189 Open source projects that are alternatives of or similar to ITKTubeTK

The code in this repository is from my master thesis. This project aims to automatically segment carotid from 3D MR brain image, and use the segmented carotid to extract Time-Activity-Curve from PET images. It mainly involves 3D image coregistration, vessel segmentation, partial valume correction.

Multi-modal Image Registration And Connectivity anaLysis

A Collection Python EEG (+ ECG) Analysis Utilities for OpenBCI and Muse

[MICCAI'18] Joint Learning of Motion Estimation and Segmentation for Cardiac MR Image Sequences

NEURON Simulator

Brain Modeling Toolkit

Deep learning integration for Nengo

cell detection in calcium imaging recordings

code for storing neurodata images and image annotations

TAPAS - Translational Algorithms for Psychiatry-Advancing Science

Brain Imaging Analysis Kit

MNE-CPP: A Framework for Electrophysiology

Easy whole-brain modeling for computational neuroscientists 🧠💻👩🏿‍🔬

Recordings of 10k neurons during spontaneous behaviors

Graphical experiment builder for the social sciences

A Python-based module for creating flexible and robust spike sorting pipelines.

ERPLAB Toolbox is a free, open-source Matlab package for analyzing ERP data. It is tightly integrated with EEGLAB Toolbox, extending EEGLAB’s capabilities to provide robust, industrial-strength tools for ERP processing, visualization, and analysis. A graphical user interface makes it easy for beginners to learn, and Matlab scripting provides enormous power for intermediate and advanced users.

Modular Tracking Framework

Blue Brain Python Optimisation Library

Attention Unet model with post process for retina optic disc segmention

Uncertainpy: a Python toolbox for uncertainty quantification and sensitivity analysis, tailored towards computational neuroscience.

A toolbox for integrated information theory.

An R package for experimental psychologists

C++ library for simulation of multiscale neural field dynamics

Connectome Workbench

A list of schools and researchers in computational neuroscience

EPFL summaries & cheatsheets over 5 years (computer science, communication systems, data science and computational neuroscience).

Generate custom Docker and Singularity images, and minimize existing containers

CellExplorer is a graphical user interface, a standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.

a python based software for visualization of neuroanatomical and morphological data.

The Arbor multi-compartment neural network simulation library.

Distributed, Versioned, Image-oriented Dataservice

Precision current source, with optional optical feedback, for driving LEDs and laser diodes

A multi-purpose GPU-accelerated open-source suite for brain data visualization

The PyTorch re-implement of a 3D CNN Tracker to extract coronary artery centerlines with state-of-the-art (SOTA) performance. (paper: 'Coronary artery centerline extraction in cardiac CT angiography using a CNN-based orientation classifier')

BrainFlow is a library intended to obtain, parse and analyze EEG, EMG, ECG and other kinds of data from biosensors

The PyTorch Implementation of Variable Optimizers/ Neural Variable Risk Minimization proposed in our Neural Computation paper: Artificial Neural Variability for Deep Learning: On overfitting, Noise Memorization, and Catastrophic Forgetting.

Parameterizing neural power spectra into periodic & aperiodic components.

认知计算神经联盟 讨论会

Fast spike sorting with drift correction for up to a thousand channels

🕝 Time-warped principal components analysis (twPCA)

EntroPy: complexity of time-series in Python (DEPRECATED)

Neuroscience information exchange format

Collaborative Annotation Toolkit for Massive Amounts of Image Data

Repository containing the code of one of the networks that we employed in the iSEG Grand MICCAI Challenge 2017, infant brain segmentation.

MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python

A brian2 extension to simulate spiking neural networks on GPUs

python implementations of Analyzing Neural Time Series Textbook

A publicly-editable collection of open computational neuroscience resources

Python-based module for extracting from, converting between, and interfacing with many common file formats in extracellular recording.

An implementation of the research paper "Retina Blood Vessel Segmentation Using A U-Net Based Convolutional Neural Network"

Deep Learning with Tensor Flow for EEG MNE Epoch Objects

Visualizer for large-scale and interactive ray-tracing of neurons

Platform-independent lightweight Python library for designing and conducting timing-critical behavioural and neuroimaging experiments

Python machine learning package based on sklearn API for multivariate data processing and statistical analysis of symmetric positive definite matrices via Riemannian geometry

Core tools required for running Canlab Matlab toolboxes. The heart of this toolbox is object-oriented tools that enable interactive analysis of neuroimaging data and simple scripts using high-level commands tailored to neuroimaging analysis.

Mother of All BCI Benchmarks

Elephant is the Electrophysiology Analysis Toolkit

A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.

A block modeling system for cognitive neuroscience