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Sholl Analysis

597 bytes added, 21:47, 18 October 2016
Highlight SWC-related software
In this mode, the plugin analyzes reconstructed arbors. This is particularly relevant for stainings that do not allow single-cell resolution.
# Run {{bc|color=white|Analysis|Sholl|Sholl Analysis (Tracings)...}} and specify input files: a tracing file (a <code>.swc</code> or a [[Simple Neurite Tracer]] <code>.traces</code> file, as produced by [[Simple Neurite Tracer]]) and the respective image associate to such files. # Choose the center of analysis using the drop down menu in the main promptlisting SWC tags (''axon'', ''dendrite'', ''soma'', etc.). If you have not tagged your traces, you will still be able to choose the center of the analysis through the [[Simple Neurite Tracer]] interface.
# Adjust the default [[#Parameters|Parameters]] in the ''Sholl Analysis'' prompt.
# Problems? Read the [[#FAQ|FAQs]]
Note that .swc files if you don't use [[Simple Neurite Tracer]], you can still analyze reconstructed data created by any software capable of [[#Related Resources|other programs]http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html SWC] (export such as [http://www.reading.ac.uk/neuromantic/ Neuromantic], [http://research.mssm.edu/cnic/tools-ns.html NeuronStudio], [https://sourceforge.net/projects/py3dn/ Py3DN ] or [http://www.vaa3d.org/ Vaa3D]) can also be used. If neededIn addition, [http://cng.gmu.edu:8080/Lm/ L-measure Measure], [http://neuronland.org/NL.html NLMorphologyConverter] or NLMorphologyConverter [http://www.neuron.yale.edu/neuron/ Neuron] can also be used to convert several file formats (including proprietary file formats such as the ones generated by from closed proprietary -source commercial software such as Neurolucida® (, MicroBrightField, Inc.) into swcSWC.
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== Analysis of Existing Profiles ==
[[File:BitmapSholl-CA1Compartment.png|frame|right|Linear plot for CA1 cell [[#CA1CellMask|described above]]. Using the soma as center, image was sampled twice using the [[#Restrict|Restrict analysis to hemicircle/hemisphere]] option in order to segregate apical from basal dendrites. For convenience, distances for basal branches were assigned negative values. For clarity, the binary image of the arbor was rotated, scaled and overlaid (in green) over the plot canvas. Note that it is also possible to restrict [[#MethodsTable|curve fitting]] to a sub-range of distances once [[#Importing|data is collected]].]]
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