Also, note that the initial black and white image would look the same under an inverted lookup table ( Image › Lookup Tables › Invert LUT). top-right and bottom-right corners of mask where intersections are sampled in the absence of real axons at those locations). hue ramps on upper left of Intersections mask) and 2) the program detects artifacts induced by the edges of the image (cf. ![]() The consequences of the phase inversion are twofold: 1) the program oversamples (cf. Note the reversal of output and how the intersections mask no longer decorates the axonal processes but the interstitial spaces between them. Bottom row: Aberrant segmentation (inverted image): Background is sampled. Top row: Image properly segmented: Arbor is sampled. Here is an example using an axonal arbor of a Drosophila olfactory neuron from the DIADEM dataset 3: To so, you can select the Red lookup table in the Threshold widget ( Image › Adjust › Threshold… ⇧ Shift + T) to highlight foreground from background pixels to verify that you are measuring neuronal processes and not the interstitial spaces between them. It is important to visually confirm which phase of the segmented image will be sampled, specially when using black and white (binary) lookup tables. 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 neurites. 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. Multipoint selection:A Multi-point selection (multipoint 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:
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