SciCommons Fullstack Development and AI Features
Contributor: Abhishek__Farshwal
SciCommons is an open source platform for researchers to interact, review, and discuss scientific papers. My project focuses on making the platform a...
Science and medicine
INCF
An open & FAIR neuroscience standards organization
Technologies
C++gpuJavaJavaScriptPython
Topics
brain modellingdatamachine learningneuroimage processingneuroscience
- Total projects
- 232
- Years participating
- 11
- Most recent
- 2026
Participation history
Historical projects
Explainable Spatio-Temporal Graph Evolution for Developmental Neuroscience
Contributor: Barshan Mondal
This project studies the development of a tiny worm called Caenorhabditis elegans, focusing on how its cells divide, grow, and interact during its...
EBRAINS Modular Software Environments and Service Integration
Contributor: Divyanshu Choudhury
The EBRAINS Software Distribution is a monolithic Spack environment that takes over 48 hours to build, making rapid deployment and testing difficult....
Semi-automated iEEG analysis and viewing in a clinical and research environment
Contributor: Eva Ozturk
This project aims to further develop an open-source intracranial EEG (iEEG) analysis platform by integrating clinically relevant seizure detection...
BreathState: A Cross Platform App for HRV Biofeedback and Resonance Breathing Protocols
Contributor: Faraz S
Problem: Currently, resonance frequency-based HRV training is backed by robust scientific evidence, but it remains inaccessible to the masses due to...
The Virtual Brian : New graphical widgets for JupyterLab
Contributor: Kambham Deepthi Reddy
The Virtual Brain (TVB) provides an open-source simulation framework for whole-brain network modeling. Unlike the traditional approach of using...
ActiveVision: continued development of a data and model portal for the study of goal-directed vision
Contributor: Lihong Chen
This project builds an automated benchmarking ecosystem for goal-directed vision. It implements a high-priority leaderboard featuring automatic...
Project #27: Integrating Personalized HRF in The Virtual Brain & EBRAINS
Contributor: M Srikanth
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...
Integrating velocity modelling into PCNToolkit package
Contributor: Maria Glushanina
The project aims to improve longitudinal normative modelling in PCNtoolkit by validating, debugging, and extending velocity-based models to support...
Towards a Generalized Mapping Framework For Gesture-Responsive Music and Speech Generation
Contributor: Mat Vallejo
This project proposes a modular, real-time gesture-to-sound mapping framework for the GestureCap system. It will enable users to translate hand...
Expressive Gesture to Sound Mapping Framework for GestureCap
Contributor: Mikael Molliex
This project develops an expressive gesture-to-sound mapping layer for GestureCap, enabling low-latency gesture data to control playable instruments...
Reusable DSOMM Security Pipeline for EBRAINS MIP Platform
Contributor: moghit-eou
The Medical Informatics Platform (MIP) currently lacks standardized automated governance for its federated infrastructure, leading to deployment...
Strengthening Core Workflows and Notebook Integration in AnalySim
Contributor: Mohab Elshamy
This project will improve AnalySim’s core reliability by addressing fragile user workflows, improving query and search behavior, and making the...
Contribute to LORIS: Improving reliability and maintainability in the electrophysiology browser
Contributor: Montek
This project aims to improve the reliability and maintainability of the LORIS electrophysiology browser through scoped enhancements to browser...
#40: QC-Studio-integrated quality control toolkit for MRI datasets
Contributor: Niusha Sadat Mirhakimi
MRI quality control (QC) is an essential but highly manual and repetitive process in neuroimaging research. Currently, reviewers must navigate...
ImageJ Active Segmentation platform: Parallel Engine for ASP/IJ
Contributor: Pakhi Awasthi
This project accelerates the convolution core of the Active Segmentation Plugin (ASP) in ImageJ by offloading its most compute-intensive pixel...
A Python Command Line Interface (CLI) for the CBRAIN Distributed Computing Platform
Contributor: RafsanNeloy
The project develops an improved Python-based CLI for the CBRAIN distributed computing platform, aiming on usability and modular design. It replaces...
#17 Project Experanto
Contributor: Reema Hanim Hanass
Implement an ast based behavioral filter enabling queries like `(treadmill>0 and eye is not nan) & screen == video`, and expand dataset support with...
HarmonyHub Music Education Interface: Mobile App Hardening and Relative Intonation Learning
Contributor: Renan Cavalcanti
HarmonyHub is an open-source platform designed to improve music education through interactive and technology-driven learning experiences. While the...
Project 39 NeuroSim As A Physics Constrained Model for Finite Horizon Network Control Theory
Contributor: RitamKRoy
The application of Network Control Theory to medical neuroimaging consistently faces the approximation crisis. Current tools rely on infinite-horizon...
Refactoring Synaptic Behavior in HNN-Core
Contributor: Satvik Saluja
This project focuses on improving the computational efficiency and biological realism of synaptic modeling in HNN-Core by refactoring how synapses...
Fix outstanding issues in Brian2CUDA
Contributor: Weiyuan Du
Problem: Brian2CUDA offers significant GPU acceleration for neural simulations, but its current "beta" state contains friction points that hinder...
Improving Statistical Efficiency, Methodological Coverage, and Contributor Onboarding in NiMARE
Contributor: Yu Luo
This project enhances NiMARE’s performance and developer accessibility through a dual-phase optimization strategy. The first phase modernizes the...
Conda packaging for GeNN
Contributor: Agrim Patil
GeNN is a C++ library that generates code for efficiently simulating Spiking Neural Networks (SNNs) using GPUs. In order to compile this generated...
Studying Peripheral Physiological Modulation of Brain Activity (INCF #27)
Contributor: Alex Zhao
Traditionally, brain activity has been analyzed independently from peripheral physiological measurements like the electrocardiogram (ECG), but our...
Python API for new cell types
Contributor: Chetan Kandpal
This project will involve refactoring the Human Neocortical Neurosolver (HNN-core) codebase to enable flexible development of neural circuits with...
GestureCap: Using markerless motion capture and gesture recognition for music generation
Contributor: Deepansh Goel
Last year, work on GestureCap focused on developing an Arduino-based latency measurement system and optimizing the pipeline for low-latency...
Developing standardised biophysically detailed neuronal circuit models using NeuroML
Contributor: Hengye Zhu
This project will convert Macaque auditory thalamocortical circuits model based on NetPyNE implementation into NeuroML standard formats and testing...
Developing an ISPC Backend for GeNN to Enable CPU-Based SNN Simulations
Contributor: Jash Vora
GeNN is a C++ library used for simulating Spiking Neural Networks through GPU-based code generation (CUDA/HIP). Currently, its accessibility is...
DevoTG: Dynamic Graph Neural Networks for Modeling C. elegans Development
Contributor: JayaG
The nematode Caenorhabditis elegans serves as a pivotal model organism in developmental biology due to its well-defined cell lineage, compact genome,...
3. HarmonyHub: Front-end interface refactoring and expansion for multi-instrument support
Contributor: Komal Bhalotia
HarmonyHub is an open-source, modular web application designed to revolutionize music education by integrating modern technologies and pedagogical...
MODELING NEURAL DEVELOPMENTAL PROGRAMS OF C. elegans USING GROWING HYPERGRAPH NEURAL NETWORKS
Contributor: Lalith Bharadwaj
This proposal outlines a novel computational framework for modeling neural developmental programs using Growing Hypergraph Neural Networks (Growing...
ActiveVision: a data and model portal for the study of goal-directed vision
Contributor: Lihong Chen
This project develops an open portal for goal-directed vision research, integrating eye-tracking datasets and machine learning models with tools for...
Develop Python API for Multi-Network Simulations in Human Neocortical Neurosolver (HNN)
Contributor: Maira usman
The Human Neocortical Neurosolver (HNN) is an open-source neural modeling tool designed to help researchers and clinicians interpret human brain...
A Python Command Line Interface (CLI) for the CBRAIN Distributed Computing Platform
Contributor: Md Asiful Alam
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...
BreathState: an open-source Android/iOS and PC app for breathing and heart-rate synchronization
Contributor: Michael Lewis
The project will develop the first version of an app that uses Bluetooth to connect with heart-rate and respiration sensors, calculate metrics of...
#23 SciCommons : A Social-Web Tool For Scientific Discussion, Interaction, Rating and Peer Review
Contributor: Mohd Faisal Ansari
SciCommons is an open-source platform aimed at improving the scientific peer review process through better user experience and web application...
Transitioning from Simulation-Based Inference to Automatic MCMC for Virtual Brain Inference
Contributor: Monica Paoletti
This project aims to replace Simulation-Based Inference (SBI) methods with Markov Chain Monte Carlo (MCMC) techniques for inference problems...
PROJECT #8: Brian Simulator :: Replace Brian’s just-in-time compilation mechanism
Contributor: Mrigesh_Thakur
This project aims to replace Brian’s current just-in-time (JIT) compilation system, which relies on Cython. While functional, Cython introduces slow...
Brian2Wasm: simulations in the browser
Contributor: Palash Chitnavis
This project focuses on enhancing the overall workflow by improving the detection and configuration of the Emscripten toolchain. It aims to optimize...
Harmony Hub: Using Generative AI for Adaptive Learning in Music
Contributor: PRIYANSHU2026
While music educators strive to provide personalized learning paths, existing educational tools often lack the flexibility to adapt to diverse...
Automating BIDS Dataset Registration into the EBRAINS Knowledge Graph
Contributor: Renqing Cuomao
This project aims to build an automated workflow to register BIDS-compliant neuroimaging datasets from external repositories (e.g. Public nEUro) into...
Parallel Filter Implementation for ASP/IJ
Contributor: Rikas Ilamdeen
The Active Segmentation Platform for ImageJ (ASP/IJ) aims to provide a general-purpose workbench that allows biologists and other domain experts to...
[Project 20] Build an AI Agent for KnowledgeSpace using Retrieval-Augmented Generation (RAG)
Contributor: Swastik R
This project builds an AI-powered agent for KnowledgeSpace using Retrieval-Augmented Generation (RAG) to deliver precise, context-aware, and...
19. Contribute to LORIS
Contributor: T Saket Hatwar
LORIS is a comprehensive data management platform that supports diverse datasets in neuroscience research, including imaging, behavioural, clinical,...
Fullstack cloud deployment for NiiVue
Contributor: Thuy T. Dao
NiiVue is a versatile tool for visualizing and handling neuroimaging data, but insufficient documentation creates friction in using it in deploying...
Project 28 Analysim , Preparing for beta release by adding admin section, forking datasets etc.
Contributor: Uday Biswas
Project Deliverables • Admin Section : Implement an admin dashboard to manage users, projects, and datasets. Add moderation tools for handling...
Open Source Community Sustainability
Contributor: Vidhi Rohira
SustainHub is an AI-driven simulation platform designed to study and enhance the sustainability of open-source communities. It models contributors,...
Implementation of SWC to NeuroML converter in PyNeuroML
Contributor: Aditya18
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...
Developmental Graph Neural Networks (D-GNNs) and Visualizations
Contributor: Pakhi Banchalia
DevoGraph is an open-source GNN framework designed specifically for analyzing embryogenetic data. It utilizes Graph Neural Networks (GNNs) as a...
Improving and Extending the User Interface of the Neuroptimus Parameter Optimization Software Tool
Contributor: Eslam Khaled Korany
Neuroptimus, an open-source parameter optimization software tailored for neuroscience applications, has been instrumental in advancing the...
Project 15.1 Analysim, INCF- implementing new features in project dashboard and notebook management.
Contributor: Uday Biswas
Project Deliverables • Implement a Project edit button, file and project rename functionality, fix edit project popup , allow editing list of...
Visualization and UI update for ASP/IJ
Contributor: Rikas Ilamdeen
The Active Segmentation Platform for ImageJ (ASP/IJ) aims to provide a general-purpose workbench that allows biologists and other domain experts to...
Implement batch simulation and optimization routines
Contributor: Abdul Samad Siddiqui
The Human Neocortical Neurosolver (HNN) is a computational tool that enables scientists to study brain responses at the cellular and circuit levels....
Using markerless motion capture to drive music generation
Contributor: Louis Martinez
Gesture-based music generation has existed for some years now, thanks to software such as Wekinator. However, they use machine learning methods that...
(Project Idea - 18.2)Improve-Brian's-markdown-exporter
Contributor: Sparsh_Agrawal
This proposal aims to improve the capability of markdown exporter package inorder to cover multicompartment model, and also to support generation of...
Package Brian's unit system
Contributor: Sorin Birchi
The project aims to refactor the Brain's unit system into a standalone package. Additionally, it aims to incorporate additional functionalities from...
21.1 HarmonyHub: A Web-Based Platform for Learning Variable-Pitch Musical Instruments
Contributor: Keerthi Reddy Kambham
This project aims to build HarmonyHub, a web platform for personalized and engaging learning experiences with variable-pitch instruments like wind...
A natural language interface for querying federated research data
Contributor: Raya Chakravarty
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...
A Social web tool to facilitate rating and commenting on research reports
Contributor: armaanalam
SciCommons aims to revolutionize academic publishing by providing an open peer review platform. The current system faces challenges such as time...
INCF GSoC 2024 Project 8.2 Proposal
Contributor: Jsprouse
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...
14.1 INCF Impact Visualization Portal with ML and Data Analytics (175 h)
Contributor: SuGa_XD
The proposal focuses on prospective ideas that can be employed for enhancement of the existing INCF Impact Visualization Portal. It goes into depth,...
HyperDevoGraph: Modeling C. elegans Development with Hypergraph Convolution Techniques
Contributor: Mehul Arora
This project studies the development of a tiny worm called Caenorhabditis elegans, focusing on how its cells grow and interact from its early stages....
Open Source Community Sustainability
Contributor: Sarrah Bastawala
The ‘Open Source Community Sustainability’ project is about simulating open-source community interactions to encourage conditions leading to...
1.1 - Enhancing tvb-widgets by developing new widgets
Contributor: Priyaa
TheVirtualBrain (TVB) is the first integrative neuroinformatics platform for the modeling of full brain network dynamics. TVB simulator, written in...
Scicommons: A social-web tool to facilitate rating and commenting on research reports
Contributor: Dinakar
The proposal aims to address the issue of the expensive and inaccessible research publishing industry by leveraging modern internet-based social...
LORIS Data Platform Web Modules and API Development
Contributor: Nada Ahmed Elmasry
The project aims to enhance the LORIS web platform, a widely used tool in neuroimaging research with databases utilized by research teams in 22...
Contribute to LORIS
Contributor: Ayush Bhardwaj
The proposal involves contributing to the LORIS codebase, a pivotal resource for neuroscience research. LORIS plays a crucial role in facilitating...
17.1 Semi-Automated Workflows for Physiological Signals
Contributor: Georgios Kikas
This project entails the upgrade of the existing physiopy packages, peakdet and phys2denoise, for optimized interoperability and the development of...
Incorporate new features into an advanced, cross-platform 3D viewer for NeuroML cells and networks
Contributor: Giannis D
The project is about incorporating new features into an existing 3D viewer which allows for visualisation of cells and networks using the NeuroML...
8.1 Automated In-Silico Representation of Published Literature
Contributor: Zequan Liu
Project synopsis / summary: This project is dedicated to developing a set of automated tools and processes for extracting useful neuronal...
Efficient app-based measurement of visual functions in infants and young children
Contributor: Dhruvanshu Joshi
Ensuring healthy vision in infants requires early detection of potential problems. Current Infant Visual Function Measurement Systems built in...
Integration of inference based models to Neuroptimus
Contributor: Tamogh Nekkanti
With the advent of machine learning, statistical learning and modelling becoming more prevalent in today’s world, we can estimate values for an...
Best of both worlds – let’s cherish the features of parametric AND explicit knowledge retrieval
Contributor: Barbara Strasser
The annotation of research data is essential to ensure its findability and reusability. High-quality data annotations require domain expertise, so...
LLM-assisted tool to annotate research data with machine-understandable, semantic data dictionaries
Contributor: Tvisha Vedant.
To participate in the Neurobagel query federation, datasets must conform to Neurobagel’s data model, so annotating the datasets is necessary to...
Image feature and classification database
Contributor: Aaryan Gautam
The Active Segmentation platform for ImageJ (ASP/IJ) was developed in the scope of GSOC 2016 - 2021. The plugin provides a general-purpose...
1.1 Integrate Zenodo API with The Virtual Brain
Contributor: Abhijit Deo
The Virtual Brain (TVB) is a scientific simulation platform that provides all means to generate, manipulate and visualize connectivity and network...
Idea 22.3 - Abhishek Tiwari - Code editor support for Brian model equations
Contributor: AbhishekTiwari
This project involves creating a VS Code extension that provides enhanced support for the Brian2 neural simulator. The extension aims to improve the...
Adding new workers and resource management to new dataflow engine written in Python: Pydra
Contributor: Aditya Agarwal
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...
Technical Improvements to enhance the usability of The Turing Way chapters by different user groups
Contributor: Arya A
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....
Impact visualization portal for global neuro-informatics community
Contributor: Atharva Purohit
The International Neuroinformatics Coordinating Facility (INCF) is a non-profit organization dedicated to advancing the field of neuroscience and...
GSoC 2023 Project Idea 2.2 Generalize parameter optimization routines
Contributor: Carolina Fernandez
The Human Neocortical Neurosolver (HNN) is open-source, computational neural modeling software that allows us to examine the cellular- and...
NWB File Compatibility Testing and Summary Generation via Docker
Contributor: Daksh Rathore
The "NWB File Compatibility Testing and Summary Generation via Docker" project aims to streamline the process of testing NWB (Neurodata Without...
Optimization of the computations of HOIs and integration in the Frites python package
Contributor: Dishie
Activity patterns of neurons have so far been examined both singly and in pairs. Higher order interactions (HOIs), or non-pairwise interactions...
Integration of Automated Model Testing and Parameter Fitting Tools for Neuroscience Applications.
Contributor: Eslam Khaled Korany
Biologically detailed models are essential tools in neuroscience, and automated methods are frequently used to build and validate such models based...
3.1 D-GNNs: developing DevoGraph for computational developmental biology - Himanshu
Contributor: Himanshu Chougule
This project is about using Graph Neural Networks(GNNs) as a method to discover underlying connectivity to characterize a growing network that...
Replicating Auditory Steady-State Response (ASSR) in an auditory cortex model. Project idea 9.1
Contributor: Irene Bernardi
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...
A Social web tool to facilitate rating and commenting on research reports
Contributor: Jyothi Swaroop Reddy Bommareddy
The currently available open-review portal helps in reviewing the research articles, By facilitating official reviewers to comment on the research...
Project 7.1: Working on Implementing CSV Data Browser and Querying Component
Contributor: Kshitiz Sareen
We are trying to solve the difficulty of collaboration among multiple users working on large datasets, particularly in analyzing datasets with many...
7.2 Working on improving graphical interface and user experience on AnalySim
Contributor: PON RAJA PRABHU
To Remove Bootstrap from the application and substitute the design with pure SCSS.To finish implementing the CSS global variables and add component...
Exploring Open Source Sustainability via Agent based Modelling and Reinforcement learning
Contributor: R.V.Rajagopalan
The proposed project aims to address the sustainability challenges faced by open-source software projects by using an agent-based modelling and...
Develop IO Routines for HNN-core outputs
Contributor: Rajat Partani
The idea of the project is to develop IO routines adapted from HNN-core objects while maintaining backwards compatibility with HNN-GUI. The...
Improving LORIS data platform
Contributor: Sanjay Thiyagarajan
Deliverables - Improving existing LORIS Codebase and API features, Write test cases for code changes - handling and serving the data efficiently,...
Efficient app-based measurement of visual functions in infants and young children
Contributor: Soham Mulye
The measurement of visual function in infants and young children is crucial for early detection and treatment of eye conditions that can lead to...
Improving Automatic Reviewer Assignment using Large Language Models For NBDT Journal
Contributor: Subhankar Panda
Matching papers to reviewers based on topics is a crucial task for the Neurons, Behavior, Data Analysis, and Theory (NBDT) journal. However, the...
Advancements in 3D Cellular Microscopy Imaging Through Fine-Tuned CellSAM and DevoNet Models
Contributor: Sushmanth Reddy Mereddy
This project centers on the enhancement and integration of the CellSAM and DevoNet models to elevate the analysis of 3D microscopy images stored in...
4.2 Virtual Reality for Distributed Research (Orthogonal Research and Education Lab) (175 h)
Contributor: VRUSHALI NANDURKAR
Virtual Reality for Distributed Research (VRDR) encompasses a VR showroom, immersive anatomy exploration, model organism studies, and a VR Morris...
Converting existing scientific workflows to the new dataflow engine Pydra (Python)
Contributor: Yibei Chen
Scientific workflows often require sophisticated analyses that encompass an extensive collection of algorithms. In neuroimaging, Nipype (Python) is a...
Digital Microsphere
Contributor: Harikrishna Pillai
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...
Upgrading the source code for the EEG-Notebook Experiment Library
Contributor: Parv
Conducting Cognitive Neuroscience Experiments has always been limited to research-grade EEG devices that cost tens of thousands of dollars. Since the...
23.1 An Open-Source Software Suite for EEG Artifact Annotation on Web Browsers
Contributor: garrettmflynn
Artifacts are parts of a measured signal generated from sources other than those of interest. For electroencephalography (EEG) data, artifacts from a...
NEUROsim - Cortical Simulator
Contributor: rahulsonkar
Cerebral cortex is the outermost layer of the brain and is associated with highest mental capabilities like consciousness, emotion, reasoning,...
INCF GSoC 2022 1.1. Implementation of White Matter Substrates in Disimpy
Contributor: Renata Cruz
Diffusion MRI is a non-invasive imaging technique which provides information about the cellular structure of the brain tissue at microscopic scale....
Conversion of a public neurophysiology dataset to Neurodata Without Borders (NWB) format
Contributor: Anh
The ever-growing body of data in Neuroscience, which has been enabled by the advancement of state-of-the-art techniques, calls forth collaborative...
Eye-tracker using deep learning with Python + TensorFlow/Pytorch
Contributor: Prakanshul Saxena
Eye tracking has varieties of applications ranging across usability and user experience research, gaming, driving, and gaze-based interaction for...
Efficient app-based measurement of visual functions in infants and young children
Contributor: wizofe
Accurate visual function measurements (e.g., resolution acuity) are vital for assessing vision in clinical practice. It is especially crucial for...
22.1 GNNs as Developmental Networks
Contributor: Watarungurunnn
I will seek to create GNNs that resemble actual biological networks found throughout development by analyzing time-series microscopy data. This...
1.2 Improving GPU-accelerated Monte Carlo simulations in Disimpy
Contributor: Joel Hurtado Moreno
Several attempts have been made in recent years to develop, collect and analyze data in the field of neuroscience. This proposal aims at helping...
DevoGraph: Modeling Cell Developmental Process of C. elegans using Graph Neural Network
Contributor: Jiahang Li
DevoGraph is an open-source framework that models cell developmental process as graphs, extracts and converts latent information into high-level...
21.1 A Collective Cognition Model for AI Ethics
Contributor: Himanshu Chougule
A Collective Cognition Model to serve as automated guidelines to open source communities. The model will project the activities, interrelationships,...
Eye-Tracker using Deep Learning with Python + TensorFlow/Pytorch
Contributor: Somnath Sharma
Eye tracking can be used for a range of purposes, from improving accessibility for people with disabilities to improving driver safety. However,...
Developing a tool to easily store data and study details
Contributor: Dinara Issagaliyeva
The project aims to create a user-friendly GUI to select simulation results and convert them to a BIDS-compliant structure following the BEP034...
A GPU-accelerated Model of the Mouse Primary Visual Cortex
Contributor: William Snider
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...
TVB Data Importer
Contributor: Akash Upadhyay
The Virtual Brain (TVB) is a brain stimulation platform. It offers tools for computing, simulating and analyzing functional and structural data of...
Improving Graphical Interface and User Experience for AnalySim
Contributor: Ahkeelah Lindo
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...
Ethical Regulators: Could they prove valuable for AI ethics?
Contributor: SHussainAther
During Google Summer of Code 2022, I propose a project in which these feedback loops (recurrent relationships) and causal loops (reciprocal...
Automatic reviewer matching using Natural Language Processing: Infrastructure for NBDT Journal
Contributor: Mrunal Prakash Gavali
Building recommendation engine for suggesting reviewers using Natural Language Processing and Huggingface library. I will be using the editors’...
17.1: Adding BIDS Prov to new dataflow engine written in Python: Pydra
Contributor: RyanCali
This project aims to add brain imaging data structure (BIDS) provenance to a workflow engine written in Python called ‘Pydra’. The brain imaging data...
Automatic Reviewer Matching Using Natural Language Processing: Infrastructure for NBDT Journal
Contributor: Alan (Bangyan) Zhang
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...
Simulating multiscale models of the mouse visual cortex in NeuroML
Contributor: Anuja Negi
Computational models, based on detailed neuroanatomical and electrophysiological data, are heavily used as an aid for understanding the brain. An...
Eye-tracker using deep learning with Python + TensorFlow/Pytorch
Contributor: Abhinav Venkatadri
Eye tracking has varieties of applications, ranging across usability and user experience research, gaming, driving, and gaze-based interaction for...
Contribute to LORIS: Development of modules and API
Contributor: Satvik Singh
This is a proposal to focus on general web development of LORIS modules and API, mentioning key deliverables such as familiarization with the LORIS...
AnalySim
Contributor: Joseph Ongchangco
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...
13.1 Integration of automated model testing and parameter fitting for neuroscience applications
Contributor: Martin Blazsek
Biologically detailed models are useful tools in neuroscience, and automated methods are now routinely applied to construct and validate such models...
A Collective Cognition Model for AI Ethics
Contributor: Brian McCorkle
The proposed project is an approach to the problems of sustainability and collective cognition within small open-source organizations, proceeding in...
Creating Benchmark Datasets for Object Recognition with Event-based Cameras
Contributor: Neelay Shah
Event-based vision is a subfield of computer vision that deals with data from event-based cameras. Event cameras, also known as neuromorphic cameras,...
9.1 Open source, cross simulator, large scale cortical models in NeuroML and PyNN
Contributor: Shayan Shafquat
NeuroML and PyNN are open, simulation independent formats that are used to convert large scale network models. Network models incorporating realistic...
Developing a Latex to XML pipeline and exploring a standalone platform for NBDT Journal
Contributor: Naresh Kumar B
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...
A GUI for HNN-core with ipywidgets and the calculation and visualization of CSD signals
Contributor: Huzi Cheng
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...
Modelling Axolotl Embryos (Proposal for Project Idea 22.2 Digital Microsphere)
Contributor: Karan Lohaan
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...
Developing a LaTeX to XML Pipeline and Exploring a Standalone Platform for NBDT Journal
Contributor: Amogh Johri
The platinum open access overlay neuroscience journal - Neurons, Behavior, Data Analysis, and Theory – NBDT is ready for inclusion in PubMed Central...
Automatic reviewer matching using Natural Language Processing: Infrastructure for NBDT Journal
Contributor: Varshita Kolipaka
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...
Adding more functionality to AnalySim: a data sharing and analysis platform
Contributor: Nga Tran
AnalySim is a data sharing platform similar to GitHub, but specialized for scientific projects. It seeks to simplify the analysis and visualization...
SOVABIDS: A python package for the automatic conversion of MEG/EEG datasets that makes the most out of metadata
Contributor: Yorguin Mantilla Ramos
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....
A Django Platform for comparing scientific methods for analyzing neural time series analysis methods
Contributor: Diptanshu Mittal
Time-series analysis is a broad, interdisciplinary field, and features for analyzing time-series datasets are ever-increasing. This has led to...
Maxima Demo and Documentation Tool.
Contributor: Aditya Wagh
The purpose of this project is to create functions which convert a wxMaxima worksheet to Texinfo. The functions to convert a worksheet will be...
Conversion of public neurophysiology datasets to NeuroData Without Borders format
Contributor: Steph Prince
Neuroscientists have begun to publicly share more and more datasets, however there are still barriers to making these datasets easily reusable by the...
Measure the Quality of CerebUnit Validation Tests
Contributor: Harsh Khilawala
This Project is about quantifying the quality of the Validation Tests (CerebTests), a part of CerebUnit Ecosystem for validation tests which needs to...
Improving Test Coverage and Implementing CI/CD in BrainBox
Contributor: Aditya R Rudra
The idea of the project is to extend the coverage of tests in the BrainBox project and also implement Continuous Integration and Continuous...
Eye Tracking
Contributor: Dinesh Sathia Raj
Eye tracking has many applications from driver safety to improved accessibility for people with disabilities. There exist expensive and bulky...
LORIS Codebase Maintenance and Automated Testing
Contributor: Viet Hoang
LORIS is an open source data platform that stores data important for numerous ongoing neuroscience projects. These data include brain scans, genetic...
Population-specific tractography bundle atlas creation
Contributor: David Romero Bascones
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...
Upgrading DevoLearn
Contributor: Mainak Deb
DevoLearn is a python library that contains pre-trained Deep Learning models for the segmentation/analysis of microscopy images. It is specialized...
Decentralized storage of versioned BIDS datasets with IPFS, datalad and Ceramic
Contributor: kinshuk
The objective of this project is to build a pipeline for decentralized (IPFS) storage of BIDS-compliant neuroimaging data, with support for version...
Re-creating the Leech Heartbeat Network Model Tutorial using the Neuron Simulator in Python and NeuroML
Contributor: Psyogi Soma
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...
Input/Out Workflows for Active Segmentation Platform
Contributor: Piyumal Demotte
ImageJ is extensively used in major areas of biological and material sciences. Previously developed active segmentation platform as a plugin for...
Analyzing stimulus prediction capabilities of neurons: predictive information estimation methods
Contributor: Shiven Tripathi
To guide behaviour, it has been proposed that neurons eventually learn to predict future states of sensory inputs. The project mentors have worked in...
Times Series Classification of EEG Data with Sktime
Contributor: Svea Marie Meyer
Electroencephalograms (EEG) and magnetoencephalography (MEG) are techniques for measuring, directly or indirectly, actual or relative changes in...
TVB for Jupyter and Collaboratory
Contributor: Ishan Vatsaraj
Make TVB Visualization Tools compatible with Jupyter Notebooks and Google Colaboratory
SciUnit: integration with NetPyNE and other simulation environments
Contributor: Evgeniia Karunus
(Neuro)scientific simulation environments: test-driven development?
Building a Working Prototype of the AutSPACEs website
Contributor: Anoushka Ramesh
AutSPACEs is a citizen science platform that aims to understand how sensory processing differences affect autistic people all around the world. It...
A Python toolbox for computing high-order information in neuroimaging
Contributor: Pranav Mahajan
The functioning of complex systems (i.e. the brain, and many others) depends on the interaction between different units; crucially, the resulting...
Support of the simulation-based inference with the model fitting toolbox
Contributor: Ante Lojic Kapetanovic
Unlike traditional inverse identification tools that rely on gradient and gradient-free methods, simulation-based inference has been established as...
IMPROVED MODEL DESCRIPTION FUNCTIONALITY IN BRIAN
Contributor: VIGNESWARAN C
Brian is a spiking neural networks simulator, which provides desirable syntactic sugar and flexibility to allow a wide variety of models without...
Deep learning using geometric features
Contributor: Joanna Stachera
ImageJ is an open source Java image processing and analysis library used extensively in biomedical sciences. Active Segmentation is a plugin...
XNAT Dashboards
Contributor: Mohammad Asif Hashmi
This project is about creating a responsive dashboard framework for extensive exploration, monitoring, and reviewing large neurological imaging...
Pre-trained models for Developmental Neuroscience
Contributor: Mayukh Deb
Deep neural networks are not yet being used (at scale) on microscopic images for research. With the right model architecture and training...
Improving personalized models of fMRI recordings including individual region-specific HRF in The Virtual Brain
Contributor: Amogh Johri
The Virtual Brain (TVB) is a neuroinformatics platform for the simulation of the dynamics of large-scale brain networks with biologically realistic...
MRI Registration using Deep Learning and Implementation of Thin-Plate Splines
Contributor: Sarath Chandra
Image registration is the process of finding a transformation that aligns one image to another. DIPY currently supports several numerical...
LORIS: API development and documentation
Contributor: Simon Pelletier
LORIS (Longitudinal Online Research and Imaging System) is a web-based data and project management software for neuroimaging research studies. It is...
Benchmarking modern SNN training algorithms on GeNN
Contributor: ManviAgarwal
In this proposal, I outline how I plan to implement and benchmark five learning rules - reward-modulated STDP, triplet STDP, compeititve STDP,...
OpenWorm: OpenDevoCell Integration
Contributor: Ujjwalll
This project is about integrating the resources available at the OpenWorm and DevoWorm group. This project will focus on improving the data science...
TVB: Web GUI for reconstruction pipeline
Contributor: Punit Batra
The project will focus on constructing a Web GUI for Reconstruction pipeline. The reconstruction pipeline takes RMN images as input and processes...
A reduced time-series feature library to efficiently characterize neural dynamics
Contributor: Imran Alam
Feature extraction is the core aspect of pattern recognition. In the specific domain of NeuroImaging, researchers in the past have formulated...
LORIS data visualization proposal
Contributor: Karim Hasbini
This proposal outlines the steps and experience needed for a javascript based data visualization tool for LORIS through the React framework. A method...
Unit Tests for Large-Scale Brain Network Dynamics
Contributor: Sorenza Bastiaens
The SciUnit framework was developed to help researchers create unit tests for scientific models. Currently, unit tests exist for models of single...
Upgrade and Fix tvb-gdist C++ Library
Contributor: Ayan Banerjee7
While running simulation on cortical surfaces we need to calculate geodesic distance as opposed to euclidean distance due to the shape of the...
Automated comparison of scientific methods for time-series analysis
Contributor: Salman Khan
Time series analysis methods are regularly being developed and we don’t have any resource at present that compares the newly developed method with...
Conversion of large scale cortical models into PyNN/NeuroML
Contributor: Ronaldo Nunes
The project Conversion of large scale cortical models into PyNN/NeuroML involves the conversion of published large scale network models into open,...
LORIS Automated Testing
Contributor: Alexandra Livadas
This project aims to improve the automated testing of the LORIS codebase. This will be achieved through writing both unit and integration tests, as...
OSB: Conversion of public neurophysiology datasets to NeuroData Without Borders format
Contributor: Vergil Haynes
Neuroscience data comes in multiple different data formats and structures. These differences provide a major technical barrier to sharing data...
Python-based electroencephalography (EEG) and deep learning workflow system
Contributor: Ronak Doshi
The Workflow Designer is a prototype web-based application allowing drag-and-drop creating, editing, and running workflows from a predefined library...
SciUnit Bifurcation analysis
Contributor: S. Hussain Ather
Extending SciUnit model testing to bifurcation models of spin-glass-like neuron network. I would propose to use model parameter optimization based on...
Cell Tracking Using Geometric Features
Contributor: Raghavendra
The project aims to provide a robust mechanism for cell tracking using 2D raw image object.Through the use of Viterbi Dynamic Programming based...
16.4 Open Data for OpenWorm
Contributor: Emily Thomas
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....
Web-based GUI for deep learning continuous workflows
Contributor: Yijie Huang
This project is a continuous work for the GSoC2018 Dynamic Signal Processing Workflow Designer. The previous existing project is a Web-based GUI to...
Continuous Integration of Research Data
Contributor: Mrinal Wahal
A GIN micro-service which allows the users to design efficient workflows for their work - probably by automating Snakemake, and build the workflows...
Improve LORIS Automated Testing
Contributor: Alexandra Livadas
LORIS, or Longitudinal Online Research and Imaging System, is a research data platform (github.com/aces/LORIS) for neuroscience studies. It is a...
Implementing automatic white matter parcellation in Nighres
Contributor: Leevi Kerkelä
Nighres is an open-source Python package that enables high-resolution neuroimaging data to be easily and efficiently processed. Diffusion MRI is an...
Project: 4.3 The Virtual Brain (TVB) Demo Packages for clinical case studies reports
Contributor: Simone L.
The project is to provide a set of demo packages, including sample python code and user-friendly webpages to clinical researchers for the...
Model Fitting
Contributor: Aleksandra Teska
Brian 2 is the new version of Brian software. In 2010 the ModelFitting toolbox was developed for the original version...
Modeling Neural Development with Braitenberg Vehicles
Contributor: Stefan Dvoretskii
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",...
"Future-Proofing" Tedana
Contributor: Monica Yao
For tedana to expand, more extensive test cases are needed. A new contributor could have introduced an unknown bug into the codebase, but without...
Deep Learning in Spiking Neural Networks using GeNN
Contributor: Ajay Subramanian
Building a library that enables conversion of Tensorflow deep neural network models to corresponding Spiking Neural Network architectures, with...
Running FindSim experiments on cloud servers
Contributor: Hou Chen
The project is about implementing the computing extensive FindSim program on a cloud server and building communication between the web server and the...
Semantic Image Processing for Developmental Data Science.
Contributor: Vinay Varma Nadimpalli
ImageJ is an OpenSource image processing tool written in Java which has been extremely helpful in the analysis of scientific images especially...
Simulating bob_robotics models using Gazebo
Contributor: Shinjan Mitra
Brains on Board (http://brainsonboard.co.uk) is an inter-university project with the aim of developing an autonomous flying robot with the learning...
Maxima to Python Translator
Contributor: Lakshya A Agrawal
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...
Visualize a large Connectome in 3D using HTML5
Contributor: Nakul Bharti
Data visualization plays a crucial role in TVB's neuroinformatics platform, and a Structural Connectivity (connectome) is a core datatype, modelling...
Project 16.1: P2P File Sharing framework for PyOpenWorm.
Contributor: Jaideep Seth
The PyOpenWorm data management tool aids in creating, storing, and sharing information about Caenorhabditis elegans and about the evidence...
Producing publication-ready brain network analysis results and visualisations from the command line
Contributor: Ruslan Yermakov
Many scientists around the world perform structural network analyses on the MRI data during neuroscience experiments or studies. Scona was designed...
Contextual Geometric Representations of Cultural Behavior
Contributor: CHENG-HSUN HSUEH
The project is about turning a set of mathematical models based on the paper “Contextual Geometric Structures: modeling the fundamental components of...
Implementation of Two Neural Mass Models on the Open Source Brain Platform
Contributor: Jessica Dafflon
Different computational models have been developed in neuroscience to simulate neural systems, however, these models often use different programming...
Importing NeuroML morphologies into Brian
Contributor: kapilkd13
Brian is a free, open source simulator for spiking neural networks. It is written in the Python programming language and is available on multiple...
Building high-resolution 3D models of brain vasculature
Contributor: Laura Bilicz
In this project, we seek to develop 3D meshing and visualization techniques that are better adapted to the complexity of vascular structures.
A PyNN interface to GeNN
Contributor: Anton Komissarov
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...
Easy BIDS: Starter Kit for Brain Imaging Data Structure
Contributor: Patrick Park
Neuroimaging scans can be costly in both time and money to acquire. This creates a barrier for many underfunded researchers without access to the...
2.3 Monitor Sensors signal in 2D and 3D
Contributor: Xiangxiu Meng
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...
Modular Machine Learning and Classification Toolbox for ImageJ
Contributor: getsanjeev
ACTIVE SEGMENTATION is an ImageJ plugin that provides a general-purpose environment that allows biologists and other domain experts to use...
MRI Defacing Detector
Contributor: Wazeer Zulfikar
In the global community for Magnetic Resonance Imaging (MRI) related research, datasets are often shared publicly due to its expensive acquisition...
Physics-based XML Model building for mosaic embryogenesis of Caenorhabditis elegans
Contributor: Arnab Banerjee
The Openworm foundation is building the world's first digital organism.(a worm matrix!) The DevoWorm project(under Openworm) is building a...
Contextual Geometric Representations of Cultural Behavior
Contributor: Sam
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...
Building a portable open pipeline to detect the hemodynamic response function at rest
Contributor: madhur.tandon
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)....
Dynamic Signal Processing Workflow Designer
Contributor: Joey Pinto
INCF is using EEG event-related potential signal processing and machine learning methods for building assistive systems for motor impaired people....
Add support for Neurodata Without Borders 2.0 to Geppetto
Contributor: Afonso Pinto
The release of a new NWB version makes it necessary the reintegration of this format into the awesome open-source in-browser neuroscientific...
Building a Neural Network Animation tool using Python and Blender
Contributor: Alona Sakhnenko
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...
Packaging the virtual brain for the modern world
Contributor: pyc0d3r
This project is about packaging of the the virtual brain(tvb) to the scientific community, using the most used scientific software distributors such...
Implementing support for numerical integration with GSL in the Brian simulator
Contributor: Charlee Fletterman
The current project aims to implement the option to carry out the numerical integration part in the Brian simulator with integrators defined in...
In-memory Compression for Neuroscience Applications: Blue-Brain Neuromapp Research & Implementation
Contributor: Devin Bayly
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...
Adding MPI support to GeNN
Contributor: Mengchi Zhang
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...
Active Segmentation Toolbox for ImageJ
Contributor: Mukesh Gupta
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...
model completion dashboard
Contributor: shubhsingh594
The OpenWorm project is building a simulation of the C. Elegans in an open science fashion. The model completion dashboard is a web-based...
Speeding up functional network analysis on fMRI data with distributed, in-memory computation using Apache Spark
Contributor: Aldo Camargo
In order to study the fMRI images it is necessary to do a preprocessing , which consist of motion correction, slice timing and realignment, spatial...
GPU implementations for MOOSE
Contributor: Micky
Neuronal and multiscale simulations are computationally demanding, they require large numbers of very similar calculations. One of the core problems...
Conversion of a large scale hippocampal network model to NeuroML
Contributor: András Ecker
I propose to convert to NeuroML, test and validate a recent, full scale, multicompartmental CA1 hippocampus model by M. Bezaire DOI:...
Integrating CBS Tools in the Nipy community
Contributor: Julia Huntenburg
CBS Tools are specialized Java-based image processing tools for ultra-high field MRI data. Making this potent software more easily accessible to...
TVB-Modernize visualizers
Contributor: DanPop
Some of the TVB visualisers are already old and need improvement. This project aims to update three of them, more specific the Wavelet Spectrogram...
G-Node : odML Library and Editor
Contributor: Shubham Dighe
The open metaData Markup Language (odML), is a standard and organized format for recording, maintaining, and exchanging metadata in an automated...
Image processing with ImageJ (segmentation of high-resolution images)
Contributor: Siddharth Yadav
This is a project is about identifying and parameterizing the precursors of neuronal cells within early-stage embryos. We will co-register the names...
Distributed EEG data storage and processing using Apache Hadoop and Spark
Contributor: Dorian Beganovic
Currently the human assistive system collects the EEG data, processes it and trains customized classifiers. With the increasing number of tested...
Building cortical network models in NeuroML2 using procedural and declarative programming approaches
Contributor: Rokas
There is a long history of neuronal simulator-specific modelling in the fields of theoretical neuroscience and neuroinformatics. As a result, most of...
Towards Support for Reverse Engineering of Neural Circuits and Non-Linear Dimensionality Reduction in Fovea and PyDSTool
Contributor: mcneela
Computational models of neural circuitry are increasingly superseding single neuron models for understanding dynamic processes in the brain....
Optimization of neural network simulator via parallelisation
Contributor: Wenyan
SDDEKit is an algorithmic library written in c backing the neural network simulator of the Virtual Brain's project supporting the calculation of...
Importing and exporting simulator-independent model-descriptions with the Brian simulator
Contributor: dokato
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,...
Shailesh Tripathi- GSoC Project #9.2: Adding OpenCL support to GeNN
Contributor: Shailesh Tripathi
GeNN uses the power of GPU parallelism to accelerate simulations. Currently GeNN only supports CUDA limiting its use to NVIDIA GPUs only. The...
The Virtual Brain Project #2: Improving Parameter Space Exploration Tool
Contributor: Dabyly
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...
Qt5 in PISAK.org, an open system for alternative communication
Contributor: bj
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...
Image Search for Brain Maps
Contributor: Asier Erramuzpe
The brain search feature is a useful tool for researchers since it allows them to find studies from other researchers showing similar results....
ZeroMQ-based distributed messaging system in the OpenBCI brain-computer interface framework
Contributor: Alex Chrabrow
OpenBCI (https://github.com/BrainTech/openbci) is GPL-licensed framework for building brain-computer interfaces. It automates common tasks such as:...
Implementation of a HDF5 export/import to EEGBase
Contributor: Ipsita
The data produced by experiments of Electroencephalography (EEG) and Event-related potentials (ERP) is stored in web portal of EEGBase, by...
Modular Machine Learning and Classification Toolbox for ImageJ
Contributor: Sumit Vohra
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...
Modifying the current neuroshare to hdf5 converter to use the NIX format instead.
Contributor: Abhay Chaturvedi
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...