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. Author manuscript; available in PMC: 2021 Apr 7.
Published in final edited form as: J Comp Neurol. 2018 Dec 4;527(13):2122–2145. doi: 10.1002/cne.24555

Figure 2. Automated segmentation of plaque fluorescence.

Figure 2.

(a) An example ROI from a single section image in somatosensory cortex, barrel field area (SSp-bfd) showing methoxy-X04 fluorescence. A portion of the hippocampus is also visible in the bottom left corner of the image. (b) Segmented plaque signal (red) overlaid on the image section shown in (a). (c) An ROI from a different section in the same brain showing the cerebral aqueduct (AQ) and surrounding periaqueductal gray (PAG). (d) Segmented plaque signal for the image section shown in c (red) showing false positive signal along the bright tissue edge at the border of the cerebral aqueduct. Similar signal was observed in APP−/− mice. Scale = 1 mm. (e-i) Quantification of false positives as percent of structure volume for 35 image series collected from APP−/− mice without plaques to identify regions prone to segmentation artifacts. False positives are plotted for summary structures in hippocampus (e), selected midbrain regions including PAG (f), olfactory areas (g), cortical subplate (h), and isocortex (i). Red points indicate APP−/− mice that received a methoxy-X04 injection one day before perfusion. Abbreviations for summary structures in isocortex, hippocampus, olfactory areas, and cortical subplate can be found in Table 2. Abbreviations in (f) SNr: Substantia nigra, reticular part; SCm: Superior colliculus, motor related; PAG: Periaqueductal gray; RN: Red nucleus. (j) Histogram showing the difference between signal and false positive levels (% coverage in APP+/− mice - % coverage in APP−/− mice) for every structure in the Allen CCFv3 reference atlas. (k) False positive heatmap showing regions with the highest segmentation artifacts. Abbreviations: BLAa: Basolateral amygdalar nucleus, anterior part; IG: Induseum griseum; AD: Anterodorsal nucleus of the thalamus; CEA: Central amygdalar nucleus; ORBm: Medial orbital cortex; SFO: Subfornical organ; MH: Medial habenula. (l) False positive heatmap for a different anatomical location. Abbreviations: CEAm: Central amygdalar nucleus, medial part; TTv: Taenia tecta, ventral part; CA2: Hippocampal field CA2.