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Sholl Analysis

228 bytes removed, 11:09, 7 June 2016
Fix typos, wording and legacy descriptions
;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 analysis to sub-compartments of the arbor.
;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]] calculations). Suitable for cases in which [[#PrimaryBranches|inference from starting radius]] is not effective.
[[File:ShollAnalysisStartupROIs.png|frame|center|Three types of ROIs expected by the plugin. Left: Line defining center of analysis (focal point), hemisphere restriction and ending radius. Middle: Single point defining center of analysis. Right: Multi-point selection in which the first point defines the focal point while the remaining points (2 to 5) serve as counters for primary dendrites.]]
==== Output Options ====
* '''Create intersections mask''' <sup>&nbsp;</sup>If checked, a 16–bit maximum intensity projection of the analyzed image is generated in which the measured arbor is painted according to its Sholl profile. The type of data (''Raw'', i.e., sampled or ''Fitted'') is displayed in the image subtitle.<br>NB: The default Lookup Table (LUT) used by the mask is modeled after the can be changed using {{bc|color=white|Image|Lookup Tables|}}. The background color [httpgray level://www0 (black) to 255 (white)] can be set in {{bc|color=white|Analysis|Sholl|Metrics &amp; Options...}} or using the '' [[MATLAB]] "jet" color map] (a rainbow color map based on a fluid'' command in the ''More»'' drop-jet simulation by NCSA) but you down menu. It can apply also be changed at any of your favorite LUTs later point using the <span style{{bc|color="border-bottom:1px dotted #ccc;">Image▷ Lookup Tables▷</span> submenuwhite|Image|Color|Edit Lut... }} WYSIWYG versions (RGB images) of these masks can be otained using by pressing {{key press|Shift|F}} (<span style{{bc|color="border-bottom:1px dotted #ccc;">Image▷ Overlay▷ white|Image|Overlay|Flatten</span>}}) or by running <span style{{bc|color="border-bottom:1px dotted #ccc;">Analyze▷ Tools▷ white|Analyze|Tools|Calibration Bar...</span>** '''Background''' <sup>&nbsp;</sup>The background color (gray level) of the mask from 0 (black) to 255 (white). It can be changed at any later point using <span style="border-bottom:1px dotted #ccc;">Image▷ Color▷ Edit Lut...</span>}}* '''Save results in image directory ''(only available when image is saved locally)''''' <sup>&nbsp;</sup> If checked, all the results (with the exception of the ''[[#Metrics|Sholl Table]]'') are saved to the image directory. These include: 1) Sholl plots (saved as PNG images), 2) A table containing detailed data (saved according to the extension and format specified in <span style{{bc|color="border-bottom:1px dotted #cccwhite|Analysis|Sholl|Metrics &amp;">Edit▷ Options▷ Input/OutputOptions...}} (or ''Options...</span>'' command in the ''More»'' drop-down menu) , and 3) The Sholl mask (saved as a 16-bit TIFF).<p>Files are named after the image filename and analysis method. When this option is not available, profiles can always be retrieved using the ''List'', ''Save...'' and ''Copy...'' commands of plot windows.</p>
** '''Do not display saved files''' If checked, saved files are directly saved to disk and are not displayed. Activate this option when [[#Batch_Processing|batch processing]] files.
== Metrics ==
Morphometric descriptors and other properties of the arbor are printed to a dedicated table named ''Sholl Results''. Output is fully customizable using {{bc|color=white|Analysis|Sholl|Metrics &amp; Options...}} or using the ''Options...'' command in the ''More»'' drop-down menu. The first columns log analysis parameters: ''Image Directory'' and , ''filename'' and ''voxel unit'', ''Lower'' and ''Upper Threshold levels'', ''X,Y'' (in pixels) and ''Z'' (slice number) coordinates of center of analysis, ''Starting'' and ''Ending radius'', ''Radius step'', ''Number of Samples per Radius'', etc. Other parameters are described below.
[[File:BitmapSholl-Table.png|100%|center|Descriptors and metrics are listed in the Sholl Table (v2.4)]]
;<span id="CriticalRadius"></span>Critical radius
:The distance at which ''Critical value'' occurs. By default (see [[#Advanced Options|Advance Advanced Options]]), it is calculated with a precision of 1/1000 of ''Radius step size''. Abbreviation: ''r<sub>c</sub>''.
: See also [[#MaxIntersRadius|Max inters. radius]]
;<span id="MeanValueOfFunction"></span>Mean value
:The mean value<ref name="Stulic"></ref> of the fitted polynomial function [[#eq1|(1)]], representing the average of intersections over the whole area occupied by the arbor. Abbreviation ''N<sub>av</sub>''.
:On the Sholl plot, it is [[#ShollPlots|highlighted]] as the height of the rectangle that has the width of ''Enclosing radius'' − ''First intersecting radius'' and the same area of the area under the fitted curve on that discrete interval. It is analogous to [[#MeanInters|Mean inters.]], the arithmetic mean of sampled intersections throughout the arbor (cf. [[#Metrics_based_on_sampled_data|Metrics based on sampled data]]). By default (see [[#Advanced Options|Advance Advanced Options]]), it is calculated with a precision of 1/1000 of ''Radius step size''.
;<span id="SchoenenFitted"></span>Schoenen Ramification index (''Ramification index (fit)'')
== Advanced Options ==
Advanced options can be set by calling public methods of <tt>Sholl_Analysis</tt>, the main class of the plugin. Options include the ability to perform analyses without displaying plots or detailed tables, and the ability to display plots without annotations. There is also an option to specify the precision to be used in the calculations of [[#MeanValueOfFunction|Mean value]], and [[#CriticalValue|Critical value]], and [[#CriticalRadius|Critical radius]].
Changes made to these settings need to be set before running the plugin and remain in effect while ImageJ is running. For a full description of all the available options, have a look at the plugin's [ API documentation (Javadocs)].
;Python example: Display only the main ''[[#Metrics|Sholl Table]]'', ignoring remaining outputs