Difference between revisions of "Neuroanatomy"
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|{{bc|Analyze|Skeleton|Classify Particles Using Skeleton}} | |{{bc|Analyze|Skeleton|Classify Particles Using Skeleton}} | ||
| − | |Tags particles according to skeleton features. | + | |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 {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}. |
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| − | Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}. | ||
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|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Import/Export'' | |colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Import/Export'' | ||
Revision as of 08:08, 30 May 2017
| Neuroanatomy update site (Fiji) | |
|---|---|
| Author | Tiago Ferreira |
| Maintainer | Tiago Ferreira |
| Source | on GitHub |
| Initial release | April 2016 |
| Latest version | 1.0.7 February 2017 (Changelog) |
| Development status | Active |
| Category | Plugins, Analysis, Neuroanatomy |
This is the main documentation page for the hIPNAT (Image Processing for NeuroAnatomy and Tree-like Structures) plugins distributed through the Neuroanatomy update site, released in April 2016. 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) 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. 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. |
| 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 › NeuroAnatomy › Convert Traces to SWC | Batch conversion of Simple Neurite Tracer's .traces files into SWC.
Implemented as a Python script. |
| Multi-SWC renderer | Plugins › NeuroAnatomy › Render Multiple SWC Files | Renders multiple SWC files in a single image canvas or a 3D viewer universe.
Implemented as a Python script. |
| Remote File renderer | Plugins › NeuroAnatomy › Render Remote SWC File | Exemplifies how to download and access a remote (e)SWC (internet connection required).
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.
