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Sholl Analysis

6 bytes added, 24 January
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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 [httphttps://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.}}
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== Analysis of Traced Cells ==
:* Scripts from the [[BAR]] {{ListOfUpdateSites|update site}}, <span style="border-bottom:1px dotted #ccc;">BAR▷ [[BAR#Segmentation|Segmentation]]▷</span>
{{Tip
|tip = For additional image processing tools have a look at the growing list of {{ListOfUpdateSites|update sites}}. For more information on image processing have a look at [[:Category:Tutorials|tutorials]], [[:Category:Segmentation|segmentation]] and the [httphttps://imagej.net/docs/guide/ ImageJ User Guide].
}}
<source lang="java">
// Recording Sholl Analysis version 3.4.3
// Visit httphttps://imagej.net/Sholl_Analysis#Batch_Processing for scripting examples
run("Sholl Analysis...", "starting=10 ending=400 radius_step=0 infer fit linear polynomial=[8th degree] semi-log normalizer=Volume create save do");
</source>
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The plugin does not parse RGB images, but will process any grayscale image (8/16-bit), including multi-channel (composite) images. This is intentional: RGB images are inflexible and images of fluorescence-labeled cells are typically non-RGB images. As explained in the [httphttps://imagej.net/docs/guide/ ImageJ User Guide], RGB images can be converted using {{bc|color=white|Image|Color|Channels Tool...}} or {{bc|color=white|Image|Type|}} commands.
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This option is only available if an orthogonal line has been created by holding {{key press|Shift}} when using the <span style="border-bottom:1px dotted #ccc;">Straight Line Selection Tool</span>. See the [httphttps://imagej.net/docs/guide/ ImageJ User Guide] for the full list of key modifiers that can be used while creating straight line ROIs.
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Select the table, then choose <span style="border-bottom:1px dotted #ccc;">File▷ Save As…</span>The filename extension can be specified using the ''More » Options...'' command (see the [httphttps://imagej.net/docs/guide/ ImageJ User Guide] for details). Single cells cannot be modified from within ImageJ, but custom extensions (e.g., .csv, .xls or .ods) will allow the table to be imported by other spreadsheet applications.
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