Biological Image Analysis
144 items from hallvaaw/awesome-biological-image-analysis ★198
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3D Slicer github.com
Free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research.
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ImageJ2 github.com
A Rewrite of ImageJ for multidimensional image data, with a focus on scientific imaging.
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SimpleITK github.com
Open-source multi-dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++.
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Fiji github.com
A "batteries-included" distribution of ImageJ — a popular, free scientific image processing application.
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HoVer-Net github.com
A multi-branch network for nuclear instance segmentation and classification with pre-trained weights.
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MicroSAM github.com
Tools for segmentation and tracking in microscopy build on top of SegmentAnything. Segment and track objects in microscopy images interactively.
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Brainrender github.com
Python package for the visualization of three dimensional neuro-anatomical data.
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ZeroCostDL4Mic github.com
Google Colab to develop a free and open-source toolbox for deep-Learning in microscopy.
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Squidpy github.com
Python framework that brings together tools from omics and image analysis to enable scalable description of spatial molecular data, such as transcriptome or multivariate proteins.
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DeepSlide github.com
A sliding window framework for classification of high resolution microscopy images.
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Ilastik github.com
Simple, user-friendly tool for interactive image classification, segmentation and analysis.
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PyImSegm github.com
Image segmentation - general superpixel segmentation and center detection and region growing.
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