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KNOSSOS - 3D image visualization and annotation tool

It is a tool to visualize and annotate volume image data of electron microscopy. Users can annotate objects (e.g. neurons) and skeleton structures. It provides the ability to overlaying the image data with user annotations, representing the spatial structure and the connectivity of labeled objects, and displaying a three dimensional model of it.
It can be extended by plugins written in python.
A similar, web-based implementation is being developed at webknossos.info.
Example datasets are also available.

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ilastik

ilastik (the image learning, analysis, and segmentation toolkit) provides non-experts with a menu of pre-built image analysis workflows. ilastik handles data of up to five dimensions (time, 3D space, and spectral dimension). Its workflows provide an interactive experience to give the user immediate feedback on the quality of the results yielded by her chosen parameters and/or labelings.

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ilastik - Carving

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Strahler Analysis

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TrakEM2

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