ItkInsight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
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ItkexamplesCookbook examples for the Insight Toolkit documented with Sphinx
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ItkwidgetsInteractive Jupyter widgets to visualize images, point sets, and meshes in 2D and 3D
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Grand Challenge.orgA platform for end-to-end development of machine learning solutions in biomedical imaging
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AvogadrolibsAvogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
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ViewersThe OHIF Medical Imaging Viewer is for viewing medical images. It can retrieve
and load images from most sources and formats; render sets in 2D, 3D, and
reconstructed representations; allows for the manipulation, annotation, and
serialization of observations; supports internationalization, OpenID Connect,
offline use, hotkeys, and many more features.
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PyimsegmImage segmentation - general superpixel segmentation & center detection & region growing
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BoneJ2Plugins for bone image analysis
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Openml RR package to interface with OpenML
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SimpegSimulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
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Segment OpenSegment Source Distribution
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ProjectweekWebsite for NA-MIC Project Weeks
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FmaFMA: A Dataset For Music Analysis
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OsfrR interface to the Open Science Framework (OSF)
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cucimNo description or website provided.
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ReprozipReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.
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openscienceEmpirical Software Engineering journal (EMSE) open science and reproducible research initiative
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ck-mlopsA collection of portable workflows, automation recipes and components for MLOps in a unified CK format. Note that this repository is outdated - please check the 2nd generation of the CK workflow automation meta-framework with portable MLOps and DevOps components here:
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unet-pytorchThis is the example implementation of UNet model for semantic segmentations
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GARIGARI (Genetic Algorithm for Reproducing Images) reproduces a single image using Genetic Algorithm (GA) by evolving pixel values.
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showyourworkFully reproducible, open source scientific articles in LaTeX.
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sunbeamA robust, extensible metagenomics pipeline
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go-dicomDICOM parser for golang
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squidpySpatial Single Cell Analysis in Python
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chestViewSplitAutomatically split the chest x-ray into two views
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OpenSkyStackerMulti-platform stacker for deep-sky astrophotography.
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covid19.MIScnnRobust Chest CT Image Segmentation of COVID-19 Lung Infection based on limited data
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fpzipCython bindings for fpzip, a floating point image compression algorithm.
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AutoPasAutopas is a node-level auto-tuned particle simulation library developed in the context of the TaLPas project.
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whyqddata wrangling simplicity, complete audit transparency, and at speed
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datajoint-pythonRelational data pipelines for the science lab
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boxtreeQuad/octree building for FMMs in Python and OpenCL
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PyCORNA script to extract data from ÄKTA/UNICORN result-files (.res)
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clinicadlFramework for the reproducible processing of neuroimaging data with deep learning methods
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bioportal web uiA Rails application for biological ontologies
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