Difference between revisions of "Neuroanatomy"

(Update script path)
(Provide links to source code)
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= List of commands =
 
= List of commands =
 
{| class="wikitable"
 
{| class="wikitable"
|style="vertical-align: middle;text-align:center;"|'''Name'''
+
|style="width:10%;vertical-align: middle;text-align:center;"|'''Name'''
|style="vertical-align: middle;text-align:center;"|'''Menu Path'''
+
|style="width:20%;vertical-align: middle;text-align:center;"|'''Menu Path'''
|style="vertical-align: middle;text-align:center;"|'''Description'''
+
|style="width:70%;vertical-align: middle;text-align:center;"|'''Description'''
 
|-
 
|-
 
|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Topological Skeletons''
 
|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Topological Skeletons''
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|Strahler classifier
 
|Strahler classifier
 
|{{bc|Analyze|Skeleton|Strahler Analysis...}}
 
|{{bc|Analyze|Skeleton|Strahler Analysis...}}
|Described in [[Strahler Analysis]]
+
|Described in [[Strahler Analysis]].
 +
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/skel|label=Java plugin}}.
 
|- valign="top"
 
|- valign="top"
 
|Summarize Skeleton
 
|Summarize Skeleton
 
|{{bc|Analyze|Skeleton|Summarize Skeleton}}
 
|{{bc|Analyze|Skeleton|Summarize Skeleton}}
|Bulk statistics of skeletonized images
+
|Bulk statistics of skeletonized images.
 +
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/skel|label=Java plugin}}.
 
|- valign="top"
 
|- valign="top"
 
|Particles classifier
 
|Particles classifier
 
|{{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.
Runs {{bc|Analyze|Analyze|Analyze Particles}} 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 {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/Analyze/Skeleton|label=Python script}}.
+
Runs {{bc|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 {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.
 
|-
 
|-
 
|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''
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|Tracings Importer
 
|Tracings Importer
 
| {{bc|File|Import|Tracings (Traces/(e)SWC)...}}
 
| {{bc|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
+
| Renders traced reconstructions ([[Simple_Neurite_Tracer:_.traces_File_Format|.traces]] - [[Simple Neurite Tracer]]'s format - and [http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html .swc] files) in ImageJ's [[3D Viewer]] or as skeletonized image stacks.
 +
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/|label=Java plugin}}.
 
|-
 
|-
 
|Traces converter
 
|Traces converter
 
| {{bc|Plugins|NeuroTools|Convert Traces to SWC}}
 
| {{bc|Plugins|NeuroTools|Convert Traces to SWC}}
| Batch conversion of [[Simple Neurite Tracer]]'s [[Simple_Neurite_Tracer:_.traces_File_Format|native files]] into [http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html SWC]
+
| Batch conversion of [[Simple Neurite Tracer]]'s [[Simple_Neurite_Tracer:_.traces_File_Format|.traces files]] into [http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html SWC].
 +
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.
 
|-
 
|-
 
|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Utilities''
 
|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Utilities''
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|Fractal Trees
 
|Fractal Trees
 
| {{bc|File|Open Samples|Fractal Tree}}
 
| {{bc|File|Open Samples|Fractal Tree}}
| Synthetic images (L-System Trees) useful for debugging, testing or prototyping
+
| Synthetic images ([https://en.wikipedia.org/wiki/L-system L-System] Trees) useful for debugging, testing or prototyping.
 +
Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/skel|label=Java plugin}}.
 
|}
 
|}
  

Revision as of 11:57, 17 November 2016

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:

  1. Run Help ▶ Update...
  2. Click Manage update sites
  3. Select the Neuroanatomy checkbox (see also List of update sites)
  4. 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.