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Neuroanatomy

681 bytes added, 10:57, 17 November 2016
Provide links to source code
= 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 particles according to skeleton features.
Runs {{bc|Analyze|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]]) 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}}.
|-
|colspan="3" style="background: #ddd; border-top: 1px solid gray; padding: 5px; text-align: center"|''Import/Export''
|Tracings Importer
| {{bc|File|Import|Tracings (Traces/(e)SWC)...}}
| 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
| {{bc|Plugins|NeuroTools|Convert Traces to SWC}}
| Batch conversion of [[Simple Neurite Tracer]]'s [[Simple_Neurite_Tracer:_.traces_File_Format|native .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''
|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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