![]() ![]() Linear plot for CA1 cell described above. Here is an example using an axonal arbor of a Drosophila olfactory neuron from the DIADEM dataset : Segmentation allows you to ensure that you are measuring neuronal processes and not the interstitial spaces between them. This command highlights foreground from background pixels and is particularly useful when analyzing black and white (binary) images or when using the B&W lookup table in the Threshold Widget ( Image▷ Adjust▷ Threshold. Segmentation to visually confirm which phase of the segmented image will be sampled. 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. Middle: Single point defining center of analysis. Left: Line defining center of analysis (focal point), hemisphere restriction and ending radius. Three types of ROIs expected by the plugin when analyzing images directly. Suitable for cases in which inference from starting radius is not effective. 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 ramification indices). Thus, this option is suitable for batch processing of images with different dimensions with undefined Ending radius. With single point selections, only the center of analysis is defined. Single point A single point marking the focus of the arbor using the Point Selection Tool. The advantages of using line selections are twofold: 1) Center of analysis and Ending radius are automatically set, and 2) Horizontal/vertical lines (created by holding ⇧ Shift while using the Straight Line Selection Tool) can be used to restrict analysis to sub-regions of the image. Straight line A Straight line from the focus of the arbor to its most distal point using the Straight Line Tool. The center of analysis can be specified using one of three possibilities: Please cite it when acknowledging the plugin in your published research. The manuscript uses Sholl Analysis to describe and classify morphologically challenging cells and is accompanied by a Supplementary Note that presents the software in greater detail. Tip: This program is described in Nature methods. Segmentation to visually inspect the two thresholded phases: arbor and background.
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