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Sholl Analysis

118 bytes added, 11:41, 7 June 2016
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More useful links to external resources
:* Scripts from the [[BAR]] [[List_of_update_sites|update site]], <span style="border-bottom:1px dotted #ccc;">BAR▷ [[BAR#Segmentation|Segmentation]]▷</span>
{{Tip
|tip = For additional image processing tools have a look at the growing list of [[List_of_update_sites|update sites]]. For more information on image processing have a look at the [[Cookbook]], [[:Category:Tutorials|tutorials]], the [http[://imagejdocu.tudor.lu ImageJ Information and Documentation PortalCategory:Segmentation|segmentation]] and the [http://imagej.net/docs/guide/ ImageJ User Guide].
}}
sa.setNoTable(True) # Exclude detailed table from output
</source>
;Java/BeanShell /Groovy example: Display plots without annotations
<source lang="java">
import sholl.Sholl_Analysis;
The authoritative reference for ''Sholl Analysis'' is:
* Ferreira T, Blackman A, Oyrer J, Jayabal A, Chung A, Watt A, Sjöström J, van Meyel D. ('''2014'''), [http://www.nature.com/nmeth/journal/v11/n10/full/nmeth.3125.html Neuronal morphometry directly from bitmap images], ''Nature Methods'' 11(10): 982–984.
The [[How to cite Fiji?Citing|authoritative reference]] for Fiji:
* Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. ('''2012''') [http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2019.html Fiji: an open-source platform for biological-image analysis], ''Nature Methods'' 9(7): 676-682.
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Use Fiji's built-in [[Report a Bug]] command, report it in the [http://forum.imagej.net|ImageJ Forum], the [http://imagej.net/list.html ImageJ mailing list] or file an [https://github.com/tferr/ASA/issues issue] on GitHub. Don't forget to include the [[Bug reporting best practices|steps needed to reproduce the problem]]. You may also want to check the {{GitHub|org=tferr|repo=ASA|path=Notes.md#development-builds|label=release notes}} for the latest [http://jenkins.imagej.net/job/Sholl-Analysis/lastBuild/ development version] to see if the issue has meanwhile been addressed.
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== Related Resources ==
* [[:Category:Neuroanatomy|Neuroanatomy]] resources, including:** '''[[Simple_Neurite_Tracer|Simple Neurite Tracer]] (SNT)''' Mark Longair's plugin for semi-automated three-dimensional tracing. Data from [[Simple_Neurite_Tracer:_Sholl_analysis|SNT]] can be [[#Importing|analyzed]] by the Sholl Analysis plugin.** [[Neuroanatomy|Neuroanatomy update site]]
* '''[[BAR]]''', ''B''roadly ''A''pplicable ''R''outines that complement ''Sholl Analysis''
* '''[[Strahler_Analysis|Strahler_Analysis]]''' Strahler Analysis on [[Skeletonize3D|skeletonized]] arbors.(distributed through the [[Neuroanatomy|Neuroanatomy update site]])
* '''[http://www.reading.ac.uk/neuromantic/ Neuromantic]''' Standalone program for (semi-manual/semi-automatic) neuronal reconstruction.
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