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Sholl Analysis

181 bytes added, 05:08, 28 May 2017
Document output ROIs
==== Output Options ====
[[File:ShollResultAsROIs.png|400px|thumb|right|Intersection points and sampling shells can be retrieved as ROIs using {{bc|color=white|Image|Overlay|To ROI Manager}}. Intersection points are placed at edges of detected clusters of foreground pixels, not their center.]]
* '''Create intersections mask''' <sup>&nbsp;</sup>If checked, a 16/32–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 and can be specified in {{bc|color=white|Analysis|Sholl|Metrics &amp; Options...}} or using the ''Options...'' command in the ''More»'' drop-down menu.<br>NB: The default Lookup Table (LUT) used by the mask can be changed using {{bc|color=white|Image|Lookup Tables|}}. The background color [gray level: 0 (black) to 255 (white)] can also be set in {{bc|color=white|Metrics &amp; Options...}}, or at any later point using {{bc|color=white|Image|Color|Edit Lut...}} WYSIWYG versions (RGB images) of these masks can be otained using by pressing {{key press|Shift|F}} ({{bc|color=white|Image|Overlay|Flatten}}) or by running {{bc|color=white|Analyze|Tools|Calibration Bar...}}
* '''Overlay sampling shells and intersection points'' (2D images only)''''' <sup>&nbsp;</sup>If checked, two sets of ROIS are added to the image overlay: 1) concentric shells matching sampled distances (circular ROIs or composite ROIs when using hemicircles); and 2) Multipoint ROIs at intersection sites between shells and clusters of foreground pixels. To manipulate and access these ROIs use {{bc|color=white|Image|Overlay|To ROI Manager}}.
* '''Save results to''' <sup>&nbsp;</sup> If checked, all the results (with the exception of the ''[[#Metrics|Sholl Table]]'') are saved to the specified directory. These include: 1) Sholl plots (saved as PNG images), 2) A table containing detailed data and 3) The Sholl mask. Files are named after the image filename and analysis method. Saving options can be specified in {{bc|color=white|Analysis|Sholl|Metrics &amp; Options...}} (''Options...'' command in the ''More»'' drop-down menu).
** '''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.