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Sholl Analysis

346 bytes added, 19:15, 1 July 2016
Document changes in 3.6.4
== Usage ==
The plugin requires a [[#faq:threshold|binary image or a segmented ]] [[#faq:image-types|grayscale image ]] (2D or 3D) containing a single neuron.
# Segment the neuronal arbor using <span style="border-bottom:1px dotted #ccc;">Image▷ Adjust▷ Threshold...</span> (shortcut: <span style="display:inline-block;">{{key press|Shift|T}} </span>).
==== Output Options ====
* '''Create intersections mask''' <sup>&nbsp;</sup>If checked, a 16–bit 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 subtitleand 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|Analysis|Sholl|Metrics &amp; Options...}} , or using the ''Options...'' command in the ''More»'' drop-down menu. It can also be changed 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...}}* '''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 {{bc|color=white|Analysis|Sholl|Metrics &amp; Options...}} (or ''Options...'' 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'', ''filename'' and ''voxel unit'', ''Channel'', ''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)]]
=== Metrics based on sampled data ===
[[ File:ShollOptionsPrompt.png|350px|right |Metrics &amp; Options prompt (version 3.6.04)]]
;Intersecting radii
:The number of sampling radii intersecting the arbor at least once.
Although ImageJ can threshold The plugin does not parse RGB images, the plugin can only parse but will process any grayscale images image (8/16-bit and 16), including multi-bitchannel (composite)images. Images This is intentional: RGB images are inflexible and images of fluorescence-labeled cells are typically non-RGB images. Conversions between different image types is As explained in the [ ImageJ User Guide], RGB images can be converted using {{bc|color=white|Image|Color|Channels Tool...}} or {{bc|color=white|Image|Type|}} commands.
<span id="faq:z-position"></span>'''With 3D and 4D images, how do I set the Z-position and of the center?'''
The Z-position (depth) of the center of analysis is the active Z-slice of the stack. It is With multichannel (composite) images, the active channel also defines the C-position. Both are reported in the ''Sholl Results'' table.