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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Neurosci Methods. Author manuscript; available in PMC 2013 August 15.
Published in final edited form as:
J Neurosci Methods. 2012 August 15; 209(2): 357–366.
Published online 2012 June 12. doi: 10.1016/j.jneumeth.2012.06.002

Figure 6

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Analysis method for image quantification

(A) Flow chart with example images describing image analysis technique. First, the red channel (B) is thresholded to identify the mCherry-positive extensions, while excluding more centrally localized regions that may include mitochondria (C). Next, a selection is made based on this threshold and an ROI is defined from the selection (D,E). The green channel is then made the active image and the ROI created in the red channel is applied to the green channel (F,G). The standard deviation of pixel intensity within the ROI is measured. This value for each image is used to calculate the punctate-diffuse index (H). To calculate this index, the values obtained for all control images are averaged; the value of each image is then divided by this mean. This produces an index from 0 to 1, where 0 is more diffuse and 1 is more punctate relative to the control images.

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