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Sholl Analysis

169 bytes added, 08:47, 19 October 2016
Describe overlay options
== Parameters ==
The majority of parameters is shared by all the Analysis commands in the three {{bc|color=white|Analysis|Sholl|Sholl Analysis&nbsp;}} commandssubmenu. However, some settings are specific to the type of data used as input: A segmented 2D image, A segmented 3D image, a tracing, or a previously obtained profile. When analyzing images, input values take into account the scale information of the image (which can be set using the <span style{{bc|color="border-bottom:1px dotted #ccc;">Analyze▷ white|Analyze|Set Scale...</span> }} or <span style{{bc|color="border-bottom:1px dotted #ccc;">Image▷ white|Image|Properties...</span> }} (<span style="display:inline-block;">{{key press|Shift|P}} </span>), the type of image (2D or 3D), and its [[#Startup ROI|active ROI]].
==== Definition of Shells ====
[[ File:BitmapSholl-Prompt_v3.png|320px|right |Main prompt (version 3.4.1), when input is a segmented image ({{bc|color=white|Analysis|Sholl|Sholl Analysis...}})]]
==== Multiple Samples and /Noise Reduction ====
* '''Samples per radius ''(2D images only)''''' <sup>&nbsp;</sup>Defines the number of measurements to be performed at each sampling circumference. These measurements are then combined into a single value according to the chosen [[#SamplesIntegration|integration method]]. This strategy, a break from previous approaches, increases the accuracy of non-continuos profiles by diluting out the effect of processes extending tangent to the sampling circumference.
:Visually, this option can be imagined as the "thickness" of the sampling circumference: e.g., for a radius of 100 pixels and a value of 3 ''Samples per radius'', the final number of intersections would integrate the measurements sampled at distances 99, 100 and 101.
==== Output Options ====
* '''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'' (2D images only)''''' <sup>&nbsp;</sup>If checked, concentric shells matching sampled distances are added to the image overlay as circular ROIs, or composite ROIs when using hemicircles. ROIs are named according to their radius.* '''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 (saved according to and 3) The Sholl mask. Files are named after the extension image filename and format analysis method. Saving options can be specified in {{bc|color=white|Analysis|Sholl|Metrics &amp; Options...}} (or ''Options...'' command in the ''More»'' drop-down menu), and 3) The Sholl mask. Files are named after the image filename and analysis method.
** '''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.