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Sholl Analysis

305 bytes added, 11:23, 7 June 2016
Update links and fix dead URLs
=== Non-Fiji Users ===
If you are not using Fiji, download ''Sholl_Analysis.jar'' from the direct link listed on the [[#top|top of this page]] and place it in the ''ImageJ/plugins/'' directory. Alternatively, drag the downloaded <tt>.jar</tt> file and drop it on the main ImageJ window. Restart ImageJ and run the new {{bc|color=white|Analysis|Sholl|Sholl Analysis...}} command.
Without access to the [[Update_Fiji|built-in updater]], you are strongly advised to upgrade ImageJ to its latest version ({{bc|color=white|Help|Update ImageJ...}}). To manually update the Sholl Analysis plugin you will have to monitor this page (or the {{GitHub|org=tferr|repo=ASA|path=Notes.md#release-notes-for-sholl-analysis|label=Release Notes}} page) for finding out if new updates have been released.
:'''[[Find Peaks]]:''' Retrieves local maxima under several filtering options such as peak amplitude, peak height and peak width. Can be used to retrieve secondary sites of branch density
:'''{{GitHub|org=tferr|repo=Scripts|path=Data_Analysis/README.md#fit-polynomial|label=Fit Polynomial}}:''' Fits a polynomial of any degree to sampled data. Features an heuristic algorithm for guessing a polynomial "best fit". Expands the built-in repertoire of polynomial fits up to 50<sup>th</sup> order functions. Requires the [http://commons.apache.org/proper/commons-math/ apache commons math library], distributed with Fiji. The script provides [[#Non-Fiji_Users|Non-Fiji users]] with direct download links that install all required dependencies
:'''{{GitHub|org=tferr|repo=Scripts|path=Data_Analysis/README.md#create-boxplot|label=Create BoxPlot}}:''' Allows direct comparison of metrics between groups or sets of data (specially useful when tagging images with the ''Comment'' field in {{bc|color=white|Analysis|Sholl|Metrics &amp; Options...}}):'''{{GitHub|org=tferr|repo=Scripts|path=Data_Analysis/README.md#plot-resultsxy-data|label=Plot ResultsXY Data}}:''' Whole-purpose routine that plots data from imported spreadsheets.
To install [[BAR]], run <span style="border-bottom:1px dotted #ccc;">Help▷ Update...</span> Choose ''Advance Mode'' then ''Manage update sites''. Activate the ''BAR'' checkbox in the list of update sites. See the [[BAR#Installation|BAR documentation page]] for more details.
<source lang="java">
// Recording Sholl Analysis version 3.4.3
// Visit http://fijiimagej.scnet/ShollSholl_Analysis#Batch_Processing for scripting examples
run("Sholl Analysis...", "starting=10 ending=400 radius_step=0 infer fit linear polynomial=[8th degree] semi-log normalizer=Volume create save do");
</source>
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