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Sholl Analysis

37 bytes added, 15:34, 1 April 2016
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Importing Tabular Data
*It can be used to analyze profiles obtained from traced cells in [[Simple Neurite Tracer]] (SNT), Fiji's remarkable framework for semi-automated reconstruction of neuronal arbors. This is particularly relevant for stainings that do not allow single-cell resolution.
*It can be used to re-analyze bitmap data (replot, modify fitting options, etc.) without having to re-sample the initial image.
 
To use it:
#Locate the profile generated by a previous run of the plugin or by SNT. Note that any tab or comma delimited text file (.csv or .txt) can be used.
# Run {{bc|color=white|Analysis|Sholl|Sholl Analysis (Tabular Data)...}} and indicate the file to be analyzed. Note that you can drag & drop .csv and .txt files into the main ImageJ window, or import data from the clipboard. [[#Batch Processing|Batch processing]] is also [[#Batch Analysis of Tabular Data|possible]].
=== Obtaining Profiles from Tracings ===
#Load tracings (typically a .swc or a .traces file) into [[Simple_Neurite_Tracer:_Basic_Instructions|Simple Neurite Tracer]]. Note that .swc files created by any other software (such as [[#Related Resources|Neuromantic]]) can also be used. If needed, [[#Related Resources|L-measure]] can be used to convert proprietary file formats such as the ones generated by Neurolucida® (MicroBrightField, Inc.).
#Retrieve the linear Sholl profile by following these [[Simple_Neurite_Tracer:_Sholl_analysis|instructions]]
#Export ''detailed data'' (.csv file)(Note that any tab or comma delimited text file (.csv or .txt) can also be used.#Locate the profile generated by a previous run of the plugin or by SNT. #Run {{bc|color=white|Analysis|Sholl|Sholl Analysis (Tabular Data)...}} and indicate the file to be analyzed. Note that you can drag & drop .csv and .txt files into the main ImageJ window, import data from the clipboard, or use any other table already opened by ImageJ. [[#Batch Processing|Batch processing]] is also [[#Batch Analysis of Tabular Data|possible]].
=== Parameters for Tabular Data ===
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