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Neuroanatomy

    Name

    Neuroanatomy update site

    Software

    Fiji

    Author

    Tiago Ferreira

    Maintainer

    Tiago Ferreira

    Source

    on GitHub

    Status

    Active

    Category

    Plugins, Analysis, Neuroanatomy

    The Neuroanatomy update site is used for distribution of SNT. A few other (legacy) plugins for Image Processing for NeuroAnatomy and Tree-like Structures are also included. For a list of all pages in this wiki related to Neuroanatomy have a look at :Category:Neuroanatomy.

    Installation

    The requirements to run the Neuroanatomy suite of plugins are twofold: i) Fiji (i.e., an ImageJ installation subscribed to the Fiji update site) running at least Java 8. If you are running an older version of Java, you can either i) Download the latest Fiji release (newer releases come pre-bundled with Java 8); or ii) If you have downloaded Fiji while ago and want to keep your existing installation, you will have to download Java 8 and make your Fiji installation aware of it.

    Subscribing to the Neuroanatomy update site:

    1. Run Help › Update…
    2. Click Manage update sites
    3. Select the Neuroanatomy checkbox (see also

    )

    1. Click Apply changes and Restart ImageJ

    Notes

    SNT has its own documentation. The list of Image Processing for NeuroAnatomy and Tree-like Structures (source ) is as follows:

    Name

    Menu Path

    Description

    Topological Skeletons

    Strahler classifier

    Analyze › Skeleton › Strahler Analysis...

    Described in Strahler Analysis. Implemented as a Java plugin .

    Summarize Skeleton

    Analyze › Skeleton › Summarize Skeleton

    Bulk statistics of skeletonized images. Implemented as a Java plugin .

    Particles classifier

    Analyze › Skeleton › Classify Particles Using Skeleton

    Tags particles according to skeleton features. Detects maxima on a masked image and clusters detected maxima using features of the skeletonized mask. A maxima is considered to be associated to a skeleton feature (e.g., a junction or end-point, see AnalyzeSkeleton) if the distance between its centroid and the feature is less than or equal to a cuttoff ("snap to") distance. Implemented as a Python script .

    Utilities

    Fractal Trees

    File › Open Samples › Fractal Tree

    Synthetic images (L-System Trees) useful for debugging, testing or prototyping. Implemented as a Java plugin .

    Further information

    • A list of all pages in this wiki related to image processing in the neurosciences can be found here.