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Neuroanatomy

2,105 bytes added, 18 May
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| released = April 2016
| status = Active
| 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]]
}}{{ambox | text =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]].  {{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]].
}}
# Run [[Update_Sites|{{bc|Help|Update...}}]]
# Click ''Manage update sites''
# Select the ''Neuroanatomy'' checkbox (see also [[List of update sites]]{{ListOfUpdateSites}})
# Click ''Apply changes'' and Restart ImageJ.
= List of commands =
{| class="wikitable"
|style="width:10%;vertical-align: middle;text-align:center;"|'''Name'''|style="width:20%;vertical-align: middle;text-align:center;"|'''Menu Path'''|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''
|Strahler classifier
|{{bc|Analyze|Skeleton|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"
|Summarize Skeleton
|{{bc|Analyze|Skeleton|Summarize Skeleton}}
|Bulk statistics of skeletonized images.Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/java/ipnat/skel|label=Java plugin}}.
|- valign="top"
|Particles classifier
|{{bc|Analyze|Skeleton|Classify Particles Using Skeleton}}
|Tags segmented 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}}.
|-
|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Import/Export''
|- valign="top"
|Tracings Importerimporter
| {{bc|File|Import|Tracings (Traces/(e)SWC)...}}
| Renders traced reconstructions ( [[SNT:_.traces_File_Format|.traces ]] - [[Simple Neurite TracerSNT]]'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
| {{bc|Plugins|NeuroToolsNeuroAnatomy|Convert Traces to SWC}}| Batch conversion of [[Simple Neurite Tracer]]'s native [[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}}.|-|Multi-SWC renderer| {{bc|Plugins|NeuroAnatomy|Render Multiple SWC Files}}| Renders multiple SWC files in a single image canvas or a [[3D_Viewer|3D viewer]] universe.Implemented as a {{GitHub|org=tferr|repo=hIPNAT|path=src/main/resources/scripts/|label=Python script}}.|-|Remote File renderer| {{bc|Plugins|NeuroAnatomy|Render Remote SWC File}}| 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''
|Fractal Trees
| {{bc|File|Open Samples|Fractal Tree}}
| 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}}.
|}
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