Neuroanatomy
| Neuroanatomy update site (Fiji) | |
|---|---|
| Author | Tiago Ferreira |
| Maintainer | Tiago Ferreira |
| Source | on GitHub |
| Initial release | April 2016 |
| Development status | Active |
| Category | Plugins, Analysis, 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) and ii) Java 8 (as part of an active effort to modernize ImageJ). 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:
- Run Help › Update...
- Click Manage update sites
- Select the Neuroanatomy checkbox (see also List of update sites)
- Click Apply changes and Restart ImageJ.
List of commands
| 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.
Runs Analyze › Analyze Particles on one image and clusters detected particles according to their positioning to features of a skeletonizable structure (e.g., a junction or end-point, see AnalyzeSkeleton). A particle is considered to be associated to a skeleton feature if the distance between its centroid and the feature is within a specified cuttoff ("snap to") distance. Implemented as a Python script. |
| Import/Export | ||
| Tracings Importer | File › Import › Tracings (Traces/(e)SWC)... | Renders traced reconstructions (.traces - Simple Neurite Tracer's format - and .swc files) in ImageJ's 3D Viewer or as skeletonized image stacks.
Implemented as a Java plugin. |
| Traces converter | Plugins › NeuroTools › Convert Traces to SWC | Batch conversion of Simple Neurite Tracer's .traces files into SWC.
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.