Search Results for "mri"
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Showing 103 open source projects for "mri"
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1
TorchIO
Medical imaging toolkit for deep learning
...These transforms include typical computer vision operations such as random affine transformations and also domain-specific ones such as simulation of intensity artifacts due to MRI magnetic field inhomogeneity (bias) or k-space motion artifacts. TorchIO is a Python package containing a set of tools to efficiently read, preprocess, sample, augment, and write 3D medical images in deep learning applications written in PyTorch, including intensity and spatial transforms for data augmentation and preprocessing. Transforms include typical computer vision operations such as random affine transformations and also domain-specific ones such as simulation of intensity artifacts due to MRI magnetic field inhomogeneity. -
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VR Neuroanatomy
Explore and dissect a complete brain model in VR
Understanding the anatomy of complex organs such as the human brain can be a challenge for students, so there is a definite advantage given to students who can experience the structures in a spatial way through real or virtual experiences. Since 2016, the Marquette Visualization Lab has been utilizing a dataset of 3 and 7 Tesla MRI scans from the Structural Informatics Group at University of Washington to visualize the structures of the brain in their Cave, utilizing the Unity game engine and 10 stereoscopic 3D projectors. Most MRI scans are presented as a volumetric rendering, but this dataset is unique because it was fully labelled and parcellated, allowing lab users to not only view the structures of the brain, but also virtually dissect it in a large scale, collaborative virtual reality environment. ... -
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Artichoke Ruby
Artichoke is a Ruby made with Rust
Artichoke is an experimental implementation of the Ruby programming language written primarily in Rust, aiming to provide a modern, embeddable, and portable Ruby runtime. It is designed to be compatible with MRI Ruby while exploring new approaches to performance, safety, and execution models through Rust’s systems programming capabilities. One of its key goals is to enable Ruby to run in environments where traditional implementations struggle, including WebAssembly and sandboxed or untrusted execution contexts. Artichoke features a modular architecture composed of multiple Rust crates, allowing developers to customize and embed the interpreter into their own applications. ... -
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Puma
A Ruby/Rack web server built for concurrency
...If you are using Bundler, just add Puma to your project's Gemfile. Once you've installed your bundle, start Puma. If you are not using Bundler, you can install Puma directly from the command line. On MRI, there is a Global VM Lock (GVL) that ensures only one thread can run Ruby code at a time. But if you're doing a lot of blocking IO (such as HTTP calls to external APIs like Twitter), Puma still improves MRI's throughput by allowing IO waiting to be done in parallel. -
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MIRT.jl
MIRT: Michigan Image Reconstruction Toolbox (Julia version)
MIRT.jl is a collection of Julia functions for performing image reconstruction and solving related inverse problems. It is very much still under construction, although there are already enough tools to solve useful problems like compressed sensing MRI reconstruction. Trying the demos is a good way to get started. The documentation is even more still under construction. -
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Mongoid
Ruby ODM framework for MongoDB
Mongoid is the officially supported ODM (Object-Document-Mapper) framework for MongoDB in Ruby. This Mongoid community organization is a group of open-source contributors around the Mongoid ODM not affiliated with the company, MongoDB. Mongoid is customarily configured through a mongoid.yml file that specifies options and clients. The simplest configuration is as follows, which configures Mongoid to talk to a MongoDB server at “localhost:27017” and use the database named “mongoid”. If you... -
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VoxelMorph
Unsupervised Learning for Image Registration
...Once the model has been trained, it can rapidly compute the transformation required to register new image pairs, significantly reducing computational time compared to classical registration algorithms. The framework supports both supervised and unsupervised learning approaches and is commonly used in medical imaging applications such as MRI alignment, anatomical analysis, and longitudinal studies. -
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Concurrent Ruby
Modern concurrency tools including agents, futures, promises, etc.
...Concurrent Ruby makes one of the strongest thread safety guarantees of any Ruby concurrency library, providing consistent behavior and guarantees on all four of the main Ruby interpreters (MRI/CRuby, JRuby, Rubinius, TruffleRuby). -
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Resque
Ruby library for creating background jobs and processing them
...Resque is heavily inspired by DelayedJob (which rocks) and comprises three parts, a Ruby library for creating, querying, and processing jobs, a Rake task for starting a worker which processes jobs, a Sinatra app for monitoring queues, jobs, and workers. Resque workers can be distributed between multiple machines, support priorities, are resilient to memory bloat / "leaks," are optimized for REE (but work on MRI and JRuby), tell you what they're doing, and expect failure. -
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10
Doctor Dok
Doctor Dok is an AI based medical data framework
Store, manage, and understand your medical history in one secure place that only you can access. Built to protect your privacy with full end-to-end encryption. Convert all your Blood Tests, MRI Scans, TK Scans, Visit reports, and Hospital Admission Reports to JSON, safely store in the cloud, and discuss, annotate, and translate them with AI. Doctor Dok is a secure storage, digitization, sharing, and AI discovery platform for all your family and/or folder health data. All health history - digitalized - accessible anywhere from Mobile or Desktop. ... -
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AWS X-Ray SDK for Ruby
The official AWS X-Ray Recorder SDK for Ruby
...It has experimental support for JRuby 9.2.0.0 (still forthcoming). To install the Ruby gem for your project, add it to your project Gemfile. You must also add either the Oj or JrJackson gems, for MRI and JRuby respectively, for JSON parsing. The default JSON parser will not work properly, currently. The SDKs included with X-Ray are part of a tightly integrated instrumentation solution offered by AWS. The AWS Distro for OpenTelemetry is part of a broader industry solution in which X-Ray is only one of many tracing solutions. You can implement end-to-end tracing in X-Ray using either approach, but it’s important to understand the differences in order to determine the most useful approach for you. -
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ODIN
develop, simulate and run magnetic resonance sequences
ODIN is a free software framework for rapid prototyping of magnetic resonance imaging (MRI) sequences. The sequences can be tested, simulated and executed on scanner hardware from different manufacturers. -
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iElectrodes
intracranial electrodes localization toolbox
iElectrodes is a free and open-source Matlab® toolbox to obtain intracranial electrode coordinates from MRI and CT images. Precise and reliable localization can be achieved fast and in a semiautomatic way with minimal user intervention. The toolbox works with ECoG (subdural grids and strips) and SEEG (depth) electrodes. The new GridFit algorithm can precisely localize high-density electrodes (up to 3mm). Brain parcellations (atlas) and surfaces can be imported to aid 2D and 3D visualization and anatomical localization can be done in native or normalized space. ... -
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Iso2Mesh - A 3D Mesh Generation Toolbox
A 3D surface and volumetric mesh generator for MATLAB/Octave
A simple yet powerful mesh generator based on MATLAB/GNU Octave language, creating finite-element mesh from surfaces or arbitrary 3D volumetric images (such as MRI/CT scans) with fully automatic workflows. -
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DcmStoreService
A lightweight and robust Dicom server to archive medical images
Dicom storage service - DcmStoreService is a lightweight and robust package for implementing the Dicom Storage SCP Service. The application (C++ compiled x86/x64) runs on computer as automatic MS Windows system service (24 hrs). It has a variety of customizable options. -
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SimPET
A web platform for the MC simulation of realistic brain PET data
SimPET (http://www.sim-pet.org) is an open, efficient, and user‐friendly online platform for the generation of synthetic brain PET datasets. The platform offers the ability to generate realistic activity and attenuation maps from patient's PET/CT and MRI images. These maps can then be simulated, and sinograms and simulated images can be downloaded. More advanced features can be obtained by using the SimPET scripts: https://github.com/txusser/brainviset_simset https://github.com/txusser/simpet (New version pre-alpha) You can also upload your own phantoms to simulate. Currently the platform incorporates MC models for the GE Advance, GE Discovery ST and Siemens mCT. ... -
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Medical Img Segmentation Suite
A software providing easy ways to segment structures in medical images
- 15 segmentation tools (FloodFill Strict, Adaptive Gaussian Threshold, Manual Brush (Freehand Lasso), Polygon Lasso (Click Points), Manual Bounding Box, Auto Bounding Box, Local Otsu Auto-Threshold, K-Means Clustering, Watershed, GrabCut AI, Canny Edge + Morphological Close, Morphologic Active Contours, Interactive Heatmap, Topographical Relief Map, Segment Anything AI) - Hybrid Layout (1 window with editor tools or Split-View with a preview window) - Intelligent file management (once a... -
18
x-unet
Implementation of a U-net complete with efficient attention
Implementation of a U-net complete with efficient attention as well as the latest research findings. For 3d (video or CT / MRI scans). -
19
ITKSnap
View 3D Images (also work with DICOM MRI images)
This software is used to view the 3D DICOM images. It is highly used to view 3D Medical Images (Human Brain, etc.). The official website for this software is: http://www.itksnap.org/ -
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KMedicalImageScreener1
A Medical Scanner for Computer Aided Detection of MRI Scans
This app is JSP that has been tested for use in Computer Aided Detection of MRI scans in the cranial and abdominal areas for cancer detection. There was one case study completed with a very high accuracy rate of over 95% on test data. This app is provided as-is under the GNU License with Accrediation. Let me know what you think, Diana -
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MELAGE is a neuroimaging software developed for visualizing and processing medical images, both Ultrasound and Magnetic Resonance Images (MRIs). Specially it has been prepared for neuroimaging of newborns, it is a versatile platform that allows the visualization of many types of medical images. It allows to load two, three and four-dimensional images of both techniques and in the case of 3D images it allows the simultaneous visualization of the three orthogonal planes which facilitates the...
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22
fastMRI
A large open dataset + tools to speed up MRI scans using ML
...It includes reference implementations for key MRI reconstruction architectures such as U-Net and Variational Networks (VarNet), along with example scripts for model training and evaluation using the PyTorch Lightning framework. The project also releases several fully anonymized public MRI datasets, including knee, brain, and prostate scans. -
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Enhanced SAR Compression
VOP Algorithm with improved speed and compression
***Please note that a much improved Version can be found on Github:*** https://github.com/sOrzada/VOP_Compression This work is described in: Orzada S, Fielder TM, Quick HH, Ladd ME, "A local SAR compression algorithm with improved compression, speed and flexibility", https://doi.org/10.1002/mrm.28739. This new algorithm is an iterative expansion of the exisisting local SAR compression algorithm for MRI proposed by Lee et al. ( https://doi.org/10.1002/mrm.23140) The number of VOPs is approximately halved with the new algorithm, while at the same time the compression time is reduced with speed-up factors of up to 2.5. -
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Region-based spatial normalization
Region-based spatial normalization (RBSN) for functional MRI.
Region-based spatial normalization (RBSN) for functional MRI. He, Hengda, and Qolamreza R. Razlighi. "Landmark‐guided region‐based spatial normalization for functional magnetic resonance imaging." Human Brain Mapping (2022). -
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CineTracker
CineTracker GUI for motion tracking of cine MRI
CineTracker GUI for motion tracking of cine MRI Developed by Liam Lawrence and Angus Lau, Sunnybrook Health Sciences Centre
