|Neuroanatomy update site (Fiji)|
|Initial release||April 2016|
|Category||Plugins, Analysis, Neuroanatomy|
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 ▶
- Click Manage update sites
- Select the Neuroanatomy checkbox (see also List of update sites)
- Click Apply changes and Restart ImageJ.
List of commands
|Strahler classifier||▶ ▶||Described in Strahler Analysis|
|Summarize Skeleton||▶ ▶||Bulk statistics of skeletonized images|
|Particles classifier||▶ ▶||Tags particles according to skeleton features.
Runs on one image and clusters detected particles according to their positioning to features (e.g., a junction or end-point, see ▶ ▶ AnalyzeSkeleton) of a skeletonizable image. 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.
|Tracings Importer||▶ ▶||Renders traced reconstructions ( .traces - Simple Neurite Tracer's format - and .swc files) in ImageJ's 3D Viewer or as skeletonized image stacks|
|Traces converter||▶ ▶||Batch conversion of Simple Neurite Tracer's native files into SWC|
|Fractal Trees||▶ ▶||Synthetic images (L-System Trees) useful for debugging, testing or prototyping|
- A list of all pages in this wiki related to image processing in the neurosciences can be found here.