation environments

(Neuro)scientific simulation environments: test-driven development?

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Building a Working Prototype of the AutSPACEs website

AutSPACEs is a citizen science platform that aims to understand how sensory processing differences affect autistic people all around the world. It...

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A Python toolbox for computing high-order information in neuroimaging

The functioning of complex systems (i.e. the brain, and many others) depends on the interaction between different units; crucially, the resulting...

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Support of the simulation-based inference with the model fitting toolbox

Unlike traditional inverse identification tools that rely on gradient and gradient-free methods, simulation-based inference has been established as...

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2020

21 projects

Official year page

IMPROVED MODEL DESCRIPTION FUNCTIONALITY IN BRIAN

Brian is a spiking neural networks simulator, which provides desirable syntactic sugar and flexibility to allow a wide variety of models without...

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Deep learning using geometric features

ImageJ is an open source Java image processing and analysis library used extensively in biomedical sciences. Active Segmentation is a plugin...

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XNAT Dashboards

This project is about creating a responsive dashboard framework for extensive exploration, monitoring, and reviewing large neurological imaging...

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Pre-trained models for Developmental Neuroscience

Deep neural networks are not yet being used (at scale) on microscopic images for research. With the right model architecture and training...

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Improving personalized models of fMRI recordings including individual region-specific HRF in The Virtual Brain

The Virtual Brain (TVB) is a neuroinformatics platform for the simulation of the dynamics of large-scale brain networks with biologically realistic...

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MRI Registration using Deep Learning and Implementation of Thin-Plate Splines

Image registration is the process of finding a transformation that aligns one image to another. DIPY currently supports several numerical...

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LORIS: API development and documentation

LORIS (Longitudinal Online Research and Imaging System) is a web-based data and project management software for neuroimaging research studies. It is...

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Benchmarking modern SNN training algorithms on GeNN

In this proposal, I outline how I plan to implement and benchmark five learning rules - reward-modulated STDP, triplet STDP, compeititve STDP,...

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OpenWorm: OpenDevoCell Integration

This project is about integrating the resources available at the OpenWorm and DevoWorm group. This project will focus on improving the data science...

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TVB: Web GUI for reconstruction pipeline

The project will focus on constructing a Web GUI for Reconstruction pipeline. The reconstruction pipeline takes RMN images as input and processes...

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A reduced time-series feature library to efficiently characterize neural dynamics

Feature extraction is the core aspect of pattern recognition. In the specific domain of NeuroImaging, researchers in the past have formulated...

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LORIS data visualization proposal

This proposal outlines the steps and experience needed for a javascript based data visualization tool for LORIS through the React framework. A method...

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Unit Tests for Large-Scale Brain Network Dynamics

The SciUnit framework was developed to help researchers create unit tests for scientific models. Currently, unit tests exist for models of single...

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Upgrade and Fix tvb-gdist C++ Library

While running simulation on cortical surfaces we need to calculate geodesic distance as opposed to euclidean distance due to the shape of the...

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Automated comparison of scientific methods for time-series analysis

Time series analysis methods are regularly being developed and we don’t have any resource at present that compares the newly developed method with...

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Conversion of large scale cortical models into PyNN/NeuroML

The project Conversion of large scale cortical models into PyNN/NeuroML involves the conversion of published large scale network models into open,...

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LORIS Automated Testing

This project aims to improve the automated testing of the LORIS codebase. This will be achieved through writing both unit and integration tests, as...

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OSB: Conversion of public neurophysiology datasets to NeuroData Without Borders format

Neuroscience data comes in multiple different data formats and structures. These differences provide a major technical barrier to sharing data...

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Python-based electroencephalography (EEG) and deep learning workflow system

The Workflow Designer is a prototype web-based application allowing drag-and-drop creating, editing, and running workflows from a predefined library...

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SciUnit Bifurcation analysis

Extending SciUnit model testing to bifurcation models of spin-glass-like neuron network. I would propose to use model parameter optimization based on...

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Cell Tracking Using Geometric Features

The project aims to provide a robust mechanism for cell tracking using 2D raw image object.Through the use of Viterbi Dynamic Programming based...

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2019

17 projects

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16.4 Open Data for OpenWorm

OpenWorm is an attempt to build a biophysical simulation of the model organism C. elegans via assimilation of published data from a range of sources....

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Web-based GUI for deep learning continuous workflows

This project is a continuous work for the GSoC2018 Dynamic Signal Processing Workflow Designer. The previous existing project is a Web-based GUI to...

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Continuous Integration of Research Data

A GIN micro-service which allows the users to design efficient workflows for their work - probably by automating Snakemake, and build the workflows...

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Improve LORIS Automated Testing

LORIS, or Longitudinal Online Research and Imaging System, is a research data platform (github.com/aces/LORIS) for neuroscience studies. It is a...

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Implementing automatic white matter parcellation in Nighres

Nighres is an open-source Python package that enables high-resolution neuroimaging data to be easily and efficiently processed. Diffusion MRI is an...

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Project: 4.3 The Virtual Brain (TVB) Demo Packages for clinical case studies reports

The project is to provide a set of demo packages, including sample python code and user-friendly webpages to clinical researchers for the...

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Model Fitting

Brian 2 is the new version of Brian software. In 2010 the ModelFitting toolbox was developed for the original version...

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Modeling Neural Development with Braitenberg Vehicles

This project is about building an embodied cognitive simulation, i.e. that in which robots we call vehicles have a body and a simple "mind",...

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"Future-Proofing" Tedana

For tedana to expand, more extensive test cases are needed. A new contributor could have introduced an unknown bug into the codebase, but without...

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Deep Learning in Spiking Neural Networks using GeNN

Building a library that enables conversion of Tensorflow deep neural network models to corresponding Spiking Neural Network architectures, with...

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Running FindSim experiments on cloud servers

The project is about implementing the computing extensive FindSim program on a cloud server and building communication between the web server and the...

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Semantic Image Processing for Developmental Data Science.

ImageJ is an OpenSource image processing tool written in Java which has been extremely helpful in the analysis of scientific images especially...

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Simulating bob_robotics models using Gazebo

Brains on Board (http://brainsonboard.co.uk) is an inter-university project with the aim of developing an autonomous flying robot with the learning...

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Maxima to Python Translator

Maxima is a computer algebra system, which has been growing for the past 40 years. However, given the growing use of Python in Neuroscience, under...

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Visualize a large Connectome in 3D using HTML5

Data visualization plays a crucial role in TVB's neuroinformatics platform, and a Structural Connectivity (connectome) is a core datatype, modelling...

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Project 16.1: P2P File Sharing framework for PyOpenWorm.

The PyOpenWorm data management tool aids in creating, storing, and sharing information about Caenorhabditis elegans and about the evidence...

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Producing publication-ready brain network analysis results and visualisations from the command line

Many scientists around the world perform structural network analyses on the MRI data during neuroscience experiments or studies. Scona was designed...

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2018

16 projects

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Contextual Geometric Representations of Cultural Behavior

The project is about turning a set of mathematical models based on the paper “Contextual Geometric Structures: modeling the fundamental components of...

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Implementation of Two Neural Mass Models on the Open Source Brain Platform

Different computational models have been developed in neuroscience to simulate neural systems, however, these models often use different programming...

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Importing NeuroML morphologies into Brian

Brian is a free, open source simulator for spiking neural networks. It is written in the Python programming language and is available on multiple...

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Building high-resolution 3D models of brain vasculature

In this project, we seek to develop 3D meshing and visualization techniques that are better adapted to the complexity of vascular structures.

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A PyNN interface to GeNN

PyNN is a project written in python that aims at interfacing a handful of neural network simulators. A unified high level interface means that a...

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Easy BIDS: Starter Kit for Brain Imaging Data Structure

Neuroimaging scans can be costly in both time and money to acquire. This creates a barrier for many underfunded researchers without access to the...

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2.3 Monitor Sensors signal in 2D and 3D

The project is about refactoring the current dual brain activity visualiser's 2D plots and adding new visual components to its 3D part to display...

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Modular Machine Learning and Classification Toolbox for ImageJ

ACTIVE SEGMENTATION is an ImageJ plugin that provides a general-purpose environment that allows biologists and other domain experts to use...

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MRI Defacing Detector

In the global community for Magnetic Resonance Imaging (MRI) related research, datasets are often shared publicly due to its expensive acquisition...

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Physics-based XML Model building for mosaic embryogenesis of Caenorhabditis elegans

The Openworm foundation is building the world's first digital organism.(a worm matrix!) The DevoWorm project(under Openworm) is building a...

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Contextual Geometric Representations of Cultural Behavior

The goal of this project is to create a platform that allows the user to run simulations with Contextual Geometric Structures. This model allows for...

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Building a portable open pipeline to detect the hemodynamic response function at rest

Most of the currently used data is task-based fMRI data i.e. the data acquired when the subject performs an explicit task (such as finger-tapping)....

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Dynamic Signal Processing Workflow Designer

INCF is using EEG event-related potential signal processing and machine learning methods for building assistive systems for motor impaired people....

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Add support for Neurodata Without Borders 2.0 to Geppetto

The release of a new NWB version makes it necessary the reintegration of this format into the awesome open-source in-browser neuroscientific...

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Building a Neural Network Animation tool using Python and Blender

The aim of the project is to design and develop a software that converts description files of neural networks (e.g. NineML, NeuroML, SpineML) into a...

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Packaging the virtual brain for the modern world

This project is about packaging of the the virtual brain(tvb) to the scientific community, using the most used scientific software distributors such...

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2017

13 projects

Official year page

Implementing support for numerical integration with GSL in the Brian simulator

The current project aims to implement the option to carry out the numerical integration part in the Brian simulator with integrators defined in...

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In-memory Compression for Neuroscience Applications: Blue-Brain Neuromapp Research & Implementation

State of the art computational tools are in especially high demand in the field of Neuroscience. However, bottleneck exists in terms of how much data...

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Adding MPI support to GeNN

This proposal is for adding MPI support to GeNN. GeNN is known as a GPU-enhanced Neuronal Network simulation environment based on code generation for...

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Active Segmentation Toolbox for ImageJ

The major goal of this project is to Extend the work of making plugin which was developed in last year. This year we need to come up with some...

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model completion dashboard

The OpenWorm project is building a simulation of the C. Elegans in an open science fashion. The model completion dashboard is a web-based...

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Speeding up functional network analysis on fMRI data with distributed, in-memory computation using Apache Spark

In order to study the fMRI images it is necessary to do a preprocessing , which consist of motion correction, slice timing and realignment, spatial...

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GPU implementations for MOOSE

Neuronal and multiscale simulations are computationally demanding, they require large numbers of very similar calculations. One of the core problems...

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Conversion of a large scale hippocampal network model to NeuroML

I propose to convert to NeuroML, test and validate a recent, full scale, multicompartmental CA1 hippocampus model by M. Bezaire DOI:...

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Integrating CBS Tools in the Nipy community

CBS Tools are specialized Java-based image processing tools for ultra-high field MRI data. Making this potent software more easily accessible to...

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TVB-Modernize visualizers

Some of the TVB visualisers are already old and need improvement. This project aims to update three of them, more specific the Wavelet Spectrogram...

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G-Node : odML Library and Editor

The open metaData Markup Language (odML), is a standard and organized format for recording, maintaining, and exchanging metadata in an automated...

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Image processing with ImageJ (segmentation of high-resolution images)

This is a project is about identifying and parameterizing the precursors of neuronal cells within early-stage embryos. We will co-register the names...

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Distributed EEG data storage and processing using Apache Hadoop and Spark

Currently the human assistive system collects the EEG data, processes it and trains customized classifiers. With the increasing number of tested...

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2016

12 projects

Official year page

Building cortical network models in NeuroML2 using procedural and declarative programming approaches

There is a long history of neuronal simulator-specific modelling in the fields of theoretical neuroscience and neuroinformatics. As a result, most of...

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Towards Support for Reverse Engineering of Neural Circuits and Non-Linear Dimensionality Reduction in Fovea and PyDSTool

Computational models of neural circuitry are increasingly superseding single neuron models for understanding dynamic processes in the brain....

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Optimization of neural network simulator via parallelisation

SDDEKit is an algorithmic library written in c backing the neural network simulator of the Virtual Brain's project supporting the calculation of...

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Importing and exporting simulator-independent model-descriptions with the Brian simulator

Brian simulator becomes more and more popular in neuroscience community. At the same time Python is now some kind of state-of-the-art in the field,...

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Shailesh Tripathi- GSoC Project #9.2: Adding OpenCL support to GeNN

GeNN uses the power of GPU parallelism to accelerate simulations. Currently GeNN only supports CUDA limiting its use to NVIDIA GPUs only. The...

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The Virtual Brain Project #2: Improving Parameter Space Exploration Tool

In the last decade simulation models have become more prevalent in a variety of application areas. Each of these models define a set of input...

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Qt5 in PISAK.org, an open system for alternative communication

The project is about replacing technology used by the PISAK program to the Qt5 framework, what will improve its overall quality and allow for easier...

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Image Search for Brain Maps

The brain search feature is a useful tool for researchers since it allows them to find studies from other researchers showing similar results....

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ZeroMQ-based distributed messaging system in the OpenBCI brain­-computer interface framework

OpenBCI (https://github.com/BrainTech/openbci) is GPL-licensed framework for building brain-computer interfaces. It automates common tasks such as:...

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Implementation of a HDF5 export/import to EEGBase

The data produced by experiments of Electroencephalography (EEG) and Event­-related potentials (ERP) is stored in web portal of EEGBase, by...

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Modular Machine Learning and Classification Toolbox for ImageJ

The major goal of our project is come up with new architecture of existing plugin. Our ultimate goal is to reduce the coupling and make it cohesive...

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Modifying the current neuroshare to hdf5 converter to use the NIX format instead.

I would be tweaking the current neuroshare converter so that any proprietary file that can be read with neuroshare could be converted to an open...

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