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Sholl Analysis

31 bytes added, 17:00, 25 October 2016
Mention neuTube
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== Analysis of Traced Cells ==
[[ File:ShollTracingsPrompt.png|400px|right |Main prompt (version 3.6.8), when input is traced data ({{bc|color=white|Analysis|Sholl|Sholl Analysis (Tracings)...}})]]In this mode, the plugin analyzes reconstructed arbors. This is particularly relevant for stainings that do not allow single-cell resolution. The plugin is macro recordable, and thus, [[#Batch Processing|batch processing]] is also possible.
# Run {{bc|color=white|Analysis|Sholl|Sholl Analysis (Tracings)...}} and specify a tracing file (a <code>.swc</code> or a [[Simple Neurite Tracer]] <code>.traces</code> file). If you want, you can also specify the image associated with the reconstruction. This will allow the plugin to use the image's metadata to determine spatial units and x,y,z spacing.
# Choose the center of analysis using the drop down menu in the main prompt listing SWC tags (''axon'', ''dendrite'', ''soma'', etc.). Note that if your tracings are not tagged you can do so in [[Simple Neurite Tracer]]
{{Tip
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| tip = You can use {{bc|color=white|Sholl Analysis (Tracings)...}} to analyze reconstructed data from any software capable of [http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html SWC] export such as [https://sourceforge.net/projects/py3dn/ Py3DN], [http://www.reading.ac.uk/neuromantic/ Neuromantic], [http://research.mssm.edu/cnic/tools-ns.html NeuronStudio], [httpshttp://sourceforgewww.neutracing.net/projects/py3dn/ Py3DNcom neuTube] , or [http://www.vaa3d.org/ Vaa3D]), not just [[Simple Neurite Tracer]]. In addition, [http://cng.gmu.edu:8080/Lm/ L-Measure], [http://neuronland.org/NL.html NLMorphologyConverter] or [http://www.neuron.yale.edu/neuron/ Neuron] can also be used to convert several file formats (including proprietary formats from closed-source commercial software such as Neurolucida®, MicroBrightField, Inc.) into SWC.}}
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