Monte Carlo
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Geant Human Oncology Simulation Tool (GHOST) project
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MCsquare: Fast Monte Carlo simulations for proton PBS
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Image Archives
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Open-Access Medical Image Repositories
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Brain MRI scans with Gamma Knife
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Radiation Dosimetry Tools: NCIDose
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RadImageNet: An Open Radiologic Deep Learning Research Dataset for Effective Transfer Learning
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Publicly Available Liver MRI Dataset with Liver Segmentation Masks and Series Labels
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Visualization
3D slicer image computing platform
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3D Slicer Plugin MedSAM-Lite: Segment Anything in Medical Images
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Nvidia AI-assisted annotation (AIAA) for 3D Slicer
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Slicer CAT: Creating custom applications based on 3D Slicer
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Total Segmentator AI model is now available as an extension for 3D Slicer
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NVIDIA Clara Imaging (using GPU)
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Medical Segmentation Decathlon
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ITK-SNAP - a software application used to segment structures in 3D medical images.
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The Medical Imaging Interaction Toolkit (MITK)
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Advanced Normalization Tools (ANTs)
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Fiji (ImageJ + many useful plugins)
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XNAT – a DICOM database system with many image handling tools
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Project InnerEye – Democratizing Medical Imaging AI
CERR – a viewer and radiotherapy data manipulation system in Matlab
and the associated open-source tools
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Image Viewing and Processing (FREE MEDICAL IMAGING SOFTWARE)
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Python Imaging Library (Pillow) (Link)
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PlatiPy documentation (Processing Library and Analysis Toolkit for Medical Imaging in Python)
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Legacy Bioimage Suite; BioImage Suite Web; BioImage Suite Manual; BioImage Suite
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Treatment Planning
Machine Learning
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A platform for end-to-end development of machine learning solutions in biomedical imaging.
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AI in Medical Physics: Guidelines for publication (Link)
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AI tools for analysis of PET/CT and CT studies (Link)
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Medical Open Network for Artificial Intelligence (MONAI) (Link)
MONAI – An Open Source Framework for AI Development in Medical Imaging (YoUTube Link)
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NiftyNet (Link)
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Tableau: Tableau platform is known for taking any kind of data from almost any system, and turning it into actionable insights with speed and ease. (Link)
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Coding
Plotting
Veusz – a scientific plotting package
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Matplotlib — Visualization with Python
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Gnuplot is a portable command-line driven graphing utility
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OriginLab: Data analysis and Graphing
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SciDAVis is a free application for Scientific Data Analysis and Visualization
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Prism: Data Visualization and Graphs
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Origin: Data analysis and graphing software
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LabPlot: Data Visualization and Analysis software
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Tableau: Connect, analyze, and visualize any data
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