Working Groups
Working Groups(WGs) are composed of users and developers from across the INCF network working collaboratively to develop, refine, and/or implement community standards. WGs represent short-term projects that aim to achieve a concrete deliverable. The WGs also serve as forums for getting agreement and community buy-in on the use of these standards and best practices. All community members are welcome to be WG members, regardless of their location in the world. INCF gives support with group communications, coordination between groups, and assistance with logistics and outreach.
This working group serves users and use cases of MATLAB (and Simulink) for psychophysics experimental control & data analysis, including applications in vision science, cellular neuroscience, and human brain mapping. Psychophysics software supports quantitative assessment of the…
This working group serves users and use cases of MATLAB (and Simulink) for cellular-scale neuroscience, including electrical live recordings (e.g., neural probes), optical live recordings (e.g., calcium imaging), and anatomical imaging (e.g., connectomics). The working group is attuned…
This Working Group aims to develop tools for the ARTEM-IS standard for electrophysiological methods reporting. ARTEM-IS stands for an Agreed Reporting Template for EEG Methodology - International Standard. Accurate reporting is critical for transparent, reproducible, replicable…
The NIDM Working Group is further developing the NeuroImaging Data Model (NIDM) originally conceived by the INCF Neuro Imaging DAta SHaring (NIDASH) Task Force and the BIRN…
This working group will turn the COBIDAS recommendations and guidelines into a series of checklists hosted on a website, to let users report information faster and with more detail.
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This working group is joint between OCNS and INCF. The group focuses on evaluating and testing computational neuroscience tools; finding them, testing them, learning how they work, and informing developers of issues to ensure that these tools remain in good shape by having communities…
The goal of this Working Group is to develop a set of specifications and tools that would allow standardization of a directory structure for experimental data, recorded with animal models in neuroscience. It will capitalize on the success of BIDS for human neuroimaging data, while…
The Working Group is composed of electrophysiology representatives from the INCF network, Human Brain Project (HBP), Neurodata Without Borders (NWB) Core Development Team, and Stimulating Peripheral Activity to Relieve Conditions (SPARC), sharing use cases from the respective projects.…
Countries in Asia Pacific face a major societal burden due to decline in mental abilities and health of the rapidly aging population. The technology solutions to this challenge will come from the intersection of aging neuroscience, cognitive engineering and information sciences. We…
This Working Group coordinates community efforts for the development of open, use case- driven and shared validatable data models (schemas, vocabularies) to enable the FAIR principles (Findable, Accessible, Interoperable and Reusable) for basic, computational and clinical…
This Working Group formed as the result of a merger of several INCF Working Groups working in the areas of neuroimaging and reproducibility. The group has several separate projects that all have reproducibility in neuroimaging as an overarching theme, specifically focusing on data…
The motivation for this Working Group is the ongoing development of complex data-driven models of neuronal networks, as well as the emergence of general purpose software packages and standardised formats to make it easier to build, specify and share such networks. To encourage…
This Working Group develops standards and best practices for quality control (QC) of neuroimaging data, including standardized protocols, easy to use tools and comprehensive manuals. Assessing the quality of neuroimaging data requires human visual inspection. Given the complex nature,…
This working group serves the developers and users of MatNWB, the MATLAB interface to the INCF-endorsed Neurodata without Borders (NWB) data standard. Neurodata Without Borders (NWB) is a data standard for neurophysiology, providing neuroscientists with a common standard to share,…
Metadata Schema of Common Data Elements for Traumatic Brain Injury working group aims to develop a metadata schema for federated data analysis on Traumatic Brain Injury (TBI) datasets through the Medical Informatics Platform (MIP). It is based on data elements from NINDS CDE catalog.…
This Working Group coordinates common efforts for defining and describing cell types across neuroscience, to reduce duplicate efforts and to improve interoperability and reuse of cell type-specific data collected across groups. The key focus is facilitating interactions between groups…
Agent-based Models (ABM) use both first-person and third-person perspectives. This project aims to develop an AR/VR experiment application which is compatible with all devices such as Meta quest and Web XR. This will in turn allow learners and researchers from around the world to…
DevoGraph has two stages to build a graph neural network (GNN): stage 1 is to extract centroids and we feed this to stage 2 to build a GNN. However, DevoLearn does not properly segment when cells are densely located, and thus, the volume cannot be extracted. We therefore propose a new…
This project requires building a new Structural Connectivity Editor Widget. It will have the following features (but not limited to): display connectivity matrix, normalize matrix, resect connections, resect nodes, change connection weights, and save the resultant connectivity. It will…
Matching papers to reviewers based on topics is a crucial task for the Neurons, Behavior, Data Analysis, and Theory (NBDT) journal. However, the current automatic reviewer assignment tool that uses SciBERT embeddings, cosine similarity, and linear programming may not capture the…
The measurement of visual function in infants and young children is crucial for early detection and treatment of eye conditions that can lead to visual deprivation and affect visual development. However, the limited cooperation and inability to provide verbal responses in infants make…
This project is geared towards improving the Longitudinal Online Research and Imaging System (LORIS) data platform, the web-based data and project management software for neuroimaging research studies.
The idea of the project is to develop IO routines adapted from Human Neocortical Neurosolver (HNN)-core objects while maintaining backwards compatibility with HNN-GUI. The requirement is to save various objects in newer formats while having capability to read both new and old formats.…
The proposed project aims to address the sustainability challenges faced by open-source software projects by using an agent-based modelling and simulation approach. Open-source projects often face issues such as limited resources, difficulty in attracting and retaining contributors,…
This project’s objective is to improve the overall GUI design and user experience of the AnalySim platform. From design to functionality, various features will be examined and either replaced or modified to enhance users’ interaction with datasets, code, and site navigation.
We are trying to solve the difficulty of collaboration among multiple users working on large datasets, particularly in analyzing datasets with many parameters and essential features that need to be filtered, measured, and analyzed. The solution is AnalySim, a data-sharing platform that…
The currently available open-review portal helps in reviewing the research articles, By facilitating official reviewers to comment on the research article. This may be a time-consuming process and as the number of submitted articles increases, it would be difficult for a small group of…
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 rhythm (40 Hz). A hallmark of schizophrenia is a reduction in ASSR; this project aims at reproducing this phenomenon using an auditory…
This project is about using Graph Neural Networks(GNNs) as a method to discover underlying connectivity to characterize a growing network that undergoes shape as well as size transformations for C. elegans. There are three parts to this project, all of which aim to integrate previous…
Biologically detailed models are essential tools in neuroscience, and automated methods are frequently used to build and validate such models based on experimental data. The open-source parameter optimization software Neuroptimus was developed to enable easy application of advanced…
Activity patterns of neurons have so far been examined both singly and in pairs. Higher order interactions (HOIs), or non-pairwise interactions between neurons, are being studied in an effort to improve analysis. The type and quantity of information stored in groups (pairs or…
To promote transparency and enable the reuse of the data for subsequent studies, neuroscientists are increasingly making their experimental datasets available to the public. However, these dataset are often not in an accessible format, which makes it difficult for other researchers to…
The Human Neocortical Neurosolver (HNN) is open-source, computational neural modeling software that allows us to examine the cellular- and circuit-level basis of brain responses. HNN requires the hand-tuning of a large set of parameters until a close fit between simulated and recorded…
The International Neuroinformatics Coordinating Facility (INCF) is a non-profit organization dedicated to advancing the field of neuroscience and neuroinformatics. They strive to establish and promote standards and best practices that are open, fair, and citable. INCF provides…
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. Over the last four years, the book has grown significantly, making it challenging to navigate. The team created a Python package in 2022 to…
This project 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 schedulers. The objective of this project is to create a Pydra worker class capable of submitting and monitor jobs on different HPC systems,…
This project involves creating a VS Code extension that provides enhanced support for the Brian2 neural simulator. The extension aims to improve the user experience and productivity of those working with Brian2 by offering syntax highlighting, syntax checking, auto-completion, and…
The Virtual Brain (TVB) is a scientific simulation platform that provides all means to generate, manipulate and visualize connectivity and network dynamics of the brain networks. Researchers in Computational Neuroscience use brain network models to understand the dynamic behavior of…
The feature space and the classification results produced by the platform are stored in several separate files. The idea is that the types and values of image features and classification outcomes would be stored in an SQLite database for cross-comparisons between sessions. The…
LORIS (Longitudinal Online Research and Imaging System) is a web-based data and project management software for neuroimaging research studies. It is an open source framework for storing and processing behavioural, clinical, neuroimaging and genetic data. LORIS also makes it…
The Virtual Brain (TVB) is a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. It enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic…
Open Source Brain is an online resource for sharing and collaboratively developing computational models of neural systems. Learn more at: https://www.opensourcebrain.org/
ImageJ is a public domain Java image processing program extensively used in life sciences. The program was designed with an open architecture that provides extensibility via Java plugins. User-written plugins make it possible to solve almost any image processing or analysis…
GeNN is a GPU enhanced Neuronal Network simulation environment based on NVIDIA CUDA technology. Learn more at: https://genn-team.github.io/genn/
BRIAN is a free, open source simulator for spiking neural networks. It is written in the Python programming language and is available on almost all platforms. BRIAN is designed to be easy to learn and use, highly flexible, and easily extensible. Learn more at:…
When The Virtual Brain(TVB) runs simulations on cortical surfaces, we need to be able and compute geodesic distances (distance on the surface) instead of the trivial Euclidean distances. For this calculus, we have a small C++ library, which had become outdated. We need to:…
The SciUnit framework was developed to help researchers create unit tests for scientific models. Currently, unit tests exist for models of single neurons and small networks thereof. However, unit tests for models concerned with large-scale brain network dynamics, such as meso-scale,…
Primary Goals
● To create a basic GUI interface for the reconstruction pipeline which gives the ability to users to provide input data, choose configurations, identify the outputs, and check logs in case of any problem which occurs during the whole process.…
This project is about unit tests for brains with SciUnit. We want to evaluate the strength of various models and select them among competitors for analyzing brain data.
The FitzHugh-Nagumo model (FHN) lets us study spike generation in squid giant axons using a 2-dimensional…
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Currently, XNAT comes with a native built-in GUI. This project will provide a dashboard framework to allow users to easily develop responsive dashboards, for exploring, monitoring, and reviewing datasets stored on any XNAT instance.
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The Workflow Designer is a prototype web-based application allowing drag-and-drop creating, editing, and running workflows from a predefined library of methods. Moreover, any workflow can be exported or imported in JSON format to ensure reusability and local execution of…
Recent advances in the field of computer vision and deep learning has shown great promise in their ability to decipher images and derive inferences involving classifications, detection of objects and approximation of certain values with high accuracy.
Pre-trained…
Neuroscience data comes in multiple different data formats and structures. These differences provide a major technical barrier to sharing data between labs or even within labs. Often the organization and naming conventions of neuroscience data structures …
In any open-source organization, one of the key factors to grow is how many people are involved in it. I have introduced OpenWorm in many conferences and meetups and everyone was interested in contributing to it. Many new members have also joined OpenWorm Slack in recent days…
Image registration is the process of finding a transformation that aligns one image to another. DIPY currently supports several numerical optimization-based techniques for image registration. Even though these methods perform well, they are limited by their slow registration speeds.…
“LORIS (Longitudinal Online Research and Imaging System), a web-based data and project management software for neuroimaging research studies”
( https://mcin.ca/technology/loris/ ). It is a very convenient tool…
LORIS is a web application used to manage as well as host, and visualize data with a focus on neuroscience and genomics (among other fields). Services are split into different modules offered to researchers. Frontend is written in javascript, allowing it to:
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LORIS is an open-source framework that facilitates data sharing for neuroscience labs and sites. It hosts both frontend and backend services that help facilitate data sharing and manipulation among researchers. The codebase includes many modules that perform different functionalities.…
Blood Oxygen Level Dependent (BOLD) functional Magnetic Resonance Imaging (fMRI) depicts changes in deoxyhemoglobin concentration consequent to task-induced or spontaneous modulation of neural metabolism. An increase in neural activity corresponds to a local increase in oxygenated…
Brian is a spiking neural networks simulator, which provides desirable syntactic sugar and flexibility to allow a wide variety of models without compromising rapidity. With a plethora of different sets of governing equations, neuronal models with complex biophysical properties,…
ImageJ is an open source Java image processing and analysis library used extensively in biomedical sciences. Active Segmentation is a plugin providing user interface to scientists, allowing them to use Machine Learning algorithms for segmentation and classification tasks. The aim…
Conversion of large scale cortical models into PyNN/NeuroML involves the conversion of published large scale network models into open, simulator independent and testing them across multiple simulator implementations. In the previous edition of GSOC the large scale network model for the…
The project aims to provide a robust mechanism for cell tracking using 2D raw image objects. Through the use of Mean Square Distance method the potential object displacements will be calculated. Another set of images will be fed as time lapse protocol. Trajectory estimate…
GeNN is a GPU-enhanced Neuronal Network simulation package in C++, that combines the ease of code generation, primarily for the purpose of setting up the parameters of the simulation through a model definition, with the flexibility of user-defined code, to actually run the simulation…
Time series analysis methods are regularly being developed and we don’t have any resources at present that compare the newly developed method with the methods that already exist to help the user determine the similarity between new and pre-existing methods. In this project, we are…
Psychiatric disorders are diagnosed based on symptom scores from clinical interviews, there are no existing gold standards that can be used for definitive validation. Brain functional neuroimaging techniques including functional magnetic resonance imaging (fMRI…
Bhalla lab develops and maintains the simulator MOOSE, the Multiscale Object-Oriented Simulation Environment. It is designed to simulate neural systems ranging from biochemical signaling to complex models of single neurons, circuits, and large networks. A typical use case is to model…
The INCF German Node (G-Node) provides various services and tools to facilitate data access, data management, and data sharing. Focusing on the development and free distribution of tools for handling and analyzing neurophysiological data. Learn more:…
We measure and evaluate electrical activity in the human brain and investigate human behavior in stressful and repetitive situations. We provide services for the collection, storage, description, analysis and sharing of large data sets from biomedicine, particularly the signals from…