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Sholl Analysis

1,400 bytes removed, 10:46, 29 September 2016
Remove contents on non-Fiji installations, as we no longer support them. Update Release version
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{{Infobox
| software = ImageJ/Fiji
| name = Sholl Analysis
| author = {{Person|Tiago}}
| maintainer = {{Person|Tiago}}
| source = {{GitHub|org=tferr|repo=ASA}}
| filename = [http://jenkins.imagej.net/job/Sholl-Analysis/118/artifact/target/Sholl_Analysis-3.6.4.jar Sholl_Analysis.jar]
| released = December 2012
| latest version = '''3.6.4 July 5 August 2016''' | status = Active ({{GitHub|org=tferr|repo=ASA|path=Notes.md#release-notes-for-sholl-analysis|label=Release Notes}})| status = Active. See [[#Release Notes and Pre-releases|Pre-releases]] and {{GitHub|org=tferr|repo=ASA|path=Notes.md#development-builds|label=Development Notes}}
| category = [[:Category:Plugins|Plugins]], [[:Category:Analysis|Analysis]], [[:Category:Neuroanatomy|Neuroanatomy]]
}}
;Segmentation issues?:Jump to [[#Cf. Segmentation|Cf. Segmentation]] or [[#Pre-processing|Pre-processing]]
;Having Problems?:Jump to [[#FAQ|FAQs]]
;Non-Fiji User?:Jump to [[#Non-Fiji_Users|Installation notes]]
</div>
</div>{{TOC}}
== Installation ==
=== The plugin is distributed with Fiji Users ===If you using Fiji, you already have the plugin . It is installed under {{bc|color=white|Analysis|Sholl|&nbsp;}}. However, as part of an active effort to [[2015-12-22_-_The_road_to_Java_8|modernize ImageJ]] (see also this [[2015-06-15_-_Major_updates_in_the_works|announcement]]), '''you need to [[How_to_follow_a_3rd_party_update_site#Add_update_sites | subscribe]] to the Java 8 update site to access the latest plugin version''' (this will also allow you to access the newest [[2015-12-22_-_The_road_to_Java_8#Components_which_have_already_migrated|ImageJ capabilities]]). To do so, you can either:
* [[Downloads|Download the latest Fiji release]]. Newer releases come pre-bundled with Java 8, and are already subscribed to the [[User:Java-8|Java-8 update site]].
* If you have downloaded Fiji while ago and want to keep your existing installation, you will have to download Java 8 and make your [[Troubleshooting#Checking_the_Java_version|Fiji installation aware of it]]. Then subscribe to the [[User:Java-8|Java-8 update site]].
Note that the plugin runs fine with older versions of Java, so you can [[#Non-Fiji_Users|update it manually]] if you do not want (or can't) use Java 8. However, it will have to be compiled for older versions of Java. === 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 .jar 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.
== Usage ==
;Data analysis tools:
:'''[[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-xy-data|label=Plot XY Data}}:''' Whole-purpose routine that plots data from imported spreadsheets.
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