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Sholl Analysis

167 bytes added, 13:44, 25 October 2016
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Analysis of Traced Cells
<span id="Traces"></span>
== 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 input files: a tracing file (a <code>.swc</code> or a [[Simple Neurite Tracer]] <code>.traces</code> file). The command is macro recordableIf 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 thusx,y, [[#Batch Processing|batch processing]] is also possiblez 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]]
# Adjust the default [[#Parameters|Parameters]]
# Problems? Read the [[#FAQ|FAQs]]
 
{{Tip
| id = external-traces
| 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 [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]), 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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== 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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