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Sholl Analysis

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<div style="font-size:175%;border-bottom:1px dotted #ccc;margin-bottom:0.55em;">Quick links</div>
;Analysis of traced arbors?:Jump to [[#Analysis of Traced Cells|Traced Cells]]
;Segmentation issues?:Jump to [[#Cf. Segmentation|Cf. Segmentation]] or [[#Pre-processing|Pre-processing]]
;Having Problems?:Jump to [[#FAQ|FAQs]]
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</div>{{TOC}}
Automated and multithreaded bitmap Sholl for direct analysis of fluorescent images of neuronal arborsor traced morphologies. Features powerful quantifications based on curve fitting. Analysis of traced arbors and analysis of previously obtained profiles is also possible.
== Introduction ==
=== Startup ROI ===
The center of analysis can be specified using one of three possibilities:
;Straight line: A Straight line from the focus of the arbor to its most distal point using the Straight Line Tool. The advantages of using line selections are twofold: 1) Center of analysis and [[#EndRadius|Ending radius]] are automatically set, and 2) Horizontal/vertical lines (created by holding {{key press|Shift}} while using the Straight Line Selection Tool) can be used to [[#Restrict|restrict analysis to sub-compartments regions]] of the arborimage.
;Single point: A single point marking the focus of the arbor using the Point Selection Tool. With single point selections, only the center of analysis is defined. Thus, this option is suitable for [[#Batch_Processing|batch processing]] of images with different dimensions with undefined [[#EndRadius|Ending radius]].
;Multi-point selection:A Multi-point selection (multi-point counter) in which the first point marks the center of analysis while the remaining points mark (count) the number of primary branches required for the calculation of [[#SchoenenSampled|ramification indices]]). Suitable for cases in which [[#PrimaryBranches|inference from starting radius]] is not effective.
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{{Tip
| tip = With binary images, ''Sholl Analysis'' treats zero intensities as the background, independently of the image lookup table or the state of the ''Black background option'' in <span style="border-bottom:1px dotted #ccc;">Process▷ Binary▷ Options...</span> As with any other [http://imagej.net/docs/guide/146-29.html#infobox:blackBackground ImageJ routine], confusing background with foreground pixels will lead to aberrant results, including: 1) overestimation of branches and 2) artifacts at distances intersecting the boundaries of the image canvas.}}
== Analysis of Traced Cells ==
In this mode, the plugin analyzes reconstructed arbors. This is particularly relevant for stainings that do not allow single-cell resolution.
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