Difference between revisions of "Neuroanatomy"

(Improve documentation of Classify Particles Using Skeleton)
 
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| released  = April 2016
 
| released  = April 2016
 
| status    = Active
 
| status    = Active
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| latest version = '''1.0.10 May 2017''' ({{GitHub|org=tferr|repo=hIPNAT/releases|label=Changelog}})
 
| category  = [[:Category:Plugins|Plugins]], [[:Category:Analysis|Analysis]], [[:Category:Neuroanatomy|Neuroanatomy]]
 
| category  = [[:Category:Plugins|Plugins]], [[:Category:Analysis|Analysis]], [[:Category:Neuroanatomy|Neuroanatomy]]
}}{{ambox | text =
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}}
This is the main documentation page for the hIPNAT (''Image Processing for NeuroAnatomy and Tree-like Structures'') plugins distributed through the [[User:Neuroanatomy|Neuroanatomy update site]], released in [http://forum.imagej.net/t/launch-of-the-neuroanatomy-update-site/1377?u=tferr April 2016].
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This is the main documentation page for the hIPNAT (''Image Processing for NeuroAnatomy and Tree-like Structures'') plugins distributed through the [[User:Neuroanatomy|Neuroanatomy update site]], released in [http://forum.imagej.net/t/launch-of-the-neuroanatomy-update-site/1377?u=tferr April 2016]. For a list of all pages in this wiki related to Neuroanatomy have a look at [[:Category:Neuroanatomy]].
 
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{{ambox | text =Please note that, at this time, these tools are under heavy development: some features are experimental and documentation remains incomplete. Also, some of this work has been meanwhile migrated to core-Fiji plugins, such as [[Simple_Neurite_Tracer|Simple Neurite Tracer]].
 
 
Please note that, at this time, these tools are under heavy development: some features are experimental and documentation remains incomplete.
 
 
}}
 
}}
  
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# Run [[Update_Sites|{{bc|Help|Update...}}]]
 
# Run [[Update_Sites|{{bc|Help|Update...}}]]
 
# Click ''Manage update sites''
 
# Click ''Manage update sites''
# Select the ''Neuroanatomy'' checkbox (see also [[List of update sites]])
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# Select the ''Neuroanatomy'' checkbox (see also {{ListOfUpdateSites}})
 
# Click ''Apply changes'' and Restart ImageJ.
 
# Click ''Apply changes'' and Restart ImageJ.
  
 
= List of commands =
 
= List of commands =
 
{| class="wikitable"
 
{| class="wikitable"
|style="vertical-align: middle;text-align:center;"|'''Name'''
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|style="width:10%;vertical-align: middle;text-align:center;"|'''Name'''
|style="vertical-align: middle;text-align:center;"|'''Menu Path'''
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|style="width:20%;vertical-align: middle;text-align:center;"|'''Menu Path'''
|style="vertical-align: middle;text-align:center;"|'''Description'''
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|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]]
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|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
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|Bulk statistics of skeletonized images.
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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.
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|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}}.
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) of a [[AnalyzeSkeleton|tagged skeleton]] [produced by {{bc|Analyze|Analyze|Skeleton (2D/3D)}}] in another 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=Scripts/Analyze/Skeleton|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''
 
|- valign="top"
 
|- valign="top"
|Tracings Importer
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|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
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| Renders traced reconstructions ([[SNT:_.traces_File_Format|.traces]] - [[SNT]]'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}}
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| {{bc|Plugins|NeuroAnatomy|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]
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| 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}}.
 +
|-
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|Multi-SWC renderer
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| {{bc|Plugins|NeuroAnatomy|Render Multiple SWC Files}}
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| Renders multiple SWC files in a single image canvas or a [[3D_Viewer|3D viewer]] universe.
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Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.
 +
|-
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|Remote File renderer
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| {{bc|Plugins|NeuroAnatomy|Render Remote SWC File}}
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| Exemplifies how to download and access a remote (e)SWC (internet connection required).
 +
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
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| 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}}.
 
|}
 
|}
  

Latest revision as of 16:33, 18 May 2019

Neuroanatomy update site (Fiji)
Author Tiago Ferreira
Maintainer Tiago Ferreira
Source on GitHub
Initial release April 2016
Latest version 1.0.10 May 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:

  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. 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 - SNT'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.