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Working Groups

Working Groups are composed of users and developers from across the INCF network working collaboratively to develop, refine, and/or implement community standards. Working Groups are composed of members working on short-term funded projects that aim to achieve a concrete deliverable.

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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…

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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…

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Open Source Brain is an online resource for sharing and collaboratively developing computational models of neural systems. Learn more at: https://www.opensourcebrain.org/

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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…

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GeNN is a GPU enhanced Neuronal Network simulation environment based on NVIDIA CUDA technology. Learn more at: https://genn-team.github.io/genn/

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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:…

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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 For this calculus, we have a small C++ library, which had become outdated.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:…

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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,…

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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.…

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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…

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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…

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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 …

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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…

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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.…

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“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…

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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.…

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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…

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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,…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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:…

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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…