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Sholl Analysis

36 bytes removed, 00:29, 28 October 2016
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Automated and multithreaded bitmap Sholl for direct analysis of fluorescent images of neuronal arbors or and traced morphologies. Features powerful quantifications based on curve fitting. Analysis of data obtained outside of ImageJ is also possible.
== Introduction ==
== 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 [[#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>, a <code>.eswc</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]]
# Adjust the default [[#Parameters|Parameters]]
=== Batch Analysis of Tabular Data ===
If you already have [[#Importing|obtained profiles]] (either from previous runs or from [[#Obtaining Profiles from TracingsAnalysis of Traced Cells|traced cells]]) and would like to extract new [[#Metrics|metrics]] from such data, you can use the {{bc|color=white|Analysis|Sholl|Sholl Analysis (Existing Profile)...}}. Here is an example macro that runs the plugin over a folder of .csv files containing Sholl profiles produced by [[Simple_Neurite_Tracer:_Sholl_analysis|Simple Neurite Tracer]]:
<source lang="java">
== Advanced Usage ==
Advanced options can be set by through the <tt>Sholl_Analysis</tt> [ APIcalls]. Here are some examples:
3D analysis of an image stack (Python):